Publications

Y. Huang, A. Wipat, J. Bacardit

Transcriptional biomarker discovery toward building a load stress reporting system for engineered Escherichia coli strains

in Biotechnology and Bioengineering, 121(1):355-365, January 2024

@ARTICLE{Huang2023a,
  title = {Transcriptional biomarker discovery toward building a load stress reporting system for engineered Escherichia coli strains},
  author = {Huang, Yiming and Wipat, Anil and Bacardit, Jaume},
  year = 2024,
  doi = {10.1002/bit.28567},
  month = jan,
  journal = {Biotechnology and Bioengineering},
  volume = {121},
  number = {1},
  pages = {355--365}
}

C. Atallah, K. James, Z. Ou, J. Skelton, D. Markham, M.S. Burridge, J. Finnigan, S. Charnock, A. Wipat

A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem

in Biosystems, 236(C):105105, February 2024

@ARTICLE{Atallah2023,
  title = {A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem},
  author = {Atallah, Christian and James, Katherine and Ou, Zhen and Skelton, James and Markham, David and Burridge, Matt S. and Finnigan, James and Charnock, Simon and Wipat, Anil},
  year = 2024,
  doi = {10.1016/j.biosystems.2023.105105},
  month = feb,
  journal = {Biosystems},
  volume = {236},
  number = {C},
  pages = {105105}
}

L. Xiao, L. Jia, J. Dai, Y. Cao, Y. Li, Q. Zhu, J. Li, M. Liu

Design and Analysis of a Novel Distributed Gradient Neural Network for Solving Consensus Problems in a Predefined Time

in IEEE Transactions on Neural Networks and Learning Systems, 35(3):3478-3487, March 2024

@ARTICLE{Xiao2022a,
  title = {Design and Analysis of a Novel Distributed Gradient Neural Network for Solving Consensus Problems in a Predefined Time},
  author = {Xiao, Lin and Jia, Lei and Dai, Jianhua and Cao, Yingkun and Li, Yiwei and Zhu, Quanxin and Li, Jichun and Liu, Min},
  year = 2024,
  doi = {10.1109/TNNLS.2022.3193429},
  month = mar,
  journal = {IEEE Transactions on Neural Networks and Learning Systems},
  volume = {35},
  number = {3},
  pages = {3478--3487}
}

DOI
C. Turner, L.M. Pardo, D.A. Gunn, R. Zillmer, S. Mekić, F. Liu, M.A. Ikram, C.C.W. Klaver, P.H. Croll, A. Goedegebure, K. Trajanoska, F. Rivadeneira, M. Kavousi, G.G.O. Brusselle, M. Kayser, T. Nijsten, J. Bacardit

Deep learning predicted perceived age is a reliable approach for analysis of facial ageing: A proof of principle study

in Journal of the European Academy of Dermatology and Venereology, available online since October 2024

C. Siachisumo, S. Luzzi, S. Aldalaqan, G. Hysenaj, C. Dalgliesh, K. Cheung, M.R. Gazzara, I.D. Yonchev, K. James, M. Kheirollahi Chadegani, I.E. Ehrmann, G.R. Smith, S.J. Cockell, J. Munkley, S.A. Wilson, Y. Barash, D.J. Elliott

An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression

in eLife, 12, October 2024

@ARTICLE{Siachisumo2024,
  title = {An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression},
  author = {Siachisumo, Chileleko and Luzzi, Sara and Aldalaqan, Saad and Hysenaj, Gerald and Dalgliesh, Caroline and Cheung, Kathleen and Gazzara, Matthew R and Yonchev, Ivaylo D and James, Katherine and Kheirollahi Chadegani, Mahsa and Ehrmann, Ingrid E and Smith, Graham R and Cockell, Simon J and Munkley, Jennifer and Wilson, Stuart A and Barash, Yoseph and Elliott, David J},
  year = 2024,
  doi = {10.7554/eLife.89705.3},
  month = oct,
  journal = {eLife},
  volume = {12}

2023

S. Scheidegger, S. Mingo Barba, H. Fellermann, U. Gaipl

Influence of the Antigen Pattern Vector on the Dynamics in a Perceptron-Based Artificial Immune - Tumour- Ecosystem During and After Radiation Therapy

in Artificial Life and Evolutionary Computation. WIVACE 2021, p.195-206, Cham., January 2023

@INPROCEEDINGS{Scheidegger2023,
  title = {Influence of the Antigen Pattern Vector on the Dynamics in a Perceptron-Based Artificial Immune - Tumour- Ecosystem During and After Radiation Therapy},
  author = {Scheidegger, Stephan and Mingo Barba, Sergio and Fellermann, Harold and Gaipl , Udo},
  year = 2023,
  month = jan,
  booktitle = {Artificial Life and Evolutionary Computation. WIVACE 2021},
  pages = {195--206},
  address = {Cham.}
}

M. Papaiakovou, N. Fraija-Fernández, K. James, A.G. Briscoe, A. Hall, T.P. Jenkins, J. Dunn, B. Levecke, Z. Mekonnen, P. Cools, S.R. Doyle, C. Cantacessi, D.T. Littlewood

Evaluation of genome skimming to detect and characterise human and livestock helminths

in International Journal for Parasitology, 53(2):69-79, February 2023

@ARTICLE{Papaiakovou2023,
  title = {Evaluation of genome skimming to detect and characterise human and livestock helminths},
  author = {Papaiakovou, Marina and Fraija-Fernández, Natalia and James, Katherine and Briscoe, Andrew G. and Hall, Andie and Jenkins, Timothy P. and Dunn, Julia and Levecke, Bruno and Mekonnen, Zeleke and Cools, Piet and Doyle, Stephen R. and Cantacessi, Cinzia and Littlewood, D. T.j.},
  year = 2023,
  doi = {10.1016/j.ijpara.2022.12.002},
  month = feb,
  journal = {International Journal for Parasitology},
  volume = {53},
  number = {2},
  pages = {69--79}
}

A. McKavanagh, A. Ridzuan-Allen, B.A.K. Kreilkamp, Y. Chen, J.V. Manjón, P. Coupé, M. Bracewell, K. Das, P.N. Taylor, A.G. Marson, S.S. Keller

Midbrain structure volume, estimated myelin and functional connectivity in idiopathic generalised epilepsy

in Epilepsy & Behavior, 140(C):109084, March 2023

@ARTICLE{McKavanagh2023,
  title = {Midbrain structure volume, estimated myelin and functional connectivity in idiopathic generalised epilepsy},
  author = {McKavanagh, Andrea and Ridzuan-Allen, Adam and Kreilkamp, Barbara A. K. and Chen, Yachin and Manjón, José V. and Coupé, Pierrick and Bracewell, Martyn and Das, Kumar and Taylor, Peter N. and Marson, Anthony G. and Keller, Simon S.},
  year = 2023,
  doi = {10.1016/j.yebeh.2023.109084},
  month = mar,
  journal = {Epilepsy & Behavior},
  volume = {140},
  number = {C},
  pages = {109084}
}

T.W. Owen, G.M. Schroeder, V. Janiukstyte, G.R. Hall, A. McEvoy, A. Miserocchi, J. de Tisi, J.S. Duncan, F. Rugg‐Gunn, Y. Wang, P.N. Taylor

MEG abnormalities and mechanisms of surgical failure in neocortical epilepsy

in Epilepsia, 64(3):692-704, March 2023

@ARTICLE{Owen2023,
  title = {MEG abnormalities and mechanisms of surgical failure in neocortical epilepsy},
  author = {Owen, Thomas W. and Schroeder, Gabrielle M. and Janiukstyte, Vytene and Hall, Gerard R. and McEvoy, Andrew and Miserocchi, Anna and de Tisi, Jane and Duncan, John S. and Rugg‐Gunn, Fergus and Wang, Yujiang and Taylor, Peter N.},
  year = 2023,
  doi = {10.1111/epi.17503},
  month = mar,
  journal = {Epilepsia},
  volume = {64},
  number = {3},
  pages = {692--704}
}

Y. Huang, N. Sinha, A. Wipat, J. Bacardit

A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis

in Synthetic and Systems Biotechnology, 8(1):97-106, March 2023

@ARTICLE{Huang2023,
  title = {A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis},
  author = {Huang, Yiming and Sinha, Nishant and Wipat, Anil and Bacardit, Jaume},
  year = 2023,
  doi = {10.1016/j.synbio.2022.12.001},
  month = mar,
  journal = {Synthetic and Systems Biotechnology},
  volume = {8},
  number = {1},
  pages = {97--106}
}

I. Montenegro-Rojas, G. Yañez, E. Skog, O. Guerrero-Calvo, M. Andaur-Lobos, L. Dolfi, A. Cellerino, M. Cerda, M.L. Concha, C. Bertocchi, N.O. Rojas, A. Ravasio, T.J. Rudge

A computational framework for testing hypotheses of the minimal mechanical requirements for cell aggregation using early annual killifish embryogenesis as a model

in Frontiers in Cell and Developmental Biology, 11, March 2023

@ARTICLE{Montenegro-Rojas2023,
  title = {A computational framework for testing hypotheses of the minimal mechanical requirements for cell aggregation using early annual killifish embryogenesis as a model},
  author = {Montenegro-Rojas, Ignacio and Yañez, Guillermo and Skog, Emily and Guerrero-Calvo, Oscar and Andaur-Lobos, Martin and Dolfi, Luca and Cellerino, Alessandro and Cerda, Mauricio and Concha, Miguel L. and Bertocchi, Cristina and Rojas, Nicolás O. and Ravasio, Andrea and Rudge, Timothy J.},
  year = 2023,
  doi = {10.3389/fcell.2023.959611},
  month = mar,
  journal = {Frontiers in Cell and Developmental Biology},
  volume = {11}

N. Partridge

Research Briefing - Governing synthetic biology: A food policy approach

Newcastle University technical report, 1, March 2023

@TECHREPORT{Partridge2023,
  title = {Research Briefing - Governing synthetic biology: A food policy approach},
  author = {Partridge, Natalie},
  year = 2023,
  doi = {10.5281/zenodo.10804432},
  month = mar,
  number = {1},
  institution = {Newcastle University}
}

L. Buecherl, T. Mitchell, J. Scott-Brown, P. Vaidyanathan, G. Vidal, H. Baig, B. Bartley, J. Beal, M. Crowther, P. Fontanarrosa, T. Gorochowski, R. Grünberg, V. Kulkarni, J. McLaughlin, G. Mısırlı, E. Oberortner, A. Wipat, C. Myers

Synthetic biology open language (SBOL) version 3.1.0

in Journal of Integrative Bioinformatics, 20(1), March 2023

@ARTICLE{Buecherl2023,
  title = {Synthetic biology open language (SBOL) version 3.1.0},
  author = {Buecherl, Lukas and Mitchell, Thomas and Scott-Brown, James and Vaidyanathan, Prashant and Vidal, Gonzalo and Baig, Hasan and Bartley, Bryan and Beal, Jacob and Crowther, Matthew and Fontanarrosa, Pedro and Gorochowski, Thomas and Grünberg, Raik and Kulkarni, Vishwesh and McLaughlin, James and Mısırlı, Göksel and Oberortner, Ernst and Wipat, Anil and Myers, Chris},
  year = 2023,
  doi = {10.1515/jib-2022-0058},
  month = mar,
  journal = {Journal of Integrative Bioinformatics},
  volume = {20},
  number = {1}

L. Grozinger, E. Heidrich, Á. Goñi‐Moreno

An electrogenetic toggle switch model

in Microbial Biotechnology, 16(3):546-559, March 2023

@ARTICLE{Grozinger2023,
  title = {An electrogenetic toggle switch model},
  author = {Grozinger, Lewis and Heidrich, Elizabeth and Goñi‐Moreno, Ángel},
  year = 2023,
  doi = {10.1111/1751-7915.14153},
  month = mar,
  journal = {Microbial Biotechnology},
  volume = {16},
  number = {3},
  pages = {546--559}
}

L.P. Binding, D. Dasgupta, P.N. Taylor, P.J. Thompson, A.G. O'Keeffe, J. de Tisi, A.W. McEvoy, A. Miserocchi, G.P. Winston, J.S. Duncan, S.B. Vos

Contribution of White Matter Fiber Bundle Damage to Language Change After Surgery for Temporal Lobe Epilepsy

in Neurology, 100(15):e1621-e1633, April 2023

@ARTICLE{Binding2023,
  title = {Contribution of White Matter Fiber Bundle Damage to Language Change After Surgery for Temporal Lobe Epilepsy},
  author = {Binding, Lawrence Peter and Dasgupta, Debayan and Taylor, Peter Neal and Thompson, Pamela Jane and O'Keeffe, Aidan G. and de Tisi, Jane and McEvoy, Andrew William and Miserocchi, Anna and Winston, Gavin P. and Duncan, John S. and Vos, Sjoerd B.},
  year = 2023,
  doi = {10.1212/WNL.0000000000206862},
  month = apr,
  journal = {Neurology},
  volume = {100},
  number = {15},
  pages = {e1621--e1633}
}

E. Torelli, B. Shirt-Ediss, S.A. Navarro, M. Manzano, P. Vizzini, N. Krasnogor

Light-Up Split Broccoli Aptamer as a Versatile Tool for RNA Assembly Monitoring in Cell-Free TX-TL Systems, Hybrid RNA/DNA Origami Tagging and DNA Biosensing

in International Journal of Molecular Sciences, 24(10):8483, May 2023

@ARTICLE{Torelli2023,
  title = {Light-Up Split Broccoli Aptamer as a Versatile Tool for RNA Assembly Monitoring in Cell-Free TX-TL Systems, Hybrid RNA/DNA Origami Tagging and DNA Biosensing},
  author = {Torelli, Emanuela and Shirt-Ediss, Ben and Navarro, Silvia A. and Manzano, Marisa and Vizzini, Priya and Krasnogor, Natalio},
  year = 2023,
  doi = {10.3390/ijms24108483},
  month = may,
  journal = {International Journal of Molecular Sciences},
  volume = {24},
  number = {10},
  pages = {8483}
}

S. Konur, M. Gheorghe, N. Krasnogor

Verifiable biology

in Journal of The Royal Society Interface, 20(202), May 2023

@ARTICLE{Konur2023,
  title = {Verifiable biology},
  author = {Konur, Savas and Gheorghe, Marian and Krasnogor, Natalio},
  year = 2023,
  doi = {10.1098/rsif.2023.0019},
  month = may,
  journal = {Journal of The Royal Society Interface},
  volume = {20},
  number = {202}

C. Taylor, J. Guy, J. Bacardit

Estimating individual-level pig growth trajectories from group-level weight time series using machine learning

in Computers and Electronics in Agriculture, 208(C):107790, May 2023

@ARTICLE{Taylor2023,
  title = {Estimating individual-level pig growth trajectories from group-level weight time series using machine learning},
  author = {Taylor, Christian and Guy, Jonathan and Bacardit, Jaume},
  year = 2023,
  doi = {10.1016/j.compag.2023.107790},
  month = may,
  journal = {Computers and Electronics in Agriculture},
  volume = {208},
  number = {C},
  pages = {107790}
}

P. Vizzini, E. Beltrame, N. Coppedè, F. Vurro, F. Andreatta, E. Torelli, M. Manzano

Detection of Listeria monocytogenes in foods with a textile organic electrochemical transistor biosensor

in Applied Microbiology and Biotechnology, 107(11):3789-3800, June 2023

@ARTICLE{Vizzini2023,
  title = {Detection of Listeria monocytogenes in foods with a textile organic electrochemical transistor biosensor},
  author = {Vizzini, Priya and Beltrame, Elena and Coppedè, Nicola and Vurro, Filippo and Andreatta, Francesco and Torelli, Emanuela and Manzano, Marisa},
  year = 2023,
  doi = {10.1007/s00253-023-12543-y},
  month = jun,
  journal = {Applied Microbiology and Biotechnology},
  volume = {107},
  number = {11},
  pages = {3789--3800}
}

D. Todd, N. Krasnogor

Homebrew Photolithography for the Rapid and Low-Cost, “Do It Yourself” Prototyping of Microfluidic Devices

in ACS Omega, 8(38):35393-35409, September 2023

@ARTICLE{Todd2023,
  title = {Homebrew Photolithography for the Rapid and Low-Cost, “Do It Yourself” Prototyping of Microfluidic Devices},
  author = {Todd, Daniel and Krasnogor, Natalio},
  year = 2023,
  doi = {10.1021/acsomega.3c05544},
  month = sep,
  journal = {ACS Omega},
  volume = {8},
  number = {38},
  pages = {35393--35409}
}

L. Xiao, W. Huang, X. Li, F. Sun, Q. Liao, L. Jia, J. Li, S. Liu

ZNNs With a Varying-Parameter Design Formula for Dynamic Sylvester Quaternion Matrix Equation

in IEEE Transactions on Neural Networks and Learning Systems, 34(12):9981-9991, December 2023

@ARTICLE{Xiao2022,
  title = {ZNNs With a Varying-Parameter Design Formula for Dynamic Sylvester Quaternion Matrix Equation},
  author = {Xiao, Lin and Huang, Wenqian and Li, Xiaopeng and Sun, Fuchun and Liao, Qing and Jia, Lei and Li, Jichun and Liu, Sai},
  year = 2023,
  doi = {10.1109/TNNLS.2022.3163293},
  month = dec,
  journal = {IEEE Transactions on Neural Networks and Learning Systems},
  volume = {34},
  number = {12},
  pages = {9981--9991}
}

P. Widera, P.M.J. Welsing, S.O. Danso, S. Peelen, M. Kloppenburg, M. Loef, A.C. Marijnissen, E.M. van Helvoort, F.J. Blanco, J. Magalhães, F. Berenbaum, I.K. Haugen, A. Bay-Jensen, A. Mobasheri, C. Ladel, J. Loughlin, F.P.J. Lafeber, A. Lalande, J. Larkin, H. Weinans, J. Bacardit

Development and validation of a machine learning-supported strategy of patient selection for osteoarthritis clinical trials: the IMI-APPROACH study

in Osteoarthritis and Cartilage Open, 5(4):100406, December 2023

@ARTICLE{Widera2023,
  title = {Development and validation of a machine learning-supported strategy of patient selection for osteoarthritis clinical trials: the IMI-APPROACH study},
  author = {Widera, Paweł and Welsing, Paco M. J. and Danso, Samuel O. and Peelen, Sjaak and Kloppenburg, Margreet and Loef, Marieke and Marijnissen, Anne C. and van Helvoort, Eefje M. and Blanco, Francisco J. and Magalhães, Joana and Berenbaum, Francis and Haugen, Ida K. and Bay-Jensen, Anne-Christine and Mobasheri, Ali and Ladel, Christoph and Loughlin, John and Lafeber, Floris P. J.G. and Lalande, Agnès and Larkin, Jonathan and Weinans, Harrie and Bacardit, Jaume},
  year = 2023,
  doi = {10.1016/j.ocarto.2023.100406},
  month = dec,
  journal = {Osteoarthritis and Cartilage Open},
  volume = {5},
  number = {4},
  pages = {100406}
}

B. Shirt-Ediss, J. Connolly, J. Elezgaray, E. Torelli, S.A. Navarro, J. Bacardit, N. Krasnogor

Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists

in Computational and Structural Biotechnology Journal, 21(C):3615-3626, 2023

@ARTICLE{Shirt-Ediss2023,
  title = {Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists},
  author = {Shirt-Ediss, Ben and Connolly, Jordan and Elezgaray, Juan and Torelli, Emanuela and Navarro, Silvia Adriana and Bacardit, Jaume and Krasnogor, Natalio},
  year = 2023,
  doi = {10.1016/j.csbj.2023.07.011},
  journal = {Computational and Structural Biotechnology Journal},
  volume = {21},
  number = {C},
  pages = {3615--3626}
}

2022

S.M. Sisodiya, C.D. Whelan, S.N. Hatton, K. Huynh, A. Altmann, M. Ryten, A. Vezzani, M.E. Caligiuri, A. Labate, A. Gambardella, V. Ives‐Deliperi, S. Meletti, B.C. Munsell, L. Bonilha, M. Tondelli, M. Rebsamen, C. Rummel, A.E. Vaudano, R. Wiest, A.R. Balachandra, N. Bargalló, E. Bartolini, A. Bernasconi, N. Bernasconi, B. Bernhardt, B. Caldairou, S.J.A. Carr, G.L. Cavalleri, F. Cendes, L. Concha, P.M. Desmond, M. Domin, et al.

The ENIGMA‐Epilepsy working group: Mapping disease from large data sets

in Human Brain Mapping, 43(1):113-128, January 2022

@ARTICLE{Sisodiya2022,
title = {The ENIGMA‐Epilepsy working group: Mapping disease from large data sets},
author = {Sisodiya, Sanjay M. and Whelan, Christopher D. and Hatton, Sean N. and Huynh, Khoa and Altmann, Andre and Ryten, Mina and Vezzani, Annamaria and Caligiuri, Maria Eugenia and Labate, Angelo and Gambardella, Antonio and Ives‐Deliperi, Victoria and Meletti, Stefano and Munsell, Brent C. and Bonilha, Leonardo and Tondelli, Manuela and Rebsamen, Michael and Rummel, Christian and Vaudano, Anna Elisabetta and Wiest, Roland and Balachandra, Akshara R. and Bargalló, Núria and Bartolini, Emanuele and Bernasconi, Andrea and Bernasconi, Neda and Bernhardt, Boris and Caldairou, Benoit and Carr, Sarah J. A. and Cavalleri, Gianpiero L. and Cendes, Fernando and Concha, Luis and Desmond, Patricia M. and Domin, Martin and Duncan, John S. and Focke, Niels K. and Guerrini, Renzo and Hamandi, Khalid and Jackson, Graeme D. and Jahanshad, Neda and Kälviäinen, Reetta and Keller, Simon S. and Kochunov, Peter and Kowalczyk, Magdalena A. and Kreilkamp, Barbara A. K. and Kwan, Patrick and Lariviere, Sara and Lenge, Matteo and Lopez, Seymour M. and Martin, Pascal and Mascalchi, Mario and Moreira, José C. V. and Morita‐Sherman, Marcia E. and Pardoe, Heath R. and Pariente, Jose C. and Raviteja, Kotikalapudi and Rocha, Cristiane S. and Rodríguez‐Cruces, Raúl and Seeck, Margitta and Semmelroch, Mira K. H.G. and Sinclair, Benjamin and Soltanian‐Zadeh, Hamid and Stein, Dan J. and Striano, Pasquale and Taylor, Peter N. and Thomas, Rhys H. and Thomopoulos, Sophia I. and Velakoulis, Dennis and Vivash, Lucy and Weber, Bernd and Yasuda, Clarissa Lin and Zhang, Junsong and Thompson, Paul M. and McDonald, Carrie R. and Abela, Eugenio and Absil, Julie and Adams, Sophia and Alhusaini, Saud and Alvim, Marina and Balestrini, Simona and Bender, Benjamin and Bergo, Felipe and Bernardes, Tauana and Calvo, Anna and Carreno, Mar and Cherubini, Andrea and David, Philippe and Davoodi‐Bojd, Esmaeil and Delanty, Norman and Depondt, Chantal and Devinsky, Orrin and Doherty, Colin and França, Wendy Caroline and Franceschet, Leticia and Hibar, Derrek P. and Ishikawa, Akari and Kaestner, Erik and Langner, Soenke and Liu, Min and Mirandola, Laura and Naylor, Jillian and Nazem‐Zadeh, Mohammad‐reza and O'Brien, Terence J. and Ribeiro, Letícia F. and Richardson, Mark and Rosenow, Felix and Severino, Mariasavina and Shuai, Chen and Tortora, Domenico and von Podewils, Felix and Vos, Sjoerd B. and Wagner, Jan and Zhang, Guohao},
year = 2022,
doi = {10.1002/hbm.25037},
month = jan,
journal = {Human Brain Mapping},
volume = {43},
number = {1},
pages = {113--128}
}

P. Darke, S. Cassidy, M. Catt, R. Taylor, P. Missier, J. Bacardit

Curating a longitudinal research resource using linked primary care EHR data—a UK Biobank case study

in Journal of the American Medical Informatics Association, 29(3):546-552, January 2022

@ARTICLE{Darke2021,
  title = {Curating a longitudinal research resource using linked primary care EHR data—a UK Biobank case study},
  author = {Darke, Philip and Cassidy, Sophie and Catt, Michael and Taylor, Roy and Missier, Paolo and Bacardit, Jaume},
  year = 2022,
  doi = {10.1093/jamia/ocab260},
  month = jan,
  journal = {Journal of the American Medical Informatics Association},
  volume = {29},
  number = {3},
  pages = {546--552}
}

S. Jiang, I. Otero-Muras, J.R. Banga, Y. Wang, M. Kaiser, N. Krasnogor

OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production

in ACS Synthetic Biology, 11(4):1531-1541, April 2022

@ARTICLE{Jiang2022,
  title = {OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production},
  author = {Jiang, Shouyong and Otero-Muras, Irene and Banga, Julio R. and Wang, Yong and Kaiser, Marcus and Krasnogor, Natalio},
  year = 2022,
  doi = {10.1021/acssynbio.1c00610},
  month = apr,
  journal = {ACS Synthetic Biology},
  volume = {11},
  number = {4},
  pages = {1531--1541}
}

P.N. Taylor, C.A. Papasavvas, T.W. Owen, G.M. Schroeder, F.E. Hutchings, F.A. Chowdhury, B. Diehl, J.S. Duncan, A.W. McEvoy, A. Miserocchi, J. de Tisi, S.B. Vos, M.C. Walker, Y. Wang

Normative brain mapping of interictal intracranial EEG to localize epileptogenic tissue

in Brain, 145(3):939-949, April 2022

@ARTICLE{Taylor2022a,
  title = {Normative brain mapping of interictal intracranial EEG to localize epileptogenic tissue},
  author = {Taylor, Peter N and Papasavvas, Christoforos A and Owen, Thomas W and Schroeder, Gabrielle M and Hutchings, Frances E and Chowdhury, Fahmida A and Diehl, Beate and Duncan, John S and McEvoy, Andrew W and Miserocchi, Anna and de Tisi, Jane and Vos, Sjoerd B and Walker, Matthew C and Wang, Yujiang},
  year = 2022,
  doi = {10.1093/brain/awab380},
  month = apr,
  journal = {Brain},
  volume = {145},
  number = {3},
  pages = {939--949}
}

K. James, J. Muñoz-Muñoz

Computational Network Inference for Bacterial Interactomics

in mSystems, 7(2), April 2022

@ARTICLE{James2022,
  title = {Computational Network Inference for Bacterial Interactomics},
  author = {James, Katherine and Muñoz-Muñoz, Jose},
  year = 2022,
  doi = {10.1128/msystems.01456-21},
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C. A Papasavvas, P. Neal Taylor, Y. Wang

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G. Vidal, C. Vidal-Céspedes, T.J. Rudge

LOICA: Integrating Models with Data for Genetic Network Design Automation

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F. Angelini, P. Widera, A. Mobasheri, J. Blair, A. Struglics, M. Uebelhoer, Y. Henrotin, A.C. Marijnissen, M. Kloppenburg, F.J. Blanco, I.K. Haugen, F. Berenbaum, C. Ladel, J. Larkin, A.C. Bay-Jensen, J. Bacardit

Osteoarthritis endotype discovery via clustering of biochemical marker data

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H. Fellermann, R.M. Füchslin

Editorial: The 2019 Conference on Artificial Life Special Issue

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M. Panagiotopoulou, C.A. Papasavvas, G.M. Schroeder, R.H. Thomas, P.N. Taylor, Y. Wang

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E. Torelli, B. Shirt-Ediss, S.A. Navarro, M. Manzano, P. Vizzini, N. Krasnogor

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K. James, A. Wipat, S.J. Cockell

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G.M. Schroeder, F.A. Chowdhury, M.J. Cook, B. Diehl, J.S. Duncan, P.J. Karoly, P.N. Taylor, Y. Wang

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A. McKavanagh, B.A.K. Kreilkamp, Y. Chen, C. Denby, M. Bracewell, K. Das, C. De Bezenac, A.G. Marson, P.N. Taylor, S.S. Keller

Altered Structural Brain Networks in Refractory and Nonrefractory Idiopathic Generalized Epilepsy

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Z. Wang, J. Li, I. Daly, J. Li

Machine Learning for Multi-Action Classification of Lower Limbs for BCI

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G. Vidal, C. Vitalis, M. Muñoz Silva, C. Castillo-Passi, G. Yáñez Feliú, F. Federici, T.J. Rudge

Accurate characterization of dynamic microbial gene expression and growth rate profiles

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C. Taylor, J. Guy, J. Bacardit

Prediction of growth in grower-finisher pigs using recurrent neural networks

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Event‐based modeling in temporal lobe epilepsy demonstrates progressive atrophy from cross‐sectional data

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C. Atallah, K. James, Z. Ou, J. Skelton, D. Markham, J. Finnigan, S. Charnock, A. Wipat

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F. Shmarov, G.R. Smith, S.C. Weatherhead, N.J. Reynolds, P. Zuliani

Individualised computational modelling of immune mediated disease onset, flare and clearance in psoriasis

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Y. Xia, P.G. Jayathilake, B. Li, P. Zuliani, D. Deehan, J. Longyear, P. Stoodley, J. Chen

Coupled CFD‐DEM modeling to predict how EPS affects bacterial biofilm deformation, recovery and detachment under flow conditions

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H. Danesh, D.H. Steel, J. Hogg, F. Ashtari, W. Innes, J. Bacardit, A. Hurlbert, J.C.A. Read, R. Kafieh

Synthetic OCT Data Generation to Enhance the Performance of Diagnostic Models for Neurodegenerative Diseases

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S.P. Samineni, G. Vidal, C. Vidal-Céspedes, G. Yañez-Feliú, T.J. Rudge, C.J. Myers, J. Mante

Experimental Data Connector (XDC): Integrating the Capture of Experimental Data and Metadata Using Standard Formats and Digital Repositories

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K. James, A. Alsobhe, S.J. Cockell, A. Wipat, M. Pocock

Integration of probabilistic functional networks without an external Gold Standard

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T.J. Rudge, G. Vidal

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J. Tellechea-Luzardo, L. Hobbs

Versioning biological cells for trustworthy cell engineering

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J.J. Horsley, G.M. Schroeder, R.H. Thomas, J. de Tisi, S.B. Vos, G.P. Winston, J.S. Duncan, Y. Wang, P.N. Taylor

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B. Li, N. Mackenzie, B. Shirt-Ediss, N. Krasnogor, P. Zuliani

Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking

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R.M. Füchslin, J. Ambühl, A. Faggian, H.M. Fellermann, D. Flumini, A. Geller, M.M. Hanczyc, A. Klinkert, P. Krütli, H. Matuttis, T. Ott, S. Scheidegger, G.B. Schmid, T. Smieszek, J.J. Schneider, A. Steiner, M.S. Weyland

Ethical Aspects of Computational Modelling in Science, Decision Support and Communication

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2021

V. de Lorenzo, N. Krasnogor, M. Schmidt

For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!

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H. Tas, L. Grozinger, R. Stoof, V. de Lorenzo, Á. Goñi-Moreno

Contextual dependencies expand the re-usability of genetic inverters

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Y. Xia, P.G. Jayathilake, B. Li, P. Zuliani, J. Chen

CFD–DEM modelling of biofilm streamer oscillations and their cohesive failure in fluid flow

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K. Georgopoulos, C. Emary, P. Zuliani

Comparison of quantum-walk implementations on noisy intermediate-scale quantum computers

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T.W. Owen, J. Tisi, S.B. Vos, G.P. Winston, J.S. Duncan, Y. Wang, P.N. Taylor

Multivariate white matter alterations are associated with epilepsy duration

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Y. Huang, W. Smith, C. Harwood, A. Wipat, J. Bacardit

Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis

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A.M. Mitchell, V. Gogulancea, W. Smith, A. Wipat, I.D. Ofiţeru

Recombinant Protein Production with Escherichia coli in Glucose and Glycerol Limited Chemostats

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B. Little, O. Alshabrawy, D. Stow, I.N. Ferrier, R. McNaney, D.G. Jackson, K. Ladha, C. Ladha, T. Ploetz, J. Bacardit, P. Olivier, P. Gallagher, J.T. O'Brien

Deep learning-based automated speech detection as a marker of social functioning in late-life depression

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@ARTICLE{Little2020,
  title = {Deep learning-based automated speech detection as a marker of social functioning in late-life depression},
  author = {Little, Bethany and Alshabrawy, Ossama and Stow, Daniel and Ferrier, I. Nicol and McNaney, Roisin and Jackson, Daniel G. and Ladha, Karim and Ladha, Cassim and Ploetz, Thomas and Bacardit, Jaume and Olivier, Patrick and Gallagher, Peter and O'Brien, John T.},
  year = 2021,
  doi = {10.1017/S0033291719003994},
  month = jul,
  journal = {Psychological Medicine},
  volume = {51},
  number = {9},
  pages = {1441--1450}
}

S. Konur, L. Mierla, H. Fellermann, C. Ladroue, B. Brown, A. Wipat, J. Twycross, B.P. Dun, S. Kalvala, M. Gheorghe, N. Krasnogor

Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation

in ACS Synthetic Biology, 10(8):1931-1945, August 2021

@ARTICLE{Konur2021,
  title = {Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation},
  author = {Konur, Savas and Mierla, Laurentiu and Fellermann, Harold and Ladroue, Christophe and Brown, Bradley and Wipat, Anil and Twycross, Jamie and Dun, Boyang Peter and Kalvala, Sara and Gheorghe, Marian and Krasnogor, Natalio},
  year = 2021,
  doi = {10.1021/acssynbio.1c00143},
  month = aug,
  journal = {ACS Synthetic Biology},
  volume = {10},
  number = {8},
  pages = {1931--1945}
}

A. Lopiccolo, B. Shirt-Ediss, E. Torelli, A.F.A. Olulana, M. Castronovo, H. Fellermann, N. Krasnogor

A last-in first-out stack data structure implemented in DNA

in Nature Communications, 12(1), August 2021

@ARTICLE{Lopiccolo2021,
  title = {A last-in first-out stack data structure implemented in DNA},
  author = {Lopiccolo, Annunziata and Shirt-Ediss, Ben and Torelli, Emanuela and Olulana, Abimbola Feyisara Adedeji and Castronovo, Matteo and Fellermann, Harold and Krasnogor, Natalio},
  year = 2021,
  doi = {10.1038/s41467-021-25023-6},
  month = aug,
  journal = {Nature Communications},
  volume = {12},
  number = {1}

N. Partridge

Towards greater transparency: Digital opportunities to promote traceability in genetic engineering.

Newcastle University technical report, 1, August 2021

This Policy Brief is an output from the N8 AgriFood Food Systems Policy Hub. It is one of a collection produced by participants on the Rapid Evidence Synthesis Training (REST) programme. REST was delivered through a collaboration between the University of Leeds, Newcastle University and the N8 AgriFood Programme, supported by Research England QR-SPF funds from the University of Leeds and the University of York.

@TECHREPORT{Partridge2021,
  title = {Towards greater transparency: Digital opportunities to promote traceability in genetic engineering.},
  author = {Partridge, Natalie},
  year = 2021,
  doi = {10.5281/zenodo.5343358},
  note = {This Policy Brief is an output from the N8 AgriFood Food Systems Policy Hub. It is one of a collection produced by participants on the Rapid Evidence Synthesis Training (REST) programme. REST was delivered through a collaboration between the University of Leeds, Newcastle University and the N8 AgriFood Programme, supported by Research England QR-SPF funds from the University of Leeds and the University of York.},
  month = aug,
  number = {1},
  institution = {Newcastle University}
}

H. Tas, L. Grozinger, A. Goñi-Moreno, V. de Lorenzo

Automated design and implementation of a NOR gate in Pseudomonas putida

in Synthetic Biology, 6(1), October 2021

@ARTICLE{Tas2021a,
  title = {Automated design and implementation of a NOR gate in Pseudomonas putida},
  author = {Tas, Huseyin and Grozinger, Lewis and Goñi-Moreno, Angel and de Lorenzo, Victor},
  year = 2021,
  doi = {10.1093/synbio/ysab024},
  month = oct,
  journal = {Synthetic Biology},
  volume = {6},
  number = {1}

E. Velázquez, Y. Al-Ramahi, J. Tellechea-Luzardo, N. Krasnogor, V. de Lorenzo

Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection

in ACS Synthetic Biology, 10(10):2552-2565, October 2021

@ARTICLE{Velazquez2021,
  title = {Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection},
  author = {Velázquez, Elena and Al-Ramahi, Yamal and Tellechea-Luzardo, Jonathan and Krasnogor, Natalio and de Lorenzo, Víctor},
  year = 2021,
  doi = {10.1021/acssynbio.1c00199},
  month = oct,
  journal = {ACS Synthetic Biology},
  volume = {10},
  number = {10},
  pages = {2552--2565}
}

S.W. Choo, W.K. Mohammed, N.V.R. Mutha, N. Rostami, H. Ahmed, N. Krasnogor, G.Y.A. Tan, N.S. Jakubovics

Transcriptomic Responses to Coaggregation between Streptococcus gordonii and Streptococcus oralis

in Applied and Environmental Microbiology, 87(22), October 2021

@ARTICLE{Choo2021,
  title = {Transcriptomic Responses to Coaggregation between Streptococcus gordonii and Streptococcus oralis},
  author = {Choo, Siew Woh and Mohammed, Waleed K. and Mutha, Naresh V. R. and Rostami, Nadia and Ahmed, Halah and Krasnogor, Natalio and Tan, Geok Yuan Annie and Jakubovics, Nicholas S.},
  year = 2021,
  doi = {10.1128/AEM.01558-21},
  month = oct,
  journal = {Applied and Environmental Microbiology},
  volume = {87},
  number = {22}

N. Watson, N. Wilson, F. Shmarov, P. Zuliani, N.J. Reynolds, S.C. Weatherhead

The use of psoriasis biomarkers, including trajectory of clinical response, to predict clearance and remission duration to UVB phototherapy

in Journal of the European Academy of Dermatology and Venereology, 35(11):2250-2258, November 2021

@ARTICLE{Watson2021,
  title = {The use of psoriasis biomarkers, including trajectory of clinical response, to predict clearance and remission duration to UVB phototherapy},
  author = {Watson, N. and Wilson, N. and Shmarov, F. and Zuliani, P. and Reynolds, N. J. and Weatherhead, S. C.},
  year = 2021,
  doi = {10.1111/jdv.17519},
  month = nov,
  journal = {Journal of the European Academy of Dermatology and Venereology},
  volume = {35},
  number = {11},
  pages = {2250--2258}
}

G. Mısırlı, B. Yang, K. James, A. Wipat

Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits

in ACS Synthetic Biology, 10(12):3304-3315, December 2021

Portabolomics paper

@ARTICLE{Msrl2021,
  title = {Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits},
  author = {Mısırlı, Göksel and Yang, Bill and James, Katherine and Wipat, Anil},
  year = 2021,
  doi = {10.1021/acssynbio.1c00157},
  note = {Portabolomics paper},
  month = dec,
  journal = {ACS Synthetic Biology},
  volume = {10},
  number = {12},
  pages = {3304--3315}
}

A. Guyet, A. Alofi, R. Daniel

Insights into the role of lipoteichoic acids in Bacillus subtilis- a new function for MprF

in Biorxiv, N/A(N/A):1, December 2021

@ARTICLE{Guyet2021,
  title = {Insights into the role of lipoteichoic acids in Bacillus subtilis- a new function for MprF},
  author = {Guyet, Aurelie and Alofi, Amirah and Daniel, Richard},
  year = 2021,
  doi = {10.1101/2021.12.12.472321},
  month = dec,
  journal = {Biorxiv},
  volume = {N/A},
  number = {N/A},
  pages = {1}
}

M.M. Callaghan, B. Koch, K.T. Hackett, A.K. Klimowicz, R.E. Schaub, N. Krasnogor, J.P. Dillard

Expression, Localization, and Protein Interactions of the Partitioning Proteins in the Gonococcal Type IV Secretion System

in Frontiers in Microbiology, 12, December 2021

@ARTICLE{Callaghan2021,
  title = {Expression, Localization, and Protein Interactions of the Partitioning Proteins in the Gonococcal Type IV Secretion System},
  author = {Callaghan, Melanie M. and Koch, Birgit and Hackett, Kathleen T. and Klimowicz, Amy K. and Schaub, Ryan E. and Krasnogor, Natalio and Dillard, Joseph P.},
  year = 2021,
  doi = {10.3389/fmicb.2021.784483},
  month = dec,
  journal = {Frontiers in Microbiology},
  volume = {12}

K. Georgopoulos, C. Emary, P. Zuliani

Modeling and simulating the noisy behavior of near-term quantum computers

in Physical Review A, 104(6), December 2021

@ARTICLE{Georgopoulos2021,
  title = {Modeling and simulating the noisy behavior of near-term quantum computers},
  author = {Georgopoulos, Konstantinos and Emary, Clive and Zuliani, Paolo},
  year = 2021,
  doi = {10.1103/PhysRevA.104.062432},
  month = dec,
  journal = {Physical Review A},
  volume = {104},
  number = {6}

2020

D. Zerti, B. Dorgau, M. Felemban, A.E. Ghareeb, M. Yu, Y. Ding, N. Krasnogor, M. Lako

Developing a simple method to enhance the generation of cone and rod photoreceptors in pluripotent stem cell-derived retinal organoids

in STEM CELLS, 38(1):45-51, January 2020

@ARTICLE{Zerti2020,
  title = {Developing a simple method to enhance the generation of cone and rod photoreceptors in pluripotent stem cell-derived retinal organoids},
  author = {Zerti, Darin and Dorgau, Birthe and Felemban, Majed and Ghareeb, Ali E. and Yu, Min and Ding, Yuchun and Krasnogor, Natalio and Lako, Majlinda},
  year = 2020,
  doi = {10.1002/stem.3082},
  month = jan,
  journal = {STEM CELLS},
  volume = {38},
  number = {1},
  pages = {45--51}
}

A. Riaz-Bradley, K. James, Y. Yuzenkova

High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors

in Nucleic Acids Research, 48(3):1341-1352, February 2020

@ARTICLE{Riaz-Bradley2020,
  title = {High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors},
  author = {Riaz-Bradley, Amber and James, Katherine and Yuzenkova, Yulia},
  year = 2020,
  doi = {10.1093/nar/gkz1130},
  month = feb,
  journal = {Nucleic Acids Research},
  volume = {48},
  number = {3},
  pages = {1341--1352}
}

J. Tellechea-Luzardo, C. Winterhalter, P. Widera, J. Kozyra, V. de Lorenzo, N. Krasnogor

Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering

in ACS Synthetic Biology, 9(3):536-545, March 2020

@ARTICLE{Tellechea-Luzardo2020,
  title = {Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering},
  author = {Tellechea-Luzardo, Jonathan and Winterhalter, Charles and Widera, Paweł and Kozyra, Jerzy and de Lorenzo, Víctor and Krasnogor, Natalio},
  year = 2020,
  doi = {10.1021/acssynbio.9b00400},
  month = mar,
  journal = {ACS Synthetic Biology},
  volume = {9},
  number = {3},
  pages = {536--545}
}

S. Jiang, H. Li, J. Guo, M. Zhong, S. Yang, M. Kaiser, N. Krasnogor

AREA: An adaptive reference-set based evolutionary algorithm for multiobjective optimisation

in Information Sciences, 515(C):365-387, April 2020

@ARTICLE{Jiang2020a,
  title = {AREA: An adaptive reference-set based evolutionary algorithm for multiobjective optimisation},
  author = {Jiang, Shouyong and Li, Hongru and Guo, Jinglei and Zhong, Mingjun and Yang, Shengxiang and Kaiser, Marcus and Krasnogor, Natalio},
  year = 2020,
  doi = {10.1016/j.ins.2019.12.011},
  month = apr,
  journal = {Information Sciences},
  volume = {515},
  number = {C},
  pages = {365--387}
}

G. Mısırlı, J. Beal, T.E. Gorochowski, G. Stan, A. Wipat, C.J. Myers

SBOL Visual 2 Ontology

in ACS Synthetic Biology, 9(4):972-977, April 2020

@ARTICLE{Misirli2020,
  title = {SBOL Visual 2 Ontology},
  author = {Mısırlı, Göksel and Beal, Jacob and Gorochowski, Thomas E. and Stan, Guy-Bart and Wipat, Anil and Myers, Chris J.},
  year = 2020,
  doi = {10.1021/acssynbio.0c00046},
  month = apr,
  journal = {ACS Synthetic Biology},
  volume = {9},
  number = {4},
  pages = {972--977}
}

S.L. Armour, S.J. Anderson, S.J. Richardson, Y. Ding, C. Carey, J. Lyon, R.R. Maheshwari, N. Al-Jahdami, N. Krasnogor, N.G. Morgan, P. MacDonald, J.A.M. Shaw, M.G. White

Reduced Expression of the Co-regulator TLE1 in Type 2 Diabetes Is Associated with Increased Islet α-Cell Number

in Endocrinology, 161(4), April 2020

@ARTICLE{Armour2020,
  title = {Reduced Expression of the Co-regulator TLE1 in Type 2 Diabetes Is Associated with Increased Islet α-Cell Number},
  author = {Armour, Sarah L and Anderson, Scott J and Richardson, Sarah J and Ding, Yuchun and Carey, Chris and Lyon, James and Maheshwari, Rashmi R and Al-Jahdami, Najwa and Krasnogor, Natalio and Morgan, Noel G and MacDonald, Patrick and Shaw, James A M and White, Michael G},
  year = 2020,
  doi = {10.1210/endocr/bqaa011},
  month = apr,
  journal = {Endocrinology},
  volume = {161},
  number = {4}

M. Crowther, L. Grozinger, M. Pocock, C.P.D. Taylor, J.A. McLaughlin, G. Mısırlı, B.A. Bartley, J. Beal, A. Goñi-Moreno, A. Wipat

ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL)

in ACS Synthetic Biology, 9(4):962-966, April 2020

@ARTICLE{Crowther2020,
  title = {ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL)},
  author = {Crowther, Matthew and Grozinger, Lewis and Pocock, Matthew and Taylor, Christopher P. D. and McLaughlin, James A. and Mısırlı, Göksel and Bartley, Bryan A. and Beal, Jacob and Goñi-Moreno, Angel and Wipat, Anil},
  year = 2020,
  doi = {10.1021/acssynbio.9b00470},
  month = apr,
  journal = {ACS Synthetic Biology},
  volume = {9},
  number = {4},
  pages = {962--966}
}

M.G. White, R.R. Maheshwari, S.J. Anderson, R. Berlinguer-Palmini, C. Jones, S.J. Richardson, P.G. Rotti, S.L. Armour, Y. Ding, N. Krasnogor, J.F. Engelhardt, M.A. Gray, N.G. Morgan, J.A.M. Shaw

In Situ Analysis Reveals That CFTR Is Expressed in Only a Small Minority of β-Cells in Normal Adult Human Pancreas

in The Journal of Clinical Endocrinology & Metabolism, 105(5):1366-1374, May 2020

@ARTICLE{White2020,
  title = {In Situ Analysis Reveals That CFTR Is Expressed in Only a Small Minority of β-Cells in Normal Adult Human Pancreas},
  author = {White, Michael G and Maheshwari, Rashmi R and Anderson, Scott J and Berlinguer-Palmini, Rolando and Jones, Claire and Richardson, Sarah J and Rotti, Pavana G and Armour, Sarah L and Ding, Yuchun and Krasnogor, Natalio and Engelhardt, John F and Gray, Mike A and Morgan, Noel G and Shaw, James A M},
  year = 2020,
  doi = {10.1210/clinem/dgz209},
  month = may,
  journal = {The Journal of Clinical Endocrinology & Metabolism},
  volume = {105},
  number = {5},
  pages = {1366--1374}
}

DOI eprint data BibTeX

P. Widera, P.M.J. Welsing, C. Ladel, J. Loughlin, F.P.F.J. Lafeber, F. Petit Dop, J. Larkin, H. Weinans, A. Mobasheri, J. Bacardit

Multi-classifier prediction of knee osteoarthritis progression from incomplete imbalanced longitudinal data

in Scientific Reports, 10(1), May 2020

@ARTICLE{Widera2020,
  title = {Multi-classifier prediction of knee osteoarthritis progression from incomplete imbalanced longitudinal data},
  author = {Widera, Paweł and Welsing, Paco M. J. and Ladel, Christoph and Loughlin, John and Lafeber, Floris P. F. J. and Petit Dop, Florence and Larkin, Jonathan and Weinans, Harrie and Mobasheri, Ali and Bacardit, Jaume},
  year = 2020,
  doi = {10.1038/s41598-020-64643-8},
  month = may,
  journal = {Scientific Reports},
  volume = {10},
  number = {1}

N.J. Kenny, S.A. McCarthy, O. Dudchenko, K. James, E. Betteridge, C. Corton, J. Dolucan, D. Mead, K. Oliver, A.D. Omer, S. Pelan, Y. Ryan, Y. Sims, J. Skelton, M. Smith, J. Torrance, D. Weisz, A. Wipat, E.L. Aiden, K. Howe, S.T. Williams

The gene-rich genome of the scallop Pecten maximus

in GigaScience, 9(5), May 2020

@ARTICLE{Kenny2020,
  title = {The gene-rich genome of the scallop Pecten maximus},
  author = {Kenny, Nathan J and McCarthy, Shane A and Dudchenko, Olga and James, Katherine and Betteridge, Emma and Corton, Craig and Dolucan, Jale and Mead, Dan and Oliver, Karen and Omer, Arina D and Pelan, Sarah and Ryan, Yan and Sims, Ying and Skelton, Jason and Smith, Michelle and Torrance, James and Weisz, David and Wipat, Anil and Aiden, Erez L and Howe, Kerstin and Williams, Suzanne T},
  year = 2020,
  doi = {10.1093/gigascience/giaa037},
  month = may,
  journal = {GigaScience},
  volume = {9},
  number = {5}

S. Jiang, Y. Wang, M. Kaiser, N. Krasnogor

NIHBA: a network interdiction approach for metabolic engineering design

in Bioinformatics, 36(11):3482-3492, June 2020

@ARTICLE{Jiang2020,
  title = {NIHBA: a network interdiction approach for metabolic engineering design},
  author = {Jiang, Shouyong and Wang, Yong and Kaiser, Marcus and Krasnogor, Natalio},
  year = 2020,
  doi = {10.1093/bioinformatics/btaa163},
  month = jun,
  journal = {Bioinformatics},
  volume = {36},
  number = {11},
  pages = {3482--3492}
}

S. Jiang, M. Kaiser, S. Yang, S. Kollias, N. Krasnogor

A Scalable Test Suite for Continuous Dynamic Multiobjective Optimization

in IEEE Transactions on Cybernetics, 50(6):2814-2826, June 2020

@ARTICLE{Jiang2019,
  title = {A Scalable Test Suite for Continuous Dynamic Multiobjective Optimization},
  author = {Jiang, Shouyong and Kaiser, Marcus and Yang, Shengxiang and Kollias, Stefanos and Krasnogor, Natalio},
  year = 2020,
  doi = {10.1109/TCYB.2019.2896021},
  month = jun,
  journal = {IEEE Transactions on Cybernetics},
  volume = {50},
  number = {6},
  pages = {2814--2826}
}

T.E. Gorochowski, S. Hauert, J. Kreft, L. Marucci, N.R. Stillman, T.-.D. Tang, L. Bandiera, V. Bartoli, D.O.R. Dixon, A.J.H. Fedorec, H. Fellermann, A.G. Fletcher, T. Foster, L. Giuggioli, A. Matyjaszkiewicz, S. McCormick, S. Montes Olivas, J. Naylor, A. Rubio Denniss, D. Ward

Toward Engineering Biosystems With Emergent Collective Functions

in Frontiers in Bioengineering and Biotechnology, 8, June 2020

@ARTICLE{Gorochowski2020,
  title = {Toward Engineering Biosystems With Emergent Collective Functions},
  author = {Gorochowski, Thomas E. and Hauert, Sabine and Kreft, Jan-Ulrich and Marucci, Lucia and Stillman, Namid R. and Tang, T. -Y. Dora and Bandiera, Lucia and Bartoli, Vittorio and Dixon, Daniel O. R. and Fedorec, Alex J. H. and Fellermann, Harold and Fletcher, Alexander G. and Foster, Tim and Giuggioli, Luca and Matyjaszkiewicz, Antoni and McCormick, Scott and Montes Olivas, Sandra and Naylor, Jonathan and Rubio Denniss, Ana and Ward, Daniel},
  year = 2020,
  doi = {10.3389/fbioe.2020.00705},
  month = jun,
  journal = {Frontiers in Bioengineering and Biotechnology},
  volume = {8}

E. Torelli, J. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor

Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami

in ACS Synthetic Biology, 9(7):1682-1692, July 2020

@ARTICLE{Torelli2020,
  title = {Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami},
  author = {Torelli, Emanuela and Kozyra, Jerzy and Shirt-Ediss, Ben and Piantanida, Luca and Voïtchovsky, Kislon and Krasnogor, Natalio},
  year = 2020,
  doi = {10.1021/acssynbio.0c00009},
  month = jul,
  journal = {ACS Synthetic Biology},
  volume = {9},
  number = {7},
  pages = {1682--1692}
}

E.M. van Helvoort, W.E. van Spil, M.P. Jansen, P.M.J. Welsing, M. Kloppenburg, M. Loef, F.J. Blanco, I.K. Haugen, F. Berenbaum, J. Bacardit, C.H. Ladel, J. Loughlin, A.C. Bay-Jensen, A. Mobasheri, J. Larkin, J. Boere, H.H. Weinans, A. Lalande, A.C.A. Marijnissen, F.P.J.G. Lafeber

Cohort profile: The Applied Public-Private Research enabling OsteoArthritis Clinical Headway (IMI-APPROACH) study: a 2-year, European, cohort study to describe, validate and predict phenotypes of osteoarthritis using clinical, imaging and biochemical markers

in BMJ Open, 10(7):e035101, July 2020

@ARTICLE{Helvoort2020,
  title = {Cohort profile: The Applied Public-Private Research enabling OsteoArthritis Clinical Headway (IMI-APPROACH) study: a 2-year, European, cohort study to describe, validate and predict phenotypes of osteoarthritis using clinical, imaging and biochemical markers},
  author = {van Helvoort, Eefje M and van Spil, Willem E and Jansen, Mylène P and Welsing, Paco M J and Kloppenburg, Margreet and Loef, Marieke and Blanco, Francisco J and Haugen, Ida K and Berenbaum, Francis and Bacardit, Jaume and Ladel, Christoph H and Loughlin, John and Bay-Jensen, Anne C and Mobasheri, Ali and Larkin, Jonathan and Boere, Janneke and Weinans, Harrie H and Lalande, Agnes and Marijnissen, Anne C A and Lafeber, Floris P J G},
  year = 2020,
  doi = {10.1136/bmjopen-2019-035101},
  month = jul,
  journal = {BMJ Open},
  volume = {10},
  number = {7},
  pages = {e035101}
}

A. Alameer, I. Kyriazakis, J. Bacardit

Automated recognition of postures and drinking behaviour for the detection of compromised health in pigs

in Scientific Reports, 10(1), August 2020

@ARTICLE{Alameer2020a,
  title = {Automated recognition of postures and drinking behaviour for the detection of compromised health in pigs},
  author = {Alameer, Ali and Kyriazakis, Ilias and Bacardit, Jaume},
  year = 2020,
  doi = {10.1038/s41598-020-70688-6},
  month = aug,
  journal = {Scientific Reports},
  volume = {10},
  number = {1}

L.J. Wu, S. Lee, S. Park, L.E. Eland, A. Wipat, S. Holden, J. Errington

Geometric principles underlying the proliferation of a model cell system

in Nature Communications, 11(1), August 2020

@ARTICLE{Wu2020,
  title = {Geometric principles underlying the proliferation of a model cell system},
  author = {Wu, Ling Juan and Lee, Seoungjun and Park, Sungshic and Eland, Lucy E. and Wipat, Anil and Holden, Séamus and Errington, Jeff},
  year = 2020,
  doi = {10.1038/s41467-020-17988-7},
  month = aug,
  journal = {Nature Communications},
  volume = {11},
  number = {1}

M.A. Franco, N. Krasnogor, J. Bacardit

Automatic Tuning of Rule-Based Evolutionary Machine Learning via Problem Structure Identification

in IEEE Computational Intelligence Magazine, 15(3):28-46, August 2020

@ARTICLE{Franco2020,
  title = {Automatic Tuning of Rule-Based Evolutionary Machine Learning via Problem Structure Identification},
  author = {Franco, Maria A. and Krasnogor, Natalio and Bacardit, Jaume},
  year = 2020,
  doi = {10.1109/MCI.2020.2998232},
  month = aug,
  journal = {IEEE Computational Intelligence Magazine},
  volume = {15},
  number = {3},
  pages = {28--46}
}

B. Brown, B. Bartley, J. Beal, J.E. Bird, Á. Goñi-Moreno, J.A. McLaughlin, G. Mısırlı, N. Roehner, D.J. Skelton, C.L. Poh, I.D. Ofiteru, K. James, A. Wipat

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)

in ACS Synthetic Biology, 9(9):2410-2417, September 2020

@ARTICLE{Brown2020,
  title = {Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)},
  author = {Brown, Bradley and Bartley, Bryan and Beal, Jacob and Bird, Jasmine E. and Goñi-Moreno, Ángel and McLaughlin, James Alastair and Mısırlı, Göksel and Roehner, Nicholas and Skelton, David James and Poh, Chueh Loo and Ofiteru, Irina Dana and James, Katherine and Wipat, Anil},
  year = 2020,
  doi = {10.1021/acssynbio.0c00176},
  month = sep,
  journal = {ACS Synthetic Biology},
  volume = {9},
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  pages = {2410--2417}
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J.A. McLaughlin, J. Beal, G. Mısırlı, R. Grünberg, B.A. Bartley, J. Scott-Brown, P. Vaidyanathan, P. Fontanarrosa, E. Oberortner, A. Wipat, T.E. Gorochowski, C.J. Myers

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering

in Frontiers in Bioengineering and Biotechnology, 8, September 2020

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A. Alameer, I. Kyriazakis, H.A. Dalton, A.L. Miller, J. Bacardit

Automatic recognition of feeding and foraging behaviour in pigs using deep learning

in Biosystems Engineering, 197(C):91-104, September 2020

@ARTICLE{Alameer2020,
  title = {Automatic recognition of feeding and foraging behaviour in pigs using deep learning},
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B. Koch, M.M. Callaghan, J. Tellechea‐Luzardo, A.Y. Seeger, J.P. Dillard, N. Krasnogor

Protein interactions within and between two F‐type type IV secretion systems

in Molecular Microbiology, 114(5):823-838, November 2020

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P.D. Olson, A. Tracey, A. Baillie, K. James, S.R. Doyle, S.K. Buddenborg, F.H. Rodgers, N. Holroyd, M. Berriman

Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection

in BMC Biology, 18(1), December 2020

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M. Vasileva, F. Shmarov, P. Zuliani

Probabilistic Reachability for Uncertain Stochastic Hybrid Systems via Gaussian Processes

in 2020 18th ACM-IEEE International Conference on Formal Methods and Models for System Design (MEMOCODE), p.1-11, Jaipur, India, December 2020

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  title = {Probabilistic Reachability for Uncertain Stochastic Hybrid Systems via Gaussian Processes},
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K. James, P.D. Olson

The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma

in BMC Genomics, 21(1), December 2020

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F. Shmarov, S. Soudjani, N. Paoletti, E. Bartocci, S. Lin, S.A. Smolka, P. Zuliani

Automated Synthesis of Safe Digital Controllers for Sampled-Data Stochastic Nonlinear Systems

in IEEE Access, 8:180825-180843, 2020

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D. Flumini, M.S. Weyland, J.J. Schneider, H. Fellermann, R.M. Füchslin

Towards Programmable Chemistries

in Artificial Life and Evolutionary Computation, Communications in Computer and Information Science 1200, p.145-157, 2020

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S. Scheidegger, A. Mikos, H. Fellermann

Modelling Artificial Immune – Tumor Ecosystem Interaction During Radiation Therapy Using a Perceptron – Based Antigen Pattern Recognition

in The 2020 Conference on Artificial Life, p.541-548, Online, 2020

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  title = {Modelling Artificial Immune – Tumor Ecosystem Interaction During Radiation Therapy Using a Perceptron – Based Antigen Pattern Recognition},
  author = {Scheidegger, Stephan and Mikos, Alexander and Fellermann, Harold},
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2019

O.K. Oyebamiji, D.J. Wilkinson, B. Li, P.G. Jayathilake, P. Zuliani, T.P. Curtis

Bayesian emulation and calibration of an individual-based model of microbial communities

in Journal of Computational Science, 30(C):194-208, January 2019

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I. Ehrmann, J.H. Crichton, M.R. Gazzara, K. James, Y. Liu, S.N. Grellscheid, T. Curk, D. de Rooij, J.S. Steyn, S. Cockell, I.R. Adams, Y. Barash, D.J. Elliott

An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning

in eLife, 8, January 2019

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Z. Johanson, K. Martin, G. Fraser, K. James

The Synarcual of the Little Skate, Leucoraja erinacea: Novel Development Among the Vertebrates

in Frontiers in Ecology and Evolution, 7, February 2019

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  title = {The Synarcual of the Little Skate, Leucoraja erinacea: Novel Development Among the Vertebrates},
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C. Thornton, F. Hutchings, M. Kaiser

The Virtual Electrode Recording Tool for EXtracellular Potentials (VERTEX) Version 2.0: Modelling in vitro electrical stimulation of brain tissue

in Wellcome Open Research, 4:20, February 2019

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  title = {The Virtual Electrode Recording Tool for EXtracellular Potentials (VERTEX) Version 2.0: Modelling in vitro electrical stimulation of brain tissue},
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C. Thomas, A. Datta, M. Kaiser, F. Hutchings

Towards modeling the influence of transcranial direct current stimulation on neuronal response

in Brain Stimulation, 12(2):583, March 2019

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B. Dorgau, M. Felemban, G. Hilgen, M. Kiening, D. Zerti, N.C. Hunt, M. Doherty, P. Whitfield, D. Hallam, K. White, Y. Ding, N. Krasnogor, J. Al-Aama, H.Z. Asfour, E. Sernagor, M. Lako

Decellularised extracellular matrix-derived peptides from neural retina and retinal pigment epithelium enhance the expression of synaptic markers and light responsiveness of human pluripotent stem cell derived retinal organoids

in Biomaterials, 199(C):63-75, April 2019

@ARTICLE{Dorgau2019,
  title = {Decellularised extracellular matrix-derived peptides from neural retina and retinal pigment epithelium enhance the expression of synaptic markers and light responsiveness of human pluripotent stem cell derived retinal organoids},
  author = {Dorgau, Birthe and Felemban, Majed and Hilgen, Gerrit and Kiening, Martin and Zerti, Darin and Hunt, Nicola Claire and Doherty, Mary and Whitfield, Phil and Hallam, Dean and White, Kathryn and Ding, Yuchun and Krasnogor, Natalio and Al-Aama, Jumana and Asfour, Hani Z. and Sernagor, Evelyne and Lako, Majlinda},
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N.V.R. Mutha, W.K. Mohammed, N. Krasnogor, G.Y.A. Tan, W.Y. Wee, Y. Li, S.W. Choo, N.S. Jakubovics

Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq

in Scientific Reports, 9(1), May 2019

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J.S. Hallinan, A. Wipat, R. Kitney, S. Woods, K. Taylor, A. Goñi-Moreno

Future-proofing synthetic biology: educating the next generation

in Engineering Biology, 3(2):25-31, June 2019

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B. Corominas-Murtra, H. Fellermann, R. Solé

Protocell Cycles as Thermodynamic Cycles

in The Energetics of Computing in Life and Machines, p.149-167, June 2019

@INCOLLECTION{Corominas-Murtra2019,
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J. Schumacher, L.R. Peraza, M. Firbank, A.J. Thomas, M. Kaiser, P. Gallagher, J.T. O’Brien, A.M. Blamire, J. Taylor

Dysfunctional brain dynamics and their origin in Lewy body dementia

in Brain, 142(6):1767-1782, June 2019

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J. Schumacher, R. Cromarty, P. Gallagher, M.J. Firbank, A.J. Thomas, M. Kaiser, A.M. Blamire, J.T. O’Brien, L.R. Peraza, J. Taylor

Structural correlates of attention dysfunction in Lewy body dementia and Alzheimer’s disease: an ex-Gaussian analysis

in Journal of Neurology, 266(7):1716-1726, July 2019

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H. Fellermann, B. Shirt-Ediss, J. Kozyra, M. Linsley, D. Lendrem, J. Isaacs, T. Howard

Design of experiments and the virtual PCR simulator: An online game for pharmaceutical scientists and biotechnologists

in Pharmaceutical Statistics, 18(4):402-406, July 2019

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  author = {Fellermann, Harold and Shirt-Ediss, Ben and Kozyra, Jerzy and Linsley, Matt and Lendrem, Dennis and Isaacs, John and Howard, Thomas},
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W.S. Smith, S. Coleman, J. Bacardit, S. Coxon

Insight from data analytics with an automotive aftermarket SME

in Quality and Reliability Engineering International, 35(5):1396-1407, July 2019

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  title = {Insight from data analytics with an automotive aftermarket SME},
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L.E. Eland, R.J. Davenport, A.B.d. Santos, C.R. Mota Filho

Molecular evaluation of microalgal communities in full-scale waste stabilisation ponds

in Environmental Technology, 40(15):1969-1976, July 2019

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J. Beal, T. Nguyen, T.E. Gorochowski, A. Goñi-Moreno, J. Scott-Brown, J.A. McLaughlin, C. Madsen, B. Aleritsch, B. Bartley, S. Bhakta, M. Bissell, S. Castillo Hair, K. Clancy, A. Luna, N. Le Novère, Z. Palchick, M. Pocock, H. Sauro, J.T. Sexton, J.J. Tabor, C.A. Voigt, Z. Zundel, C. Myers, A. Wipat

Communicating Structure and Function in Synthetic Biology Diagrams

in ACS Synthetic Biology, 8(8):1818-1825, August 2019

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  title = {Communicating Structure and Function in Synthetic Biology Diagrams},
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R. Stoof, A. Wood, Á. Goñi-Moreno

A Model for the Spatiotemporal Design of Gene Regulatory Circuits

in ACS Synthetic Biology, 8(9):2007-2016, September 2019

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  title = {A Model for the Spatiotemporal Design of Gene Regulatory Circuits},
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P.G. Jayathilake, B. Li, P. Zuliani, T. Curtis, J. Chen

Modelling bacterial twitching in fluid flows: a CFD-DEM approach

in Scientific Reports, 9(1), October 2019

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  title = {Modelling bacterial twitching in fluid flows: a CFD-DEM approach},
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D.J. Swan, D. Aschenbrenner, C.A. Lamb, K. Chakraborty, J. Clark, S. Pandey, K.R. Engelhardt, R. Chen, A. Cavounidis, Y. Ding, N. Krasnogor, C.D. Carey, M. Acres, S. Needham, A.J. Cant, P.D. Arkwright, A. Chandra, K. Okkenhaug, H.H. Uhlig, S. Hambleton

Immunodeficiency, autoimmune thrombocytopenia and enterocolitis caused by autosomal recessive deficiency of PIK3CD -encoded phosphoinositide 3-kinase δ

in Haematologica, 104(10):e483-e486, October 2019

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J.R. Tarn, N. Howard-Tripp, D.W. Lendrem, X. Mariette, A. Saraux, V. Devauchelle-Pensec, R. Seror, A.J. Skelton, K. James, P. McMeekin, S. Al-Ali, K.L. Hackett, B.C. Lendrem, B. Hargreaves, J. Casement, S. Mitchell, S.J. Bowman, E. Price, C.T. Pease, P. Emery, P. Lanyon, J. Hunter, M. Gupta, M. Bombardieri, N. Sutcliffe, C. Pitzalis, J. McLaren, A. Cooper, M. Regan, I. Giles, D. Isenberg, V. Saravanan, et al.

Symptom-based stratification of patients with primary Sjögren's syndrome: multi-dimensional characterisation of international observational cohorts and reanalyses of randomised clinical trials

in The Lancet Rheumatology, 1(2):e85-e94, October 2019

@ARTICLE{Tarn2019,
  title = {Symptom-based stratification of patients with primary Sjögren's syndrome: multi-dimensional characterisation of international observational cohorts and reanalyses of randomised clinical trials},
  author = {Tarn, Jessica R and Howard-Tripp, Nadia and Lendrem, Dennis W and Mariette, Xavier and Saraux, Alain and Devauchelle-Pensec, Valerie and Seror, Raphaele and Skelton, Andrew J and James, Katherine and McMeekin, Peter and Al-Ali, Shereen and Hackett, Katie L and Lendrem, B Clare and Hargreaves, Ben and Casement, John and Mitchell, Sheryl and Bowman, Simon J and Price, Elizabeth and Pease, Colin T and Emery, Paul and Lanyon, Peter and Hunter, John and Gupta, Monica and Bombardieri, Michele and Sutcliffe, Nurhan and Pitzalis, Costantino and McLaren, John and Cooper, Annie and Regan, Marian and Giles, Ian and Isenberg, David and Saravanan, Vadivelu and Coady, David and Dasgupta, Bhaskar and McHugh, Neil and Young-Min, Steven and Moots, Robert and Gendi, Nagui and Akil, Mohammed and Griffiths, Bridget and Johnsen, Svein J A and Norheim, Katrine B and Omdal, Roald and Stocken, Deborah and Everett, Colin and Fernandez, Catherine and Isaacs, John D and Gottenberg, Jacques-Eric and Ng, Wan-Fai and Devauchelle-Pensec, Valerie and Dieude, Philippe and Dubost, Jean Jacques and Fauchais, Anne-Laure and Goeb, Vincent and Hachulla, Eric and Larroche, Claire and Le Guern, Véronique and Morel, Jacques and Perdriger, Aleth and Puéchal, Xavier and Rist, Stephanie and Sen, Damien and Sibilia, Jean and Vittecoq, Olivier and Benessiano, Joelle and Tubiana, Sarah and Inamo, Karine and Gaete, Stanie and Batouche, Djilali and Molinari, Domitille and Randrianandrasana, Mickael and Pane, Isabelle and Abbe, Adeline and Baron, Gabriel and Ravaud, Philippe and Gottenberg, Jacques-Eric and Ravaud, Philippe and Puéchal, Xavier and Le Guern, Véronique and Sibilia, Jean and Larroche, Claire and Saraux, Alain and Devauchelle-Pensec, Valérie and Morel, Jacques and Hayem, Gilles and Hatron, Pierre and Perdriger, Aleth and Sene, Damien and Zarnitsky, Charles and Batouche, Djilali and Furlan, Valérie and Benessiano, Joelle and Perrodeau, Elodie and Seror, Raphaele and Mariette, Xavier and Brown, S and Navarro, N Coy and Pitzalis, C and Emery, P and Pavitt, S and Gray, J and Hulme, C and Hall, F and Busch, R and Smith, P and Dawson, L and Bombardieri, M and Ng, W-f and Pease, C and Price, E and Sutcliffe, N and Woods, C and Ruddock, S and Everett, C and Reynolds, C and Skinner, E and Poveda-Gallego, A and Rout, J and Macleod, I and Rauz, S and Bowman, S and Ng, Wan-Fai and Bowman, Simon J and Griffiths, Bridget and Hall, Frances and Bacaba, Elalaine C and Frankland, Helen and Moots, Robert and Chadravarty, Kuntal and Lamabadusuriya, Shamin and Bombardieri, Michele and Pitzalis, Constantino and Sutcliffe, Nurhan and Breston, Celia and Gendi, Nagui and Culfear, Karen and Riddell, Claire and Hamburger, John and Richards, Andrea and Rauz, Saaeh and Brailsford, Sue and Dasgin, Joanne and Logan, Joanne and Mulherin, Diarmuid and Andrews, Jacqueline and Emery, Pau and McManus, Alison and Pease, Colin and Pickles, David and Booth, Alison and Regan, Marian and Kin, Jon King and Holt, Amanda and Dimitroulas, Theodoros and Kadiki, Lucy and Kaur, Daljit and Kitas, George and Khan, Abdul and Cosier, Tracey and Panthakalam, Panthakala and Mintrim, Kell and Lloyd, Mark and Moore, Lisa and Gordon, Esther and Lawson, Cathy and Gupta, Monica and Hunter, John and Stirton, Lesley and Ortiz, Gill and Price, Elizabeth and Pelger, Suzannah and Gorman, Claire and Hans, Balinder and Clunie, Gavin and Lane, Suzanne and Rose, Ginny and Cuckow, Sue and Batley, Michael and Einosas, Ruby and Knight, Susan and Symmons, Deborah and Jones, Beverley and Carr, Andrew and Edgar, Suzanne and Figuereido, Francisco and Foggo, Heather and Lendrem, Dennis and Macleod, Iain and Mitchell, Sheryl and Downie, Christine and Tarn, Jessica and Locke, James and Al-Ali, Shereen and Legg, Sarah and Mirza, Kamran and Hargreaves, Ben and Hetherington, Laura and Jones, Adrian and Lanyon, Peter and Muir, Alice and White, Paula and Young-Min, Steven and Pugmire, Susan and Vadivelu, Saravanan and Cooper, Annie and Watkins, Marianne and Field, Anne and Kaye, Stephen and Mewar, Devesh and Medcalf, Patricia and Tomlinson, Pamela and Whiteside, Debbie and McHugh, Neil and Pauling, John and James, Julie and Dowden, Andrea and Akil, Mohammed and McDermott, Jayne and Godia, Olivia and Coady, David and Kidd, Elizabeth and Palmer, Lynne and Li, Charles and Bartrum, Sarah and Mead, De and Dasgupta, Bhaskar and Katsande, Victoria and Long, Pamela and Vermaak, Erin and Turner, Janet and Chandra, Usha and MacKay, Kirsten and Fedele, Stefano and Ferenkeh-Koroma, Ada and Giles, Ian and Isenberg, David and MaConnell, Helena and Ahwiren, Nyarko and Porter, Stephen and Allcoa, Paul and McLaren, John},
  year = 2019,
  doi = {10.1016/s2665-9913(19)30042-6},
  month = oct,
  journal = {The Lancet Rheumatology},
  volume = {1},
  number = {2},
  pages = {e85--e94}
}

J. Naylor, H. Fellermann, N. Krasnogor

Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations

in Bioinformatics, 35(19):3859-3860, October 2019

@ARTICLE{Naylor2019,
  title = {Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations},
  author = {Naylor, Jonathan and Fellermann, Harold and Krasnogor, Natalio},
  year = 2019,
  doi = {10.1093/bioinformatics/btz131},
  month = oct,
  journal = {Bioinformatics},
  volume = {35},
  number = {19},
  pages = {3859--3860}
}

D. Popescu, R.A. Botting, E. Stephenson, K. Green, S. Webb, L. Jardine, E.F. Calderbank, K. Polanski, I. Goh, M. Efremova, M. Acres, D. Maunder, P. Vegh, Y. Gitton, J. Park, R. Vento-Tormo, Z. Miao, D. Dixon, R. Rowell, D. McDonald, J. Fletcher, E. Poyner, G. Reynolds, M. Mather, C. Moldovan, L. Mamanova, F. Greig, M.D. Young, K.B. Meyer, S. Lisgo, J. Bacardit, A. Fuller, et al.

Decoding human fetal liver haematopoiesis

in Nature, 574(7778):365-371, October 2019

@ARTICLE{Popescu2019,
  title = {Decoding human fetal liver haematopoiesis},
  author = {Popescu, Dorin-Mirel and Botting, Rachel A. and Stephenson, Emily and Green, Kile and Webb, Simone and Jardine, Laura and Calderbank, Emily F. and Polanski, Krzysztof and Goh, Issac and Efremova, Mirjana and Acres, Meghan and Maunder, Daniel and Vegh, Peter and Gitton, Yorick and Park, Jong-Eun and Vento-Tormo, Roser and Miao, Zhichao and Dixon, David and Rowell, Rachel and McDonald, David and Fletcher, James and Poyner, Elizabeth and Reynolds, Gary and Mather, Michael and Moldovan, Corina and Mamanova, Lira and Greig, Frankie and Young, Matthew D. and Meyer, Kerstin B. and Lisgo, Steven and Bacardit, Jaume and Fuller, Andrew and Millar, Ben and Innes, Barbara and Lindsay, Susan and Stubbington, Michael J. T. and Kowalczyk, Monika S. and Li, Bo and Ashenberg, Orr and Tabaka, Marcin and Dionne, Danielle and Tickle, Timothy L. and Slyper, Michal and Rozenblatt-Rosen, Orit and Filby, Andrew and Carey, Peter and Villani, Alexandra-Chloé and Roy, Anindita and Regev, Aviv and Chédotal, Alain and Roberts, Irene and Göttgens, Berthold and Behjati, Sam and Laurenti, Elisa and Teichmann, Sarah A. and Haniffa, Muzlifah},
  year = 2019,
  doi = {10.1038/s41586-019-1652-y},
  month = oct,
  journal = {Nature},
  volume = {574},
  number = {7778},
  pages = {365--371}
}

L. Grozinger, M. Amos, T.E. Gorochowski, P. Carbonell, D.A. Oyarzún, R. Stoof, H. Fellermann, P. Zuliani, H. Tas, A. Goñi-Moreno

Pathways to cellular supremacy in biocomputing

in Nature Communications, 10(1), November 2019

@ARTICLE{Grozinger2019,
  title = {Pathways to cellular supremacy in biocomputing},
  author = {Grozinger, Lewis and Amos, Martyn and Gorochowski, Thomas E. and Carbonell, Pablo and Oyarzún, Diego A. and Stoof, Ruud and Fellermann, Harold and Zuliani, Paolo and Tas, Huseyin and Goñi-Moreno, Angel},
  year = 2019,
  doi = {10.1038/s41467-019-13232-z},
  month = nov,
  journal = {Nature Communications},
  volume = {10},
  number = {1}

L.R. Peraza, A. Díaz-Parra, O. Kennion, D. Moratal, J. Taylor, M. Kaiser, R. Bauer

Structural connectivity centrality changes mark the path toward Alzheimer's disease

in Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring, 11(C):98-107, December 2019

@ARTICLE{Peraza2019,
  title = {Structural connectivity centrality changes mark the path toward Alzheimer's disease},
  author = {Peraza, Luis R. and Díaz-Parra, Antonio and Kennion, Oliver and Moratal, David and Taylor, John-Paul and Kaiser, Marcus and Bauer, Roman},
  year = 2019,
  doi = {10.1016/j.dadm.2018.12.004},
  month = dec,
  journal = {Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring},
  volume = {11},
  number = {C},
  pages = {98--107}
}

N. Sinha, Y. Wang, J. Dauwels, M. Kaiser, T. Thesen, R. Forsyth, P.N. Taylor

Computer modelling of connectivity change suggests epileptogenesis mechanisms in idiopathic generalised epilepsy

in NeuroImage: Clinical, 21(C):101655, 2019

@ARTICLE{Sinha2019,
  title = {Computer modelling of connectivity change suggests epileptogenesis mechanisms in idiopathic generalised epilepsy},
  author = {Sinha, Nishant and Wang, Yujiang and Dauwels, Justin and Kaiser, Marcus and Thesen, Thomas and Forsyth, Rob and Taylor, Peter Neal},
  year = 2019,
  doi = {10.1016/j.nicl.2019.101655},
  journal = {NeuroImage: Clinical},
  volume = {21},
  number = {C},
  pages = {101655}
}

J. Schumacher, L.R. Peraza, M. Firbank, A.J. Thomas, M. Kaiser, P. Gallagher, J.T. O'Brien, A.M. Blamire, J. Taylor

Dynamic functional connectivity changes in dementia with Lewy bodies and Alzheimer's disease

in NeuroImage: Clinical, 22(C):101812, 2019

@ARTICLE{Schumacher2019a,
  title = {Dynamic functional connectivity changes in dementia with Lewy bodies and Alzheimer's disease},
  author = {Schumacher, Julia and Peraza, Luis R. and Firbank, Michael and Thomas, Alan J. and Kaiser, Marcus and Gallagher, Peter and O'Brien, John T. and Blamire, Andrew M. and Taylor, John-Paul},
  year = 2019,
  doi = {10.1016/j.nicl.2019.101812},
  journal = {NeuroImage: Clinical},
  volume = {22},
  number = {C},
  pages = {101812}
}

H. Fellermann, J. Bacardit, A. Goñi-Moreno, R.M. Füchslin

Artificial Life in a Challenged World

in The 2019 Conference on Artificial Life, p.1-3, Newcastle, United Kingdom, 2019

@INPROCEEDINGS{Fellermann2019b,
  title = {Artificial Life in a Challenged World},
  author = {Fellermann, Harold and Bacardit, Jaume and Goñi-Moreno, Angel and Füchslin, Rudolf M.},
  year = 2019,
  doi = {10.1162/isal_a_00123},
  booktitle = {The 2019 Conference on Artificial Life},
  pages = {1--3},
  address = {Newcastle, United Kingdom}
}

H. Fellermann, A.S. Penn, R.M. Füchslin, J. Bacardit, A. Goñi-Moreno

Towards Low-Carbon Conferencing: Acceptance of Virtual Conferencing Solutions and Other Sustainability Measures in the ALIFE Community

in The 2019 Conference on Artificial Life, p.21-27, Newcastle, United Kingdom, 2019

@INPROCEEDINGS{Fellermann2019a,
  title = {Towards Low-Carbon Conferencing: Acceptance of Virtual Conferencing Solutions and Other Sustainability Measures in the ALIFE Community},
  author = {Fellermann, Harold and Penn, Alexandra S. and Füchslin, Rudolf M. and Bacardit, Jaume and Goñi-Moreno, Angel},
  year = 2019,
  doi = {10.1162/isal_a_00133},
  booktitle = {The 2019 Conference on Artificial Life},
  pages = {21--27},
  address = {Newcastle, United Kingdom}
}

S. Scheidegger, H. Fellermann

Optimizing Radiation Therapy Treatments by Exploring Tumour Ecosystem Dynamics in – silico

in The 2019 Conference on Artificial Life, p.236-242, Newcastle, United Kingdom, 2019

@INPROCEEDINGS{Scheidegger2019,
  title = {Optimizing Radiation Therapy Treatments by Exploring Tumour Ecosystem Dynamics in – silico},
  author = {Scheidegger, Stephan and Fellermann, Harold},
  year = 2019,
  doi = {10.1162/isal_a_00167},
  booktitle = {The 2019 Conference on Artificial Life},
  pages = {236--242},
  address = {Newcastle, United Kingdom}
}

J. Cowton, I. Kyriazakis, J. Bacardit

Automated Individual Pig Localisation, Tracking and Behaviour Metric Extraction Using Deep Learning

in IEEE Access, 7:108049-108060, 2019

@ARTICLE{Cowton2019,
  title = {Automated Individual Pig Localisation, Tracking and Behaviour Metric Extraction Using Deep Learning},
  author = {Cowton, Jake and Kyriazakis, Ilias and Bacardit, Jaume},
  year = 2019,
  doi = {10.1109/ACCESS.2019.2933060},
  journal = {IEEE Access},
  volume = {7},
  pages = {108049--108060}
}

2018

eprint BibTeX

S. Jiang, S. Yang, X. Yao, K.C. Tan, M. Kaiser, N. Krasnogor

Benchmark Problems for CEC2018 Competition on Dynamic Multiobjective Optimisation

Newcastle University technical report, -, January 2018

@TECHREPORT{Jiang2018c,
  title = {Benchmark Problems for CEC2018 Competition on Dynamic Multiobjective Optimisation},
  author = {Jiang, Shouyong and Yang, Shengxiang and Yao, Xin and Tan, Kay Chen and Kaiser, Marcus and Krasnogor, Natalio},
  year = 2018,
  month = jan,
  number = {-},
  institution = {Newcastle University}
}

E. Torelli, M. Manzano, S.K. Srivastava, R.S. Marks

DNA origami nanorobot fiber optic genosensor to TMV

in Biosensors and Bioelectronics, 99(C):209-215, January 2018

@ARTICLE{Torelli2018,
  title = {DNA origami nanorobot fiber optic genosensor to TMV},
  author = {Torelli, Emanuela and Manzano, Marisa and Srivastava, Sachin K. and Marks, Robert S.},
  year = 2018,
  doi = {10.1016/j.bios.2017.07.051},
  month = jan,
  journal = {Biosensors and Bioelectronics},
  volume = {99},
  number = {C},
  pages = {209--215}
}

A. Dumuscab, W. Ng, K. James, B. Griffiths, E. Price, C.T. Pease, P. Emery, P. Lanyon, A. Jones, M. Bombardieri, N. Sutcliffe, C. Pitzalis, M. Gupta, J. McLaren, A. Cooper, I. Giles, D. Isenberg, V. Saravanan, D. Coady, B. Dasgupta, N. McHugh, S. Young-Min, R.J. Moots, N. Gendi, M. Akil, F. Barone, B.A. Fisher, S. Rauz, A. Richards, S.J. Bowman

Comparison of ESSDAI and ClinESSDAI in potential optimisation of trial outcomes in primary Sjögren’s syndrome: examination of data from the UK Primary Sjögren’s Syndrome Registry

in Swiss Medical Weekly, 148(56):w14588, February 2018

@ARTICLE{2018,
  title = {Comparison of ESSDAI and ClinESSDAI in potential optimisation of trial outcomes in primary Sjögren’s syndrome: examination of data from the UK Primary Sjögren’s Syndrome Registry},
  author = {Dumuscab, Alexandre and Ng, Wan-Fai and James, Katherine and Griffiths, Bridget and Price, Elizabeth and Pease, Colin T. and Emery, Paul and Lanyon, Peter  and Jones, Adrian and Bombardieri, Michele and Sutcliffe, Nurhan and Pitzalis, Costantino and Gupta, Monica and McLaren, John and Cooper, Annie and Giles, Ian and Isenberg, David and Saravanan, Vadivelu and Coady, David and Dasgupta, Bhaskar and McHugh, Neil and Young-Min, Steven and Moots, Robert J. and Gendi, Nagui and Akil, Mohammed and Barone, Francesca and Fisher, Benjamin A. and Rauz, Saaeha and Richards, Andrea and Bowman, Simon J.},
  year = 2018,
  doi = {10.4414/smw.2018.14588},
  month = feb,
  journal = {Swiss Medical Weekly},
  volume = {148},
  number = {56},
  pages = {w14588}
}

DOI data BibTeX

O. Markovitch, N. Krasnogor

Predicting species emergence in simulated complex pre-biotic networks

in PLOS ONE, 13(2):e0192871, February 2018

10.5281/zenodo.56534

@ARTICLE{Markovitch2018,
  title = {Predicting species emergence in simulated complex pre-biotic networks},
  author = {Markovitch, Omer and Krasnogor, Natalio},
  year = 2018,
  doi = {10.1371/journal.pone.0192871},
  note = {10.5281/zenodo.56534},
  month = feb,
  journal = {PLOS ONE},
  volume = {13},
  number = {2},
  pages = {e0192871}
}

J.A. McLaughlin, C.J. Myers, Z. Zundel, G. Mısırlı, M. Zhang, I.D. Ofiteru, A. Goñi-Moreno, A. Wipat

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology

in ACS Synthetic Biology, 7(2):682-688, February 2018

@ARTICLE{McLaughlin2018,
  title = {SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology},
  author = {McLaughlin, James Alastair and Myers, Chris J. and Zundel, Zach and Mısırlı, Göksel and Zhang, Michael and Ofiteru, Irina Dana and Goñi-Moreno, Angel and Wipat, Anil},
  year = 2018,
  doi = {10.1021/acssynbio.7b00403},
  month = feb,
  journal = {ACS Synthetic Biology},
  volume = {7},
  number = {2},
  pages = {682--688}
}

J. Schumacher, L.R. Peraza, M. Firbank, A.J. Thomas, M. Kaiser, P. Gallagher, J.T. O'Brien, A.M. Blamire, J. Taylor

Functional connectivity in dementia with Lewy bodies: A within- and between-network analysis

in Human Brain Mapping, 39(3):1118-1129, March 2018

@ARTICLE{Schumacher2018,
  title = {Functional connectivity in dementia with Lewy bodies: A within- and between-network analysis},
  author = {Schumacher, Julia and Peraza, Luis R. and Firbank, Michael and Thomas, Alan J. and Kaiser, Marcus and Gallagher, Peter and O'Brien, John T. and Blamire, Andrew M. and Taylor, John-Paul},
  year = 2018,
  doi = {10.1002/hbm.23901},
  month = mar,
  journal = {Human Brain Mapping},
  volume = {39},
  number = {3},
  pages = {1118--1129}
}

O.K. Oyebamiji, D.J. Wilkinson, P.G. Jayathilake, S.P. Rushton, B. Bridgens, B. Li, P. Zuliani

A Bayesian approach to modelling the impact of hydrodynamic shear stress on biofilm deformation

in PLOS ONE, 13(4):e0195484, April 2018

@ARTICLE{Oyebamiji2018,
  title = {A Bayesian approach to modelling the impact of hydrodynamic shear stress on biofilm deformation},
  author = {Oyebamiji, Oluwole K. and Wilkinson, Darren J. and Jayathilake, Pahala Gedara and Rushton, Steve P. and Bridgens, Ben and Li, Bowen and Zuliani, Paolo},
  year = 2018,
  doi = {10.1371/journal.pone.0195484},
  month = apr,
  journal = {PLOS ONE},
  volume = {13},
  number = {4},
  pages = {e0195484}
}

E. Torelli, J.W. Kozyra, J. Gu, U. Stimming, L. Piantanida, K. Voïtchovsky, N. Krasnogor

Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon

in Scientific Reports, 8(1), May 2018

@ARTICLE{Torelli2018a,
  title = {Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon},
  author = {Torelli, Emanuela and Kozyra, Jerzy Wieslaw and Gu, Jing-Ying and Stimming, Ulrich and Piantanida, Luca and Voïtchovsky, Kislon and Krasnogor, Natalio},
  year = 2018,
  doi = {10.1038/s41598-018-25270-6},
  month = may,
  journal = {Scientific Reports},
  volume = {8},
  number = {1}

A. Guyet, M. Dade-Robertson, A. Wipat, J. Casement, W. Smith, H. Mitrani, M. Zhang

Mild hydrostatic pressure triggers oxidative responses in Escherichia coli

in PLOS ONE, 13(7):e0200660, July 2018

@ARTICLE{Guyet2018,
  title = {Mild hydrostatic pressure triggers oxidative responses in Escherichia coli},
  author = {Guyet, Aurelie and Dade-Robertson, Martyn and Wipat, Anil and Casement, John and Smith, Wendy and Mitrani, Helen and Zhang, Meng},
  year = 2018,
  doi = {10.1371/journal.pone.0200660},
  month = jul,
  journal = {PLOS ONE},
  volume = {13},
  number = {7},
  pages = {e0200660}
}

S. Jiang, M. Torres, D. Pelta, P. Krabben, R. Daniel, J.T. Luzardo, M. Kaiser, N. Krasnogor

Improving microbial strain design via multiobjective optimisation and decision making

in FAIM Workshop on AI for Sythetic Biology 2, p.1-6, Stockholm, Sweden, July 2018

@INPROCEEDINGS{Jiang2018b,
  title = {Improving microbial strain design via multiobjective optimisation and decision making},
  author = {Jiang, Shouyong and Torres, Marina and Pelta, David and Krabben, Preben and Daniel, Richard and Luzardo, Jonathan Tellechea and Kaiser, Marcus and Krasnogor, Natalio},
  year = 2018,
  month = jul,
  booktitle = {FAIM Workshop on AI for Sythetic Biology 2},
  pages = {1--6},
  address = {Stockholm, Sweden}
}

S. Jiang, M. Kaiser, S. Wan, J. Guo, S. Yang, N. Krasnogor

An Empirical Study of Dynamic Triobjective Optimisation Problems

in 2018 IEEE Congress on Evolutionary Computation (CEC), p.1-8, Rio de Janeiro, July 2018

@INPROCEEDINGS{Jiang2018a,
  title = {An Empirical Study of Dynamic Triobjective Optimisation Problems},
  author = {Jiang, Shouyong and Kaiser, Marcus and Wan, Shuzhen and Guo, Jinglei and Yang, Shengxiang and Krasnogor, Natalio},
  year = 2018,
  doi = {10.1109/CEC.2018.8477667},
  month = jul,
  booktitle = {2018 IEEE Congress on Evolutionary Computation (CEC)},
  pages = {1--8},
  address = {Rio de Janeiro}
}

M. Felemban, B. Dorgau, N.C. Hunt, D. Hallam, D. Zerti, R. Bauer, Y. Ding, J. Collin, D. Steel, N. Krasnogor, J. Al-Aama, S. Lindsay, C. Mellough, M. Lako

Extracellular matrix component expression in human pluripotent stem cell-derived retinal organoids recapitulates retinogenesis in vivo and reveals an important role for IMPG1 and CD44 in the development of photoreceptors and interphotoreceptor matrix

in Acta Biomaterialia, 74(C):207-221, July 2018

@ARTICLE{Felemban2018,
  title = {Extracellular matrix component expression in human pluripotent stem cell-derived retinal organoids recapitulates retinogenesis  in vivo  and reveals an important role for IMPG1 and CD44 in the development of photoreceptors and interphotoreceptor matrix},
  author = {Felemban, Majed and Dorgau, Birthe and Hunt, Nicola Claire and Hallam, Dean and Zerti, Darin and Bauer, Roman and Ding, Yuchun and Collin, Joseph and Steel, David and Krasnogor, Natalio and Al-Aama, Jumana and Lindsay, Susan and Mellough, Carla and Lako, Majlinda},
  year = 2018,
  doi = {10.1016/j.actbio.2018.05.023},
  month = jul,
  journal = {Acta Biomaterialia},
  volume = {74},
  number = {C},
  pages = {207--221}
}

C. Keasar, L.J. McGuffin, B. Wallner, G. Chopra, B. Adhikari, D. Bhattacharya, L. Blake, L.O. Bortot, R. Cao, B.K. Dhanasekaran, I. Dimas, R.A. Faccioli, E. Faraggi, R. Ganzynkowicz, S. Ghosh, S. Ghosh, A. Giełdoń, L. Golon, Y. He, L. Heo, J. Hou, M. Khan, F. Khatib, G.A. Khoury, C. Kieslich, D.E. Kim, P. Krupa, G.R. Lee, H. Li, J. Li, A. Lipska, A. Liwo, et al.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

in Scientific Reports, 8(1), July 2018

@ARTICLE{Keasar2018,
title = {An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12},
author = {Keasar, Chen and McGuffin, Liam J. and Wallner, Björn and Chopra, Gaurav and Adhikari, Badri and Bhattacharya, Debswapna and Blake, Lauren and Bortot, Leandro Oliveira and Cao, Renzhi and Dhanasekaran, B. K. and Dimas, Itzhel and Faccioli, Rodrigo Antonio and Faraggi, Eshel and Ganzynkowicz, Robert and Ghosh, Sambit and Ghosh, Soma and Giełdoń, Artur and Golon, Lukasz and He, Yi and Heo, Lim and Hou, Jie and Khan, Main and Khatib, Firas and Khoury, George A. and Kieslich, Chris and Kim, David E. and Krupa, Pawel and Lee, Gyu Rie and Li, Hongbo and Li, Jilong and Lipska, Agnieszka and Liwo, Adam and Maghrabi, Ali Hassan A. and Mirdita, Milot and Mirzaei, Shokoufeh and Mozolewska, Magdalena A. and Onel, Melis and Ovchinnikov, Sergey and Shah, Anand and Shah, Utkarsh and Sidi, Tomer and Sieradzan, Adam K. and Ślusarz, Magdalena and Ślusarz, Rafal and Smadbeck, James and Tamamis, Phanourios and Trieber, Nicholas and Wirecki, Tomasz and Yin, Yanping and Zhang, Yang and Bacardit, Jaume and Baranowski, Maciej and Chapman, Nicholas and Cooper, Seth and Defelicibus, Alexandre and Flatten, Jeff and Koepnick, Brian and Popović, Zoran and Zaborowski, Bartlomiej and Baker, David and Cheng, Jianlin and Czaplewski, Cezary and Delbem, Alexandre Cláudio Botazzo and Floudas, Christodoulos and Kloczkowski, Andrzej and Ołdziej, Stanislaw and Levitt, Michael and Scheraga, Harold and Seok, Chaok and Söding, Johannes and Vishveshwara, Saraswathi and Xu, Dong and Caglar, Ahmet and Coral, Alan and MacMillan, Alison and Lubow, Allen and Failer, Barbara and Kestemont, Bruno and Landers, Catherine R. and Painter, Charles Robert and Garnier, Christophe and Sellin, Claudine and Janz, Dietmar and Wheeler, Douglas Craig and Simon, Vera and Flear, Dylan M. and Croze, Emmanuel and McIlvaine, George Victor and Beecher, Gil and Lawrie, Gordon and Ykman, Guy and Feldmann, Harald and Fuentes, Heidemarie K. and Terumasa, Hosokawa and Kovanecz, Istvan and Longino, James Absalom and Nijland, Jan Hendrik and Diderich, Jasper A. and Canfield, Jeffrey M. and Eriksson, Jesper and Slone, Jesse David and Appel, Joan Goldsworthy and Mitchell, Joanne and Mitch, John and Loots-Boiy, Jorn and Brownlee, June M. and Wilson, Karsten and Clayton, Keith T. and DeFord, Kenneth E. and Abbey, Kirk J. and Withers, Larry and Wei, Linda and Ives, Lloyd and Miller, Lori A. and Carpenter, Lynn and Sharma, Manasa G. and Ricci, Manuel and Binfield, Mark Stewart and Davids, Matthew John and Gaebel, Matthias and Cassidy, Michael D. and Fagiola, Michael and Pfützenreuter, Michael and Barlow, Nova and Triggiani, Peter John and Innes, Renton Braden Mathew and Leduc, Robert and dos Santos Gomes, Rodrigo Luccas Corrêa and Morneau, Rosemarie L. R. and Zaccanelli, Scott J. and Kleinfelter, Susan C. and van der Laan, T. J. A. and Bausewein, Thomas and George, Thomas J. and Mikhail, Varichev and Barmettler, Walter and Crivelli, Silvia N.},
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doi = {10.1038/s41598-018-26812-8},
month = jul,
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volume = {8},
number = {1}

K. James, C. Chipeta, A. Parker, S. Harding, S.J. Cockell, C.S. Gillespie, J. Hallinan, F. Barone, S.J. Bowman, W. Ng, B.A. Fisher

B-cell activity markers are associated with different disease activity domains in primary Sjögren’s syndrome

in Rheumatology, 57(7):1222-1227, July 2018

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P. Gonzalez-De-Aledo, A. Vladimirov, M. Manca, J. Baugh, R. Asai, M. Kaiser, R. Bauer

An optimization approach for agent-based computational models of biological development

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J. Munkley, T.M. Maia, N. Ibarluzea, K.E. Livermore, D. Vodak, I. Ehrmann, K. James, P. Rajan, N.L. Barbosa-Morais, D.J. Elliott

Androgen-dependent alternative mRNA isoform expression in prostate cancer cells

in F1000Research, 7:1189, August 2018

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W. Hordijk, J. Naylor, N. Krasnogor, H. Fellermann

Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World

in Life, 8(3):33, August 2018

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J. Cowton, I. Kyriazakis, T. Plötz, J. Bacardit

A Combined Deep Learning GRU-Autoencoder for the Early Detection of Respiratory Disease in Pigs Using Multiple Environmental Sensors

in Sensors, 18(8):2521, August 2018

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  title = {A Combined Deep Learning GRU-Autoencoder for the Early Detection of Respiratory Disease in Pigs Using Multiple Environmental Sensors},
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H. Fellermann, B. Shirt-Ediss, J.W. Koryza, M. Linsley, D.W. Lendrem, T.P. Howard

The PCR Simulator: an on-line application for teaching Design of Experiments and the polymerase chain reaction

in bioRxiv, 415042v2, September 2018

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A. Buskin, L. Zhu, V. Chichagova, B. Basu, S. Mozaffari-Jovin, D. Dolan, A. Droop, J. Collin, R. Bronstein, S. Mehrotra, M. Farkas, G. Hilgen, K. White, K. Pan, A. Treumann, D. Hallam, K. Bialas, G. Chung, C. Mellough, Y. Ding, N. Krasnogor, S. Przyborski, S. Zwolinski, J. Al-Aama, S. Alharthi, Y. Xu, G. Wheway, K. Szymanska, M. McKibbin, C.F. Inglehearn, D.J. Elliott, S. Lindsay, et al.

Disrupted alternative splicing for genes implicated in splicing and ciliogenesis causes PRPF31 retinitis pigmentosa

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R.A. Cromarty, J. Schumacher, S. Graziadio, P. Gallagher, A. Killen, M.J. Firbank, A. Blamire, M. Kaiser, A.J. Thomas, J.T. O’Brien, L.R. Peraza, J. Taylor

Structural Brain Correlates of Attention Dysfunction in Lewy Body Dementias and Alzheimer’s Disease

in Frontiers in Aging Neuroscience, 10, October 2018

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P.D. Olson, M. Zarowiecki, K. James, A. Baillie, G. Bartl, P. Burchell, A. Chellappoo, F. Jarero, L.Y. Tan, N. Holroyd, M. Berriman

Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms

in EvoDevo, 9(1), December 2018

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N.V.R. Mutha, W.K. Mohammed, N. Krasnogor, G.Y.A. Tan, S.W. Choo, N.S. Jakubovics

Transcriptional responses of Streptococcus gordonii and Fusobacterium nucleatum to coaggregation

in Molecular Oral Microbiology, 33(6):450-464, December 2018

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B. Shirt-Ediss, N. Krasnogor, H. Fellermann

The fittest, the common, and the dullest: Selection dynamics of exact autocatalytic replicators

in The 2018 Conference on Artificial Life, p.370-371, Tokyo, Japan, 2018

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  booktitle = {The 2018 Conference on Artificial Life},
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  address = {Tokyo, Japan}
}

M. Torres, S. Jiang, D. Pelta, M. Kaiser, N. Krasnogor

Strain Design as Multiobjective Network Interdiction Problem: A Preliminary Approach

in Advances in Artificial Intelligence, Lecture Notes in Computer Science 11160, p.273-282, 2018

@INCOLLECTION{Torres2018,
  title = {Strain Design as Multiobjective Network Interdiction Problem: A Preliminary Approach},
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  doi = {10.1007/978-3-030-00374-6_26},
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}

S. Jiang, M. Kaiser, J. Guo, S. Yang, N. Krasnogor

Less detectable environmental changes in dynamic multiobjective optimisation

in Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '18, p.673-680, Kyoto, Japan, 2018

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  title = {Less detectable environmental changes in dynamic multiobjective optimisation},
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DOI
A. Buskin, L. Zhu, V. Chichagova, B. Basu, S. MozaffariiJovin, D. Dolan, A. Droop, J. Colli, R. Bronstei, S. Mehrotr, M. Farkas, G. Hilgen, K. White, D. Hallam, K. Bialas, G. Chung, C. Mellough, Y. Ding, N. Krasnogor, S. Przyborski, J. AllAama, S. Alharthi, Y. Xu, G. Wheway, K. Szymanska, M. McKibbin, C.F. Inglehearn, D.J. Elliott, S. Lindsay, R.R. Ali, D.H. Steel, L. Armstrong, et al.

Human iPSC-Derived RPE and Retinal Organoids Reveal Impaired Alternative Splicing of Genes Involved in Pre-mRNA Splicing in PRPF31 Autosomal Dominant Retinitis Pigmentosa Type 11

in SSRN Electronic Journal, available online since 2018

J. Revell, P. Zuliani

Stochastic Rate Parameter Inference Using the Cross-Entropy Method

in Computational Methods in Systems Biology, Lecture Notes in Computer Science 11095, p.146-164, 2018

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G. Baier, R. Rosch, P.N. Taylor, Y. Wang

Design Principle for a Population-Based Model of Epileptic Dynamics

in Complexity and Synergetics, p.333-347, 2018

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P.N. Taylor, N. Sinha, Y. Wang, S.B. Vos, J. de Tisi, A. Miserocchi, A.W. McEvoy, G.P. Winston, J.S. Duncan

The impact of epilepsy surgery on the structural connectome and its relation to outcome

in NeuroImage: Clinical, 18(C):202-214, 2018

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2017

D.E. Job, D.A. Dickie, D. Rodriguez, A. Robson, S. Danso, C. Pernet, M.E. Bastin, J.P. Boardman, A.D. Murray, T. Ahearn, G.D. Waiter, R.T. Staff, I.J. Deary, S.D. Shenkin, J.M. Wardlaw

A brain imaging repository of normal structural MRI across the life course: Brain Images of Normal Subjects (BRAINS)

in NeuroImage, 144(PB):299-304, January 2017

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  title = {A brain imaging repository of normal structural MRI across the life course: Brain Images of Normal Subjects (BRAINS)},
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P.N. Taylor, Y. Wang, M. Kaiser

Within brain area tractography suggests local modularity using high resolution connectomics

in Scientific Reports, 7:39859, January 2017

@ARTICLE{Taylor2017,
  title = {Within brain area tractography suggests local modularity using high resolution connectomics},
  author = {Taylor, Peter N. and Wang, Yujiang and Kaiser, Marcus},
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  month = jan,
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  volume = {7},
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N. Sinha, J. Dauwels, M. Kaiser, S.S. Cash, M. Brandon Westover, Y. Wang, P.N. Taylor

Predicting neurosurgical outcomes in focal epilepsy patients using computational modelling

in Brain, 140(2):319-332, February 2017

@ARTICLE{Sinha2017,
  title = {Predicting neurosurgical outcomes in focal epilepsy patients using computational modelling},
  author = {Sinha, Nishant and Dauwels, Justin and Kaiser, Marcus and Cash, Sydney S. and Brandon Westover, M. and Wang, Yujiang and Taylor, Peter N.},
  year = 2017,
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Á. Goñi-Moreno, J. Kim, V. de Lorenzo

CellShape: A user-friendly image analysis tool for quantitative visualization of bacterial cell factories inside

in Biotechnology Journal, 12(2):1600323, February 2017

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  title = {CellShape: A user-friendly image analysis tool for quantitative visualization of bacterial cell factories inside},
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  doi = {10.1002/biot.201600323},
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R. Bauer, M. Kaiser

Nonlinear growth: an origin of hub organization in complex networks

in Royal Society Open Science, 4(3):160691, March 2017

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  title = {Nonlinear growth: an origin of hub organization in complex networks},
  author = {Bauer, Roman and Kaiser, Marcus},
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  month = mar,
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  volume = {4},
  number = {3},
  pages = {160691}
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L.R. Peraza, D. Nesbitt, R.A. Lawson, G.W. Duncan, A.J. Yarnall, T.K. Khoo, M. Kaiser, M.J. Firbank, J.T. O'Brien, R.A. Barker, D.J. Brooks, D.J. Burn, J. Taylor

Intra- and inter-network functional alterations in Parkinson's disease with mild cognitive impairment

in Human Brain Mapping, 38(3):1702-1715, March 2017

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  title = {Intra- and inter-network functional alterations in Parkinson's disease with mild cognitive impairment},
  author = {Peraza, Luis R. and Nesbitt, David and Lawson, Rachael A. and Duncan, Gordon W. and Yarnall, Alison J. and Khoo, Tien K. and Kaiser, Marcus and Firbank, Michael J. and O'Brien, John T. and Barker, Roger A. and Brooks, David J. and Burn, David J. and Taylor, John-Paul},
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F.E. Hutchings, C.B. Thornton, M. Kaiser

Implementation and comparison of non-invasive stimulation modalities in the VERTEX simulation tool

in Brain Stimulation, 10(2):477, March 2017

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  title = {Implementation and comparison of non-invasive stimulation modalities in the VERTEX simulation tool},
  author = {Hutchings, F. E. and Thornton, C. B. and Kaiser, M.},
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  pages = {477}
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P. Gamba, K. James, N. Zenkin

A link between transcription fidelity and pausing in vivo

in Transcription, 8(2):99-105, March 2017

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  title = {A link between transcription fidelity and pausing in vivo },
  author = {Gamba, Pamela and James, Katherine and Zenkin, Nikolay},
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  journal = {Transcription},
  volume = {8},
  number = {2},
  pages = {99--105}
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G. Baier, P.N. Taylor, Y. Wang

Understanding Epileptiform After-Discharges as Rhythmic Oscillatory Transients

in Frontiers in Computational Neuroscience, 11, April 2017

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  title = {Understanding Epileptiform After-Discharges as Rhythmic Oscillatory Transients},
  author = {Baier, Gerold and Taylor, Peter N. and Wang, Yujiang},
  year = 2017,
  doi = {10.3389/fncom.2017.00025},
  month = apr,
  journal = {Frontiers in Computational Neuroscience},
  volume = {11}

W. Ng, A. Miller, S.J. Bowman, E.J. Price, G.D. Kitas, C. Pease, P. Emery, P. Lanyon, J. Hunter, M. Gupta, I. Giles, D. Isenberg, J. McLaren, M. Regan, A. Cooper, S.A. Young-Min, N. McHugh, S. Vadivelu, R.J. Moots, D. Coady, K. MacKay, B. Dasgupta, N. Sutcliffe, M. Bombardieri, C. Pitzalis, B. Griffiths, S. Mitchell, S.T. Miyamoto, M. Trenell

Physical activity but not sedentary activity is reduced in primary Sjögren’s syndrome

in Rheumatology International, 37(4):623-631, April 2017

@ARTICLE{Ng2017,
  title = {Physical activity but not sedentary activity is reduced in primary Sjögren’s syndrome},
  author = {Ng, Wan-Fai and Miller, Ariana and Bowman, Simon J. and Price, Elizabeth J. and Kitas, George D. and Pease, Colin and Emery, Paul and Lanyon, Peter and Hunter, John and Gupta, Monica and Giles, Ian and Isenberg, David and McLaren, John and Regan, Marian and Cooper, Annie and Young-Min, Steven A. and McHugh, Neil and Vadivelu, Saravanan and Moots, Robert J. and Coady, David and MacKay, Kirsten and Dasgupta, Bhaskar and Sutcliffe, Nurhan and Bombardieri, Michele and Pitzalis, Costantino and Griffiths, Bridget and Mitchell, Sheryl and Miyamoto, Samira Tatiyama and Trenell, Michael},
  year = 2017,
  doi = {10.1007/s00296-016-3637-6},
  month = apr,
  journal = {Rheumatology International},
  volume = {37},
  number = {4},
  pages = {623--631}
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N. Sinha, J. Dauwels, M. Kaiser, S.S. Cash, M. Brandon Westover, Y. Wang, P.N. Taylor

Reply: Computer models to inform epilepsy surgery strategies: prediction of postoperative outcome

in Brain, 140(5):e31-e31, May 2017

@ARTICLE{Sinha2017a,
  title = {Reply: Computer models to inform epilepsy surgery strategies: prediction of postoperative outcome},
  author = {Sinha, Nishant and Dauwels, Justin and Kaiser, Marcus and Cash, Sydney S. and Brandon Westover, M. and Wang, Yujiang and Taylor, Peter N.},
  year = 2017,
  doi = {10.1093/brain/awx068},
  month = may,
  journal = {Brain},
  volume = {140},
  number = {5},
  pages = {e31--e31}
}

K. James, S.J. Cockell, N. Zenkin

Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics

in Methods, 120(C):76-84, May 2017

@ARTICLE{James2017,
  title = {Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics},
  author = {James, Katherine and Cockell, Simon J. and Zenkin, Nikolay},
  year = 2017,
  doi = {10.1016/j.ymeth.2017.04.016},
  month = may,
  journal = {Methods},
  volume = {120},
  number = {C},
  pages = {76--84}
}

Y. Wang, A.J. Trevelyan, A. Valentin, G. Alarcon, P.N. Taylor, M. Kaiser

Mechanisms underlying different onset patterns of focal seizures

in PLOS Computational Biology, 13(5):e1005475, May 2017

@ARTICLE{Wang2017,
  title = {Mechanisms underlying different onset patterns of focal seizures},
  author = {Wang, Yujiang and Trevelyan, Andrew J and Valentin, Antonio and Alarcon, Gonzalo and Taylor, Peter N and Kaiser, Marcus},
  year = 2017,
  doi = {10.1371/journal.pcbi.1005475},
  month = may,
  journal = {PLOS Computational Biology},
  volume = {13},
  number = {5},
  pages = {e1005475}
}

D. Forrest, K. James, Y. Yuzenkova, N. Zenkin

Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase

in Nature Communications, 8:15774, June 2017

@ARTICLE{Forrest2017,
  title = {Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase},
  author = {Forrest, David and James, Katherine and Yuzenkova, Yulia and Zenkin, Nikolay},
  year = 2017,
  doi = {10.1038/ncomms15774},
  month = jun,
  journal = {Nature Communications},
  volume = {8},
  pages = {15774}
}

A. Goñi-Moreno, A. Wipat, N. Krasnogor

CSBB: synthetic biology research at Newcastle University

in Biochemical Society Transactions, 45(3):781-783, June 2017

@ARTICLE{Goni-Moreno2017a,
  title = {CSBB: synthetic biology research at Newcastle University},
  author = {Goñi-Moreno, Angel and Wipat, Anil and Krasnogor, Natalio},
  year = 2017,
  doi = {10.1042/BST20160437},
  month = jun,
  journal = {Biochemical Society Transactions},
  volume = {45},
  number = {3},
  pages = {781--783}
}

A. Garcia-Piquer, J. Bacardit, A. Fornells, E. Golobardes

Scaling-up multiobjective evolutionary clustering algorithms using stratification

in Pattern Recognition Letters, 93(C):69-77, July 2017

@ARTICLE{Garcia-Piquer2016,
  title = {Scaling-up multiobjective evolutionary clustering algorithms using stratification},
  author = {Garcia-Piquer, Alvaro and Bacardit, Jaume and Fornells, Albert and Golobardes, Elisabet},
  year = 2017,
  doi = {10.1016/j.patrec.2016.12.001},
  month = jul,
  journal = {Pattern Recognition Letters},
  volume = {93},
  number = {C},
  pages = {69--77}
}

B. Shirt-Ediss, S. Murillo-Sánchez, K. Ruiz-Mirazo

Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research

in Beilstein Journal of Organic Chemistry, 13:1388-1395, July 2017

@ARTICLE{Shirt-Ediss2017,
  title = {Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research},
  author = {Shirt-Ediss, Ben and Murillo-Sánchez, Sara and Ruiz-Mirazo, Kepa},
  year = 2017,
  doi = {10.3762/bjoc.13.135},
  month = jul,
  journal = {Beilstein Journal of Organic Chemistry},
  volume = {13},
  pages = {1388--1395}
}

Á. Goñi-Moreno, I. Benedetti, J. Kim, V. de Lorenzo

Deconvolution of Gene Expression Noise into Spatial Dynamics of Transcription Factor–Promoter Interplay

in ACS Synthetic Biology, 6(7):1359-1369, July 2017

@ARTICLE{Goni-Moreno2017b,
  title = {Deconvolution of Gene Expression Noise into Spatial Dynamics of Transcription Factor–Promoter Interplay},
  author = {Goñi-Moreno, Ángel and Benedetti, Ilaria and Kim, Juhyun and de Lorenzo, Víctor},
  year = 2017,
  doi = {10.1021/acssynbio.6b00397},
  month = jul,
  journal = {ACS Synthetic Biology},
  volume = {6},
  number = {7},
  pages = {1359--1369}
}

DOI code BibTeX

J. Naylor, H. Fellermann, Y. Ding, W.K. Mohammed, N.S. Jakubovics, J. Mukherjee, C.A. Biggs, P.C. Wright, N. Krasnogor

Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations

in ACS Synthetic Biology, 6(7):1194-1210, July 2017

@ARTICLE{Naylor2017,
  title = {Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations},
  author = {Naylor, Jonathan and Fellermann, Harold and Ding, Yuchun and Mohammed, Waleed K. and Jakubovics, Nicholas S. and Mukherjee, Joy and Biggs, Catherine A. and Wright, Phillip C. and Krasnogor, Natalio},
  year = 2017,
  doi = {10.1021/acssynbio.6b00315},
  month = jul,
  journal = {ACS Synthetic Biology},
  volume = {6},
  number = {7},
  pages = {1194--1210}
}

J. Kozyra, A. Ceccarelli, E. Torelli, A. Lopiccolo, J. Gu, H. Fellermann, U. Stimming, N. Krasnogor

Designing Uniquely Addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami

in ACS Synthetic Biology, 6(7):1140-1149, July 2017

@ARTICLE{Kozyra2017,
  title = {Designing Uniquely Addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami},
  author = {Kozyra, Jerzy and Ceccarelli, Alessandro and Torelli, Emanuela and Lopiccolo, Annunziata and Gu, Jing-Ying and Fellermann, Harold and Stimming, Ulrich and Krasnogor, Natalio},
  year = 2017,
  doi = {10.1021/acssynbio.6b00271},
  month = jul,
  journal = {ACS Synthetic Biology},
  volume = {6},
  number = {7},
  pages = {1140--1149}
}

P.G. Jayathilake, P. Gupta, B. Li, C. Madsen, O. Oyebamiji, R. González-Cabaleiro, S. Rushton, B. Bridgens, D. Swailes, B. Allen, A.S. McGough, P. Zuliani, I.D. Ofiteru, D. Wilkinson, J. Chen, T. Curtis

A mechanistic Individual-based Model of microbial communities

in PLOS ONE, 12(8):e0181965, August 2017

@ARTICLE{Jayathilake2017,
  title = {A mechanistic Individual-based Model of microbial communities},
  author = {Jayathilake, Pahala Gedara and Gupta, Prashant and Li, Bowen and Madsen, Curtis and Oyebamiji, Oluwole and González-Cabaleiro, Rebeca and Rushton, Steve and Bridgens, Ben and Swailes, David and Allen, Ben and McGough, A. Stephen and Zuliani, Paolo and Ofiteru, Irina Dana and Wilkinson, Darren and Chen, Jinju and Curtis, Tom},
  year = 2017,
  doi = {10.1371/journal.pone.0181965},
  month = aug,
  journal = {PLOS ONE},
  volume = {12},
  number = {8},
  pages = {e0181965}
}

M. Kaiser

Mechanisms of Connectome Development

in Trends in Cognitive Sciences, 21(9):703-717, September 2017

@ARTICLE{Kaiser2017,
  title = {Mechanisms of Connectome Development},
  author = {Kaiser, Marcus},
  year = 2017,
  doi = {10.1016/j.tics.2017.05.010},
  month = sep,
  journal = {Trends in Cognitive Sciences},
  volume = {21},
  number = {9},
  pages = {703--717}
}

J. García-Betancur, A. Goñi-Moreno, T. Horger, M. Schott, M. Sharan, J. Eikmeier, B. Wohlmuth, A. Zernecke, K. Ohlsen, C. Kuttler, D. Lopez

Cell differentiation defines acute and chronic infection cell types in Staphylococcus aureus

in eLife, 6, September 2017

@ARTICLE{Garcia-Betancur2017,
  title = {Cell differentiation defines acute and chronic infection cell types in Staphylococcus aureus},
  author = {García-Betancur, Juan-Carlos and Goñi-Moreno, Angel and Horger, Thomas and Schott, Melanie and Sharan, Malvika and Eikmeier, Julian and Wohlmuth, Barbara and Zernecke, Alma and Ohlsen, Knut and Kuttler, Christina and Lopez, Daniel},
  year = 2017,
  doi = {10.7554/eLife.28023},
  month = sep,
  journal = {eLife},
  volume = {6}

O.M. Bezzina, P. Gallagher, S. Mitchell, S.J. Bowman, B. Griffiths, V. Hindmarsh, B. Hargreaves, E.J. Price, C.T. Pease, P. Emery, P. Lanyon, M. Bombardieri, N. Sutcliffe, C. Pitzalis, J. Hunter, M. Gupta, J. McLaren, A.M. Cooper, M. Regan, I.P. Giles, D.A. Isenberg, V. Saravanan, D. Coady, B. Dasgupta, N.J. McHugh, S.A. Young‐Min, R.J. Moots, N. Gendi, M. Akil, K. MacKay, W.F. Ng, L.J. Robinson

Subjective and Objective Measures of Dryness Symptoms in Primary Sjögren's Syndrome: Capturing the Discrepancy

in Arthritis Care & Research, 69(11):1714-1723, November 2017

@ARTICLE{Bezzina2017,
  title = {Subjective and Objective Measures of Dryness Symptoms in Primary Sjögren's Syndrome: Capturing the Discrepancy},
  author = {Bezzina, Oriana M. and Gallagher, Peter and Mitchell, Sheryl and Bowman, Simon J. and Griffiths, Bridget and Hindmarsh, Victoria and Hargreaves, Ben and Price, Elizabeth J. and Pease, Colin T. and Emery, Paul and Lanyon, Peter and Bombardieri, Michele and Sutcliffe, Nurhan and Pitzalis, Costantino and Hunter, John and Gupta, Monica and McLaren, John and Cooper, Anne M. and Regan, Marian and Giles, Ian P. and Isenberg, David A. and Saravanan, Vadivelu and Coady, David and Dasgupta, Bhaskar and McHugh, Neil J. and Young‐Min, Steven A. and Moots, Robert J. and Gendi, Nagui and Akil, Mohammed and MacKay, Kirsten and Ng, W. Fai and Robinson, Lucy J.},
  year = 2017,
  doi = {10.1002/acr.23165},
  month = nov,
  journal = {Arthritis Care & Research},
  volume = {69},
  number = {11},
  pages = {1714--1723}
}

H. Fellermann, S. Tanaka, S. Rasmussen

Sequence selection by dynamical symmetry breaking in an autocatalytic binary polymer model

in Physical Review E, 96(6), December 2017

@ARTICLE{Fellermann2017,
  title = {Sequence selection by dynamical symmetry breaking in an autocatalytic binary polymer model},
  author = {Fellermann, Harold and Tanaka, Shinpei and Rasmussen, Steen},
  year = 2017,
  doi = {10.1103/PhysRevE.96.062407},
  month = dec,
  journal = {Physical Review E},
  volume = {96},
  number = {6}

N. Lazzarini, J. Runhaar, A.C. Bay-Jensen, C.S. Thudium, S.M. Bierma-Zeinstra, Y. Henrotin, J. Bacardit

A machine learning approach for the identification of new biomarkers for knee osteoarthritis development in overweight and obese women

in Osteoarthritis and Cartilage, 25(12):2014-2021, December 2017

@ARTICLE{Lazzarini2017a,
  title = {A machine learning approach for the identification of new biomarkers for knee osteoarthritis development in overweight and obese women},
  author = {Lazzarini, N. and Runhaar, J. and Bay-Jensen, A. C. and Thudium, C. S. and Bierma-Zeinstra, S. M.a. and Henrotin, Y. and Bacardit, J.},
  year = 2017,
  doi = {10.1016/j.joca.2017.09.001},
  month = dec,
  journal = {Osteoarthritis and Cartilage},
  volume = {25},
  number = {12},
  pages = {2014--2021}
}

N. Lazzarini, J. Bacardit

RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers

in BMC Bioinformatics, 18(1), December 2017

@ARTICLE{Lazzarini2017,
  title = {RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers},
  author = {Lazzarini, Nicola and Bacardit, Jaume},
  year = 2017,
  doi = {10.1186/s12859-017-1729-2},
  month = dec,
  journal = {BMC Bioinformatics},
  volume = {18},
  number = {1}

S. Baron, N. Lazzarini, J. Bacardit

Characterising the Influence of Rule-Based Knowledge Representations in Biological Knowledge Extraction from Transcriptomics Data

in Applications of Evolutionary Computation, Lecture Notes in Computer Science 10199, p.125-141, 2017

@INCOLLECTION{Baron2017,
  title = {Characterising the Influence of Rule-Based Knowledge Representations in Biological Knowledge Extraction from Transcriptomics Data},
  author = {Baron, Simon and Lazzarini, Nicola and Bacardit, Jaume},
  year = 2017,
  doi = {10.1007/978-3-319-55849-3_9},
  booktitle = {Applications of Evolutionary Computation},
  publisher = {Springer International Publishing},
  volume = {10199},
  series = {Lecture Notes in Computer Science},
  pages = {125--141}
}

J. Kozyra, H. Fellermann, B. Shirt-Ediss, A. Lopiccolo, N. Krasnogor

Optimizing nucleic acid sequences for a molecular data recorder

in Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '17, p.1145-1152, Berlin, Germany, 2017

@INPROCEEDINGS{Kozyra2017a,
  title = {Optimizing nucleic acid sequences for a molecular data recorder},
  author = {Kozyra, Jerzy and Fellermann, Harold and Shirt-Ediss, Ben and Lopiccolo, Annunziata and Krasnogor, Natalio},
  year = 2017,
  doi = {10.1145/3071178.3071345},
  booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference on   - GECCO '17},
  pages = {1145--1152},
  address = {Berlin, Germany}
}

R. Bauer, M. Kaiser

Organisational Principles of Connectomes: Changes During Evolution and Development

in Brain Evolution by Design, p.387-401, 2017

@INCOLLECTION{Bauer2017a,
  title = {Organisational Principles of Connectomes: Changes During Evolution and Development},
  author = {Bauer, Roman and Kaiser, Marcus},
  year = 2017,
  doi = {10.1007/978-4-431-56469-0_17},
  booktitle = {Brain Evolution by Design},
  publisher = {Springer Japan},
  pages = {387--401}
}

S. Lim, F. Hutchings, M. Kaiser

Modeling the Impact of Lesions in the Brain

in The Rewiring Brain, p.465-484, 2017

@INCOLLECTION{Lim2017,
  title = {Modeling the Impact of Lesions in the Brain},
  author = {Lim, Sol and Hutchings, Frances and Kaiser, Marcus},
  year = 2017,
  doi = {10.1016/B978-0-12-803784-3.00022-6},
  booktitle = {The Rewiring Brain},
  publisher = {Elsevier},
  pages = {465--484}
}

F. Shmarov, N. Paoletti, E. Bartocci, S. Lin, S.A. Smolka, P. Zuliani

SMT-based Synthesis of Safe and Robust PID Controllers for Stochastic Hybrid Systems

in Hardware and Software: Verification and Testing, Lecture Notes in Computer Science 10629, p.131-146, 2017

@INCOLLECTION{Shmarov2017,
  title = {SMT-based Synthesis of Safe and Robust PID Controllers for Stochastic Hybrid Systems},
  author = {Shmarov, Fedor and Paoletti, Nicola and Bartocci, Ezio and Lin, Shan and Smolka, Scott A. and Zuliani, Paolo},
  year = 2017,
  doi = {10.1007/978-3-319-70389-3_9},
  booktitle = {Hardware and Software: Verification and Testing},
  publisher = {Springer International Publishing},
  volume = {10629},
  series = {Lecture Notes in Computer Science},
  pages = {131--146}
}

2016

J. Mullen, S.J. Cockell, H. Tipney, P.M. Woollard, A. Wipat

Mining integrated semantic networks for drug repositioning opportunities

in PeerJ, 4:e1558, January 2016

@ARTICLE{Mullen2016,
  title = {Mining integrated semantic networks for drug repositioning opportunities},
  author = {Mullen, Joseph and Cockell, Simon J. and Tipney, Hannah and Woollard, Peter M. and Wipat, Anil},
  year = 2016,
  doi = {10.7717/peerj.1558},
  month = jan,
  journal = {PeerJ},
  volume = {4},
  pages = {e1558}
}

M.A. Franco, J. Bacardit

Large-scale experimental evaluation of GPU strategies for evolutionary machine learning

in Information Sciences, 330(C):385-402, February 2016

@ARTICLE{Franco2015,
  title = {Large-scale experimental evaluation of GPU strategies for evolutionary machine learning},
  author = {Franco, María A. and Bacardit, Jaume},
  year = 2016,
  doi = {10.1016/j.ins.2015.10.025},
  month = feb,
  journal = {Information Sciences},
  volume = {330},
  number = {C},
  pages = {385--402}
}

T.B. Yehezkel, A. Rival, O. Raz, R. Cohen, Z. Marx, M. Camara, J. Dubern, B. Koch, S. Heeb, N. Krasnogor, C. Delattre, E. Shapiro

Synthesis and cell-free cloning of DNA libraries using programmable microfluidics

in Nucleic Acids Research, 44(4):e35-e35, February 2016

@ARTICLE{Yehezkel2015,
  title = {Synthesis and cell-free cloning of DNA libraries using programmable microfluidics},
  author = {Yehezkel, Tuval Ben and Rival, Arnaud and Raz, Ofir and Cohen, Rafael and Marx, Zipora and Camara, Miguel and Dubern, Jean-Frédéric and Koch, Birgit and Heeb, Stephan and Krasnogor, Natalio and Delattre, Cyril and Shapiro, Ehud},
  year = 2016,
  doi = {10.1093/nar/gkv1087},
  month = feb,
  journal = {Nucleic Acids Research},
  volume = {44},
  number = {4},
  pages = {e35--e35}
}

G. Misirli, M. Cavaliere, W. Waites, M. Pocock, C. Madsen, O. Gilfellon, R. Honorato-Zimmer, P. Zuliani, V. Danos, A. Wipat

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization

in Bioinformatics, 32(6):908-917, March 2016

@ARTICLE{Misirli2015,
  title = {Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization},
  author = {Misirli, Goksel and Cavaliere, Matteo and Waites, William and Pocock, Matthew and Madsen, Curtis and Gilfellon, Owen and Honorato-Zimmer, Ricardo and Zuliani, Paolo and Danos, Vincent and Wipat, Anil},
  year = 2016,
  doi = {10.1093/bioinformatics/btv660},
  month = mar,
  journal = {Bioinformatics},
  volume = {32},
  number = {6},
  pages = {908--917}
}

M. Ainsworth, S. Lee, M. Kaiser, J. Simonotto, N.J. Kopell, M.A. Whittington

GABA B receptor-mediated, layer-specific synaptic plasticity reorganizes gamma-frequency neocortical response to stimulation

in Proceedings of the National Academy of Sciences, 113(19):E2721-E2729, May 2016

@ARTICLE{Ainsworth2016,
  title = {GABA B receptor-mediated, layer-specific synaptic plasticity reorganizes gamma-frequency neocortical response to stimulation},
  author = {Ainsworth, Matthew and Lee, Shane and Kaiser, Marcus and Simonotto, Jennifer and Kopell, Nancy J. and Whittington, Miles A.},
  year = 2016,
  doi = {10.1073/pnas.1605243113},
  month = may,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {113},
  number = {19},
  pages = {E2721--E2729}
}

J. Mullen, S.J. Cockell, P. Woollard, A. Wipat

An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations

in PLOS ONE, 11(5):e0155811, May 2016

@ARTICLE{Mullen2016a,
  title = {An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations},
  author = {Mullen, Joseph and Cockell, Simon J. and Woollard, Peter and Wipat, Anil},
  year = 2016,
  doi = {10.1371/journal.pone.0155811},
  month = may,
  journal = {PLOS ONE},
  volume = {11},
  number = {5},
  pages = {e0155811}
}

N. Roehner, J. Beal, K. Clancy, B. Bartley, G. Misirli, R. Grünberg, E. Oberortner, M. Pocock, M. Bissell, C. Madsen, T. Nguyen, M. Zhang, Z. Zhang, Z. Zundel, D. Densmore, J.H. Gennari, A. Wipat, H.M. Sauro, C.J. Myers

Sharing Structure and Function in Biological Design with SBOL 2.0

in ACS Synthetic Biology, 5(6):498-506, June 2016

@ARTICLE{Roehner2016,
  title = {Sharing Structure and Function in Biological Design with SBOL 2.0},
  author = {Roehner, Nicholas and Beal, Jacob and Clancy, Kevin and Bartley, Bryan and Misirli, Goksel and Grünberg, Raik and Oberortner, Ernst and Pocock, Matthew and Bissell, Michael and Madsen, Curtis and Nguyen, Tramy and Zhang, Michael and Zhang, Zhen and Zundel, Zach and Densmore, Douglas and Gennari, John H. and Wipat, Anil and Sauro, Herbert M. and Myers, Chris J.},
  year = 2016,
  doi = {10.1021/acssynbio.5b00215},
  month = jun,
  journal = {ACS Synthetic Biology},
  volume = {5},
  number = {6},
  pages = {498--506}
}

A. Best, K. James, G. Hysenaj, A. Tyson-Capper, D.J. Elliott

Transformer2 proteins protect breast cancer cells from accumulating replication stress by ensuring productive splicing of checkpoint kinase 1

in Frontiers of Chemical Science and Engineering, 10(2):186-195, June 2016

@ARTICLE{Best2015,
  title = {Transformer2 proteins protect breast cancer cells from accumulating replication stress by ensuring productive splicing of checkpoint kinase 1},
  author = {Best, Andrew and James, Katherine and Hysenaj, Gerald and Tyson-Capper, Alison and Elliott, David J.},
  year = 2016,
  doi = {10.1007/s11705-015-1540-4},
  month = jun,
  journal = {Frontiers of Chemical Science and Engineering},
  volume = {10},
  number = {2},
  pages = {186--195}
}

J. Munkley, D. Vodak, K.E. Livermore, K. James, B.T. Wilson, B. Knight, P. Mccullagh, J. Mcgrath, M. Crundwell, L.W. Harries, H.Y. Leung, C.N. Robson, I.G. Mills, P. Rajan, D.J. Elliott

Glycosylation is an Androgen-Regulated Process Essential for Prostate Cancer Cell Viability

in EBioMedicine, 8(C):103-116, June 2016

@ARTICLE{Munkley2016,
  title = {Glycosylation is an Androgen-Regulated Process Essential for Prostate Cancer Cell Viability},
  author = {Munkley, Jennifer and Vodak, Daniel and Livermore, Karen E. and James, Katherine and Wilson, Brian T. and Knight, Bridget and Mccullagh, Paul and Mcgrath, John and Crundwell, Malcolm and Harries, Lorna W. and Leung, Hing Y. and Robson, Craig N. and Mills, Ian G. and Rajan, Prabhakar and Elliott, David J.},
  year = 2016,
  doi = {10.1016/j.ebiom.2016.04.018},
  month = jun,
  journal = {EBioMedicine},
  volume = {8},
  number = {C},
  pages = {103--116}
}

S. Edwin Thanarajah, C.E. Han, A. Rotarska-Jagiela, W. Singer, R. Deichmann, K. Maurer, M. Kaiser, P.J. Uhlhaas

Abnormal Connectional Fingerprint in Schizophrenia: A Novel Network Analysis of Diffusion Tensor Imaging Data

in Frontiers in Psychiatry, 7, June 2016

@ARTICLE{EdwinThanarajah2016,
  title = {Abnormal Connectional Fingerprint in Schizophrenia: A Novel Network Analysis of Diffusion Tensor Imaging Data},
  author = {Edwin Thanarajah, Sharmili and Han, Cheol E. and Rotarska-Jagiela, Anna and Singer, Wolf and Deichmann, Ralf and Maurer, Konrad and Kaiser, Marcus and Uhlhaas, Peter J.},
  year = 2016,
  doi = {10.3389/fpsyt.2016.00114},
  month = jun,
  journal = {Frontiers in Psychiatry},
  volume = {7}

A. Manu, Z. Hill, A.H. ten Asbroek, S. Soremekun, B. Weobong, T. Gyan, C. Tawiah-Agyemang, S. Danso, S. Amenga-Etego, S. Owusu-Agyei, B.R. Kirkwood

Increasing access to care for sick newborns: evidence from the Ghana Newhints cluster-randomised controlled trial

in BMJ Open, 6(6):e008107, June 2016

@ARTICLE{Manu2016,
  title = {Increasing access to care for sick newborns: evidence from the Ghana Newhints cluster-randomised controlled trial},
  author = {Manu, Alexander and Hill, Zelee and ten Asbroek, Augustinus HA and Soremekun, Seyi and Weobong, Benedict and Gyan, Thomas and Tawiah-Agyemang, Charlotte and Danso, Samuel and Amenga-Etego, Seeba and Owusu-Agyei, Seth and Kirkwood, Betty R},
  year = 2016,
  doi = {10.1136/bmjopen-2015-008107},
  month = jun,
  journal = {BMJ Open},
  volume = {6},
  number = {6},
  pages = {e008107}
}

L.R. Peraza, S.J. Colloby, L. Deboys, J.T. O'Brien, M. Kaiser, J. Taylor

Regional functional synchronizations in dementia with Lewy bodies and Alzheimer's disease

in International Psychogeriatrics, 28(07):1143-1151, July 2016

@ARTICLE{Peraza2016,
  title = {Regional functional synchronizations in dementia with Lewy bodies and Alzheimer's disease},
  author = {Peraza, Luis R. and Colloby, Sean J. and Deboys, Liam and O'Brien, John T. and Kaiser, Marcus and Taylor, John-Paul},
  year = 2016,
  doi = {10.1017/S1041610216000429},
  month = jul,
  journal = {International Psychogeriatrics},
  volume = {28},
  number = {07},
  pages = {1143--1151}
}

P.N. Taylor, R. Forsyth

Heterogeneity of trans-callosal structural connectivity and effects on resting state subnetwork integrity may underlie both wanted and unwanted effects of therapeutic corpus callostomy

in NeuroImage: Clinical, 12(C):341-347, July 2016

@ARTICLE{Taylor2016,
  title = {Heterogeneity of trans-callosal structural connectivity and effects on resting state subnetwork integrity may underlie both wanted and unwanted effects of therapeutic corpus callostomy},
  author = {Taylor, Peter Neal and Forsyth, Rob},
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  doi = {10.1016/j.nicl.2016.07.010},
  month = jul,
  journal = {NeuroImage: Clinical},
  volume = {12},
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  pages = {341--347}
}

J.A. McLaughlin, M. Pocock, G. Mısırlı, C. Madsen, A. Wipat

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization

in ACS Synthetic Biology, 5(8):874-876, August 2016

@ARTICLE{McLaughlin2016,
  title = {VisBOL: Web-Based Tools for Synthetic Biology Design Visualization},
  author = {McLaughlin, James Alastair and Pocock, Matthew and Mısırlı, Göksel and Madsen, Curtis and Wipat, Anil},
  year = 2016,
  doi = {10.1021/acssynbio.5b00244},
  month = aug,
  journal = {ACS Synthetic Biology},
  volume = {5},
  number = {8},
  pages = {874--876}
}

H. Fellermann, O. Markovitch, O. Gilfellon, C. Madsen, A. Phillips

Toward Programmable Biology

in ACS Synthetic Biology, 5(8):793-794, August 2016

@ARTICLE{Fellermann2016a,
  title = {Toward Programmable Biology},
  author = {Fellermann, Harold and Markovitch, Omer and Gilfellon, Owen and Madsen, Curtis and Phillips, Andrew},
  year = 2016,
  doi = {10.1021/acssynbio.6b00213},
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  volume = {5},
  number = {8},
  pages = {793--794}
}

D.R. Espeso, E. Martínez-García, V. de Lorenzo, Á. Goñi-Moreno

Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells

in Frontiers in Microbiology, 7, September 2016

@ARTICLE{Espeso2016,
  title = {Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells},
  author = {Espeso, David R. and Martínez-García, Esteban and de Lorenzo, Víctor and Goñi-Moreno, Ángel},
  year = 2016,
  doi = {10.3389/fmicb.2016.01437},
  month = sep,
  journal = {Frontiers in Microbiology},
  volume = {7}

A. Goñi-Moreno, M. Carcajona, J. Kim, E. Martínez-García, M. Amos, V. de Lorenzo

An Implementation-Focused Bio/Algorithmic Workflow for Synthetic Biology

in ACS Synthetic Biology, 5(10):1127-1135, October 2016

@ARTICLE{Goni-Moreno2016,
  title = {An Implementation-Focused Bio/Algorithmic Workflow for Synthetic Biology},
  author = {Goñi-Moreno, Angel and Carcajona, Marta and Kim, Juhyun and Martínez-García, Esteban and Amos, Martyn and de Lorenzo, Víctor},
  year = 2016,
  doi = {10.1021/acssynbio.6b00029},
  month = oct,
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  volume = {5},
  number = {10},
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}

N. Miskov-Zivanov, P. Zuliani, Q. Wang, E.M. Clarke, J.R. Faeder

High-level modeling and verification of cellular signaling

in 2016 IEEE International High Level Design Validation and Test Workshop (HLDVT), p.162-169, Santa Cruz, CA, USA, October 2016

@INPROCEEDINGS{Miskov-Zivanov2016,
  title = {High-level modeling and verification of cellular signaling},
  author = {Miskov-Zivanov, Natasa and Zuliani, Paolo and Wang, Qinsi and Clarke, Edmund M. and Faeder, James R.},
  year = 2016,
  doi = {10.1109/HLDVT.2016.7748271},
  month = oct,
  booktitle = {2016 IEEE International High Level Design Validation and Test Workshop (HLDVT)},
  pages = {162--169},
  address = {Santa Cruz, CA, USA}
}

G. Mısırlı, J. Hallinan, M. Pocock, P. Lord, J.A. McLaughlin, H. Sauro, A. Wipat

Data Integration and Mining for Synthetic Biology Design

in ACS Synthetic Biology, 5(10):1086-1097, October 2016

@ARTICLE{Misirli2016,
  title = {Data Integration and Mining for Synthetic Biology Design},
  author = {Mısırlı, Göksel and Hallinan, Jennifer and Pocock, Matthew and Lord, Phillip and McLaughlin, James Alastair and Sauro, Herbert and Wipat, Anil},
  year = 2016,
  doi = {10.1021/acssynbio.5b00295},
  month = oct,
  journal = {ACS Synthetic Biology},
  volume = {5},
  number = {10},
  pages = {1086--1097}
}

DOI
K. James, P. Gamba, S.J. Cockell, N. Zenkin

Misincorporation by RNA polymerase is a major source of transcription pausing in vivo

in Nucleic Acids Research, available online since October 2016

Y. Wang, J. Necus, M. Kaiser, B. Mota

Universality in human cortical folding in health and disease

in Proceedings of the National Academy of Sciences, 113(45):12820-12825, November 2016

@ARTICLE{Wang2016,
  title = {Universality in human cortical folding in health and disease},
  author = {Wang, Yujiang and Necus, Joe and Kaiser, Marcus and Mota, Bruno},
  year = 2016,
  doi = {10.1073/pnas.1610175113},
  month = nov,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {113},
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}

DOI eprint code BibTeX

N. Lazzarini, P. Widera, S. Williamson, R. Heer, N. Krasnogor, J. Bacardit

Functional networks inference from rule-based machine learning models

in BioData Mining, 9(1), December 2016

@ARTICLE{Lazzarini2016,
  title = {Functional networks inference from rule-based machine learning models},
  author = {Lazzarini, Nicola and Widera, Paweł and Williamson, Stuart and Heer, Rakesh and Krasnogor, Natalio and Bacardit, Jaume},
  year = 2016,
  doi = {10.1186/s13040-016-0106-4},
  month = dec,
  journal = {BioData Mining},
  volume = {9},
  number = {1}

M. Chavarría, Á. Goñi-Moreno, V. de Lorenzo, P.I. Nikel

A Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in Pseudomonas putida

in mSystems, 1(6):e00154-16, December 2016

@ARTICLE{Chavarria2016,
  title = {A Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in Pseudomonas putida },
  author = {Chavarría, Max and Goñi-Moreno, Ángel and de Lorenzo, Víctor and Nikel, Pablo I.},
  year = 2016,
  doi = {10.1128/mSystems.00154-16},
  month = dec,
  journal = {mSystems},
  volume = {1},
  number = {6},
  pages = {e00154--16}
}

S.O. Danso, D.E. Job, D.R. Gonzalez, D.A. Dickie, J. Palmer, J. Ure, P.M. Bath, P.A.G. Sandercock, J.M. Wardlaw

Developing an Integrated Image Bank and Metadata for Large-scale Research in Cerebrovascular Disease: Our Experience from the Stroke Image Bank Project

in Frontiers in ICT, 3, December 2016

@ARTICLE{Danso2016,
  title = {Developing an Integrated Image Bank and Metadata for Large-scale Research in Cerebrovascular Disease: Our Experience from the Stroke Image Bank Project},
  author = {Danso, Samuel O. and Job, Dominic E. and Gonzalez, David Rodriguez and Dickie, David Alexander and Palmer, Jeb and Ure, Jenny and Bath, Philip M. and Sandercock, Peter A. G. and Wardlaw, Joanna M.},
  year = 2016,
  doi = {10.3389/fict.2016.00032},
  month = dec,
  journal = {Frontiers in ICT},
  volume = {3}

E.O. Odei-Lartey, D. Boateng, S. Danso, A. Kwarteng, L. Abokyi, S. Amenga-Etego, S. Gyaase, K.P. Asante, S. Owusu-Agyei

The application of a biometric identification technique for linking community and hospital data in rural Ghana

in Global Health Action, 9(1):29854, December 2016

@ARTICLE{Odei-Lartey2016,
  title = {The application of a biometric identification technique for linking community and hospital data in rural Ghana},
  author = {Odei-Lartey, Eliezer Ofori and Boateng, Dennis and Danso, Samuel and Kwarteng, Anthony and Abokyi, Livesy and Amenga-Etego, Seeba and Gyaase, Stephaney and Asante, Kwaku Poku and Owusu-Agyei, Seth},
  year = 2016,
  doi = {10.3402/gha.v9.29854},
  month = dec,
  journal = {Global Health Action},
  volume = {9},
  number = {1},
  pages = {29854}
}

P.D. Gutiérrez, M. Lastra, J. Bacardit, J.M. Benítez, F. Herrera

GPU-SME-kNN: Scalable and memory efficient kNN and lazy learning using GPUs

in Information Sciences, 373(C):165-182, December 2016

@ARTICLE{Gutierrez2016,
  title = {GPU-SME-kNN: Scalable and memory efficient kNN and lazy learning using GPUs},
  author = {Gutiérrez, Pablo D. and Lastra, Miguel and Bacardit, Jaume and Benítez, José M. and Herrera, Francisco},
  year = 2016,
  doi = {10.1016/j.ins.2016.08.089},
  month = dec,
  journal = {Information Sciences},
  volume = {373},
  number = {C},
  pages = {165--182}
}

L. Anticoli, C. Piazza, L. Taglialegne, P. Zuliani

Towards Quantum Programs Verification: From Quipper Circuits to QPMC

in Reversible Computation, Lecture Notes in Computer Science 9720, p.213-219, 2016

@INCOLLECTION{Anticoli2016,
  title = {Towards Quantum Programs Verification: From Quipper Circuits to QPMC},
  author = {Anticoli, Linda and Piazza, Carla and Taglialegne, Leonardo and Zuliani, Paolo},
  year = 2016,
  doi = {10.1007/978-3-319-40578-0_16},
  booktitle = {Reversible Computation},
  publisher = {Springer International Publishing},
  volume = {9720},
  series = {Lecture Notes in Computer Science},
  pages = {213--219}
}

H. Fellermann, A. Lopiccolo, J. Kozyra, N. Krasnogor

In Vitro Implementation of a Stack Data Structure Based on DNA Strand Displacement

in Unconventional Computation and Natural Computation, Lecture Notes in Computer Science 9726, p.87-98, 2016

@INCOLLECTION{Fellermann2016,
  title = {In Vitro Implementation of a Stack Data Structure Based on DNA Strand Displacement},
  author = {Fellermann, Harold and Lopiccolo, Annunziata and Kozyra, Jerzy and Krasnogor, Natalio},
  year = 2016,
  doi = {10.1007/978-3-319-41312-9_8},
  booktitle = {Unconventional Computation and Natural Computation},
  publisher = {Springer International Publishing},
  volume = {9726},
  series = {Lecture Notes in Computer Science},
  pages = {87--98}
}

L.E. Eland, A. Wipat, S. Lee, S. Park, L.J. Wu

Microfluidics for bacterial imaging

in Imaging Bacterial Molecules, Structures and Cells, Methods in Microbiology 43, p.69-111, 2016

@INCOLLECTION{Eland2016,
  title = {Microfluidics for bacterial imaging},
  author = {Eland, L. E. and Wipat, A. and Lee, S. and Park, S. and Wu, L. J.},
  year = 2016,
  doi = {10.1016/bs.mim.2016.10.002},
  booktitle = {Imaging Bacterial Molecules, Structures and Cells},
  publisher = {Elsevier},
  volume = {43},
  series = {Methods in Microbiology},
  pages = {69--111}
}

F. Shmarov, P. Zuliani

Probabilistic Hybrid Systems Verification via SMT and Monte Carlo Techniques

in Hardware and Software: Verification and Testing, Lecture Notes in Computer Science 10028, p.152-168, 2016

@INCOLLECTION{Shmarov2016,
  title = {Probabilistic Hybrid Systems Verification via SMT and Monte Carlo Techniques},
  author = {Shmarov, Fedor and Zuliani, Paolo},
  year = 2016,
  doi = {10.1007/978-3-319-49052-6_10},
  booktitle = {Hardware and Software: Verification and Testing},
  publisher = {Springer International Publishing},
  volume = {10028},
  series = {Lecture Notes in Computer Science},
  pages = {152--168}
}

2015

E. Martinez-Garcia, T. Aparicio, A. Goni-Moreno, S. Fraile, V. de Lorenzo

SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities

in Nucleic Acids Research, 43(D1):D1183-D1189, January 2015

@ARTICLE{Martinez-Garcia2015,
  title = {SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities},
  author = {Martinez-Garcia, E. and Aparicio, T. and Goni-Moreno, A. and Fraile, S. and de Lorenzo, V.},
  year = 2015,
  doi = {10.1093/nar/gku1114},
  month = jan,
  journal = {Nucleic Acids Research},
  volume = {43},
  number = {D1},
  pages = {D1183--D1189}
}

DOI eprint code BibTeX

D. Sanassy, P. Widera, N. Krasnogor

Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology

in ACS Synthetic Biology, 4(1):39-47, January 2015

@ARTICLE{Sanassy2014,
  title = {Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology},
  author = {Sanassy, Daven and Widera, Paweł and Krasnogor, Natalio},
  year = 2015,
  doi = {10.1021/sb5001406},
  month = jan,
  journal = {ACS Synthetic Biology},
  volume = {4},
  number = {1},
  pages = {39--47}
}

A. Swan, D. Stekel, C. Hodgman, D. Allaway, M. Alqahtani, A. Mobasheri, J. Bacardit

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data

in BMC Genomics, 16(Suppl 1):S2, January 2015

@ARTICLE{Swan2015,
  title = {A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data},
  author = {Swan, A.L. and Stekel, D.J. and Hodgman, C. and Allaway, D. and Alqahtani, M.H. and Mobasheri, A. and Bacardit, J.},
  year = 2015,
  doi = {10.1186/1471-2164-16-S1-S2},
  month = jan,
  journal = {BMC Genomics},
  volume = {16},
  number = {Suppl 1},
  pages = {S2}
}

S. Konur, M. Gheorghe, C. Dragomir, L. Mierla, F. Ipate, N. Krasnogor

Qualitative and Quantitative Analysis of Systems and Synthetic Biology Constructs using P Systems

in ACS Synthetic Biology, 4(1):83-92, January 2015

@ARTICLE{Konur2015,
  title = {Qualitative and Quantitative Analysis of Systems and Synthetic Biology Constructs using P Systems},
  author = {Konur, Savas and Gheorghe, Marian and Dragomir, Ciprian and Mierla, Laurentiu and Ipate, Florentin and Krasnogor, Natalio},
  year = 2015,
  doi = {10.1021/sb500134w},
  month = jan,
  journal = {ACS Synthetic Biology},
  volume = {4},
  number = {1},
  pages = {83--92}
}

N. Roehner, E. Oberortner, M. Pocock, J. Beal, K. Clancy, C. Madsen, G. Misirli, A. Wipat, H. Sauro, C.J. Myers

Proposed Data Model for the Next Version of the Synthetic Biology Open Language

in ACS Synthetic Biology, 4(1):57-71, January 2015

@ARTICLE{Roehner2014,
  title = {Proposed Data Model for the Next Version of the Synthetic Biology Open Language},
  author = {Roehner, Nicholas and Oberortner, Ernst and Pocock, Matthew and Beal, Jacob and Clancy, Kevin and Madsen, Curtis and Misirli, Goksel and Wipat, Anil and Sauro, Herbert and Myers, Chris J.},
  year = 2015,
  doi = {10.1021/sb500176h},
  month = jan,
  journal = {ACS Synthetic Biology},
  volume = {4},
  number = {1},
  pages = {57--71}
}

I. Triguero, D. Peralta, J. Bacardit, S. García, F. Herrera

MRPR: A MapReduce solution for prototype reduction in big data classification

in Neurocomputing, 150(PA):331-345, February 2015

@ARTICLE{Triguero2014a,
  title = {MRPR: A MapReduce solution for prototype reduction in big data classification},
  author = {Triguero, Isaac and Peralta, Daniel and Bacardit, Jaume and García, Salvador and Herrera, Francisco},
  year = 2015,
  doi = {10.1016/j.neucom.2014.04.078},
  month = feb,
  journal = {Neurocomputing},
  volume = {150},
  number = {PA},
  pages = {331--345}
}

B. Weobong, A.H. ten Asbroek, S. Soremekun, S. Danso, S. Owusu-Agyei, M. Prince, B.R. Kirkwood

Determinants Of Postnatal Depression In Rural Ghana: Findings From The Don Population Based Cohort Study

in Depression and Anxiety, 32(2):108-119, February 2015

@ARTICLE{Weobong2015,
  title = {Determinants Of Postnatal Depression In Rural Ghana: Findings From The Don Population Based Cohort Study},
  author = {Weobong, Benedict and ten Asbroek, Augustinus HA and Soremekun, Seyi and Danso, Samuel and Owusu-Agyei, Seth and Prince, Martin and Kirkwood, Betty R.},
  year = 2015,
  doi = {10.1002/da.22218},
  month = feb,
  journal = {Depression and Anxiety},
  volume = {32},
  number = {2},
  pages = {108--119}
}

S. Lim, M. Kaiser

Developmental time windows for axon growth influence neuronal network topology

in Biological Cybernetics, 109(2):275-286, April 2015

@ARTICLE{Lim2015,
  title = {Developmental time windows for axon growth influence neuronal network topology},
  author = {Lim, Sol and Kaiser, Marcus},
  year = 2015,
  doi = {10.1007/s00422-014-0641-3},
  month = apr,
  journal = {Biological Cybernetics},
  volume = {109},
  number = {2},
  pages = {275--286}
}

P.I. Nikel, F.J. Romero-Campero, J.A. Zeidman, Á. Goñi-Moreno, V. de Lorenzo

The Glycerol-Dependent Metabolic Persistence of Pseudomonas putida KT2440 Reflects the Regulatory Logic of the GlpR Repressor

in mBio, 6(2):e00340-15, May 2015

@ARTICLE{Nikel2015,
  title = {The Glycerol-Dependent Metabolic Persistence of Pseudomonas putida KT2440 Reflects the Regulatory Logic of the GlpR Repressor},
  author = {Nikel, Pablo I. and Romero-Campero, Francisco J. and Zeidman, Joshua A. and Goñi-Moreno, Ángel and de Lorenzo, Víctor},
  year = 2015,
  doi = {10.1128/mBio.00340-15},
  month = may,
  journal = {mBio},
  volume = {6},
  number = {2},
  pages = {e00340--15}
}

M. Kaiser

Neuroanatomy: Connectome Connects Fly and Mammalian Brain Networks

in Current Biology, 25(10):R416-R418, May 2015

@ARTICLE{Kaiser2015,
  title = {Neuroanatomy: Connectome Connects Fly and Mammalian Brain Networks},
  author = {Kaiser, Marcus},
  year = 2015,
  doi = {10.1016/j.cub.2015.03.039},
  month = may,
  journal = {Current Biology},
  volume = {25},
  number = {10},
  pages = {R416--R418}
}

S. Wook Yoo, C.E. Han, J.S. Shin, S. Won Seo, D.L. Na, M. Kaiser, Y. Jeong, J. Seong

A Network Flow-based Analysis of Cognitive Reserve in Normal Ageing and Alzheimer’s Disease

in Scientific Reports, 5:10057, May 2015

@ARTICLE{WookYoo2015,
  title = {A Network Flow-based Analysis of Cognitive Reserve in Normal Ageing and Alzheimer’s Disease},
  author = {Wook Yoo, Sang and Han, Cheol E. and Shin, Joseph S. and Won Seo, Sang and Na, Duk L. and Kaiser, Marcus and Jeong, Yong and Seong, Joon-Kyung},
  year = 2015,
  doi = {10.1038/srep10057},
  month = may,
  journal = {Scientific Reports},
  volume = {5},
  pages = {10057}
}

L.T. Lui, G. Terrazas, H. Zenil, C. Alexander, N. Krasnogor

Complexity Measurement Based on Information Theory and Kolmogorov Complexity

in Artificial Life, 21(2):205-224, May 2015

@ARTICLE{Lui2015,
  title = {Complexity Measurement Based on Information Theory and Kolmogorov Complexity},
  author = {Lui, Leong Ting and Terrazas, Germán and Zenil, Hector and Alexander, Cameron and Krasnogor, Natalio},
  year = 2015,
  doi = {10.1162/ARTL_a_00157},
  month = may,
  journal = {Artificial Life},
  volume = {21},
  number = {2},
  pages = {205--224}
}

S. Lim, C.E. Han, P.J. Uhlhaas, M. Kaiser

Preferential Detachment During Human Brain Development: Age- and Sex-Specific Structural Connectivity in Diffusion Tensor Imaging (DTI) Data

in Cerebral Cortex, 25(6):1477-1489, June 2015

@ARTICLE{Lim2013,
  title = {Preferential Detachment During Human Brain Development: Age- and Sex-Specific Structural Connectivity in Diffusion Tensor Imaging (DTI) Data},
  author = {Lim, S. and Han, C. E. and Uhlhaas, P. J. and Kaiser, M.},
  year = 2015,
  doi = {10.1093/cercor/bht333},
  month = jun,
  journal = {Cerebral Cortex},
  volume = {25},
  number = {6},
  pages = {1477--1489}
}

R.J. Tomsett, M. Ainsworth, A. Thiele, M. Sanayei, X. Chen, M.A. Gieselmann, M.A. Whittington, M.O. Cunningham, M. Kaiser

Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue

in Brain Structure and Function, 220(4):2333-2353, July 2015

@ARTICLE{Tomsett2015,
  title = {Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue},
  author = {Tomsett, Richard J. and Ainsworth, Matt and Thiele, Alexander and Sanayei, Mehdi and Chen, Xing and Gieselmann, Marc A. and Whittington, Miles A. and Cunningham, Mark O. and Kaiser, Marcus},
  year = 2015,
  doi = {10.1007/s00429-014-0793-x},
  month = jul,
  journal = {Brain Structure and Function},
  volume = {220},
  number = {4},
  pages = {2333--2353}
}

P. Zuliani

Statistical model checking for biological applications

in International Journal on Software Tools for Technology Transfer, 17(4):527-536, August 2015

@ARTICLE{Zuliani2014,
  title = {Statistical model checking for biological applications},
  author = {Zuliani, Paolo},
  year = 2015,
  doi = {10.1007/s10009-014-0343-0},
  month = aug,
  journal = {International Journal on Software Tools for Technology Transfer},
  volume = {17},
  number = {4},
  pages = {527--536}
}

F. Eduati, L.M. Mangravite, T. Wang, H. Tang, J.C. Bare, R. Huang, T. Norman, M. Kellen, M.P. Menden, J. Yang, X. Zhan, R. Zhong, G. Xiao, M. Xia, N. Abdo, O. Kosyk, F. Eduati, L.M. Mangravite, J.C. Bare, T. Norman, M. Kellen, M.P. Menden, S. Friend, G. Stolovitzky, A. Dearry, R.R. Tice, R. Huang, M. Xia, A. Simeonov, N. Abdo, O. Kosyk, I. Rusyn, et al.

Prediction of human population responses to toxic compounds by a collaborative competition

in Nature Biotechnology, 33(9):933-940, August 2015

@ARTICLE{Eduati2015,
  title = {Prediction of human population responses to toxic compounds by a collaborative competition},
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B. Weobong, A.H.A. ten Asbroek, S. Soremekun, L. Gram, S. Amenga-Etego, S. Danso, S. Owusu-Agyei, M. Prince, B.R. Kirkwood

Association between probable postnatal depression and increased infant mortality and morbidity: findings from the DON population-based cohort study in rural Ghana

in BMJ Open, 5(8):e006509, August 2015

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C.A. Papasavvas, Y. Wang, A.J. Trevelyan, M. Kaiser

Gain control through divisive inhibition prevents abrupt transition to chaos in a neural mass model

in Physical Review E, 92(3), September 2015

@ARTICLE{Papasavvas2015,
  title = {Gain control through divisive inhibition prevents abrupt transition to chaos in a neural mass model},
  author = {Papasavvas, Christoforos A. and Wang, Yujiang and Trevelyan, Andrew J. and Kaiser, Marcus},
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  doi = {10.1103/PhysRevE.92.032723},
  month = sep,
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L.R. Peraza, J. Taylor, M. Kaiser

Divergent brain functional network alterations in dementia with Lewy bodies and Alzheimer's disease

in Neurobiology of Aging, 36(9):2458-2467, September 2015

@ARTICLE{Peraza2015,
  title = {Divergent brain functional network alterations in dementia with Lewy bodies and Alzheimer's disease},
  author = {Peraza, Luis R. and Taylor, John-Paul and Kaiser, Marcus},
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  month = sep,
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  volume = {36},
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H.D. Kjeldsen, M. Kaiser, M.A. Whittington

Near-field electromagnetic holography for high-resolution analysis of network interactions in neuronal tissue

in Journal of Neuroscience Methods, 253(C):1-9, September 2015

@ARTICLE{Kjeldsen2015,
  title = {Near-field electromagnetic holography for high-resolution analysis of network interactions in neuronal tissue},
  author = {Kjeldsen, Henrik D. and Kaiser, Marcus and Whittington, Miles A.},
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  volume = {253},
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Eligibility for clinical trials in primary Sjögren’s syndrome: lessons from the UK Primary Sjögren’s Syndrome Registry

in Rheumatology, available online since October 2015

Y. Lo, R. O’Dea, J.J. Crofts, C.E. Han, M. Kaiser

A geometric network model of intrinsic grey-matter connectivity of the human brain

in Scientific Reports, 5:15397, October 2015

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  title = {A geometric network model of intrinsic grey-matter connectivity of the human brain},
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I. Triguero, S. del Río, V. López, J. Bacardit, J.M. Benítez, F. Herrera

ROSEFW-RF: The winner algorithm for the ECBDL’14 big data competition: An extremely imbalanced big data bioinformatics problem

in Knowledge-Based Systems, 87(C):69-79, October 2015

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  title = {ROSEFW-RF: The winner algorithm for the ECBDL’14 big data competition: An extremely imbalanced big data bioinformatics problem},
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L.R. Peraza, S.J. Colloby, M.J. Firbank, G.S. Greasy, I.G. McKeith, M. Kaiser, J. O'Brien, J. Taylor

Resting state in Parkinson's disease dementia and dementia with Lewy bodies: commonalities and differences

in International Journal of Geriatric Psychiatry, 30(11):1135-1146, November 2015

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Z. Zhang, T. Nguyen, N. Roehner, G. Misirli, M. Pocock, E. Oberortner, M. Samineni, Z. Zundel, J. Beal, K. Clancy, A. Wipat, C.J. Myers

libSBOLj 2.0: A Java Library to Support SBOL 2.0

in IEEE Life Sciences Letters, 1(4):34-37, December 2015

@ARTICLE{Zhang2015,
  title = {libSBOLj 2.0: A Java Library to Support SBOL 2.0},
  author = {Zhang, Zhen and Nguyen, Tramy and Roehner, Nicholas and Misirli, Goksel and Pocock, Matthew and Oberortner, Ernst and Samineni, Meher and Zundel, Zach and Beal, Jacob and Clancy, Kevin and Wipat, Anil and Myers, Chris J.},
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K. James, S. Al-Ali, J. Tarn, S.J. Cockell, C.S. Gillespie, V. Hindmarsh, J. Locke, S. Mitchell, D. Lendrem, S. Bowman, E. Price, C.T. Pease, P. Emery, P. Lanyon, J.A. Hunter, M. Gupta, M. Bombardieri, N. Sutcliffe, C. Pitzalis, J. McLaren, A. Cooper, M. Regan, I. Giles, D. Isenberg, V. Saravanan, D. Coady, B. Dasgupta, N. McHugh, S. Young-Min, R. Moots, N. Gendi, M. Akil, et al.

A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome

in PLOS ONE, 10(12):e0143970, December 2015

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F. Hutchings, C.E. Han, S.S. Keller, B. Weber, P.N. Taylor, M. Kaiser

Predicting Surgery Targets in Temporal Lobe Epilepsy through Structural Connectome Based Simulations

in PLOS Computational Biology, 11(12):e1004642, December 2015

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  title = {Predicting Surgery Targets in Temporal Lobe Epilepsy through Structural Connectome Based Simulations},
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P.N. Taylor, J. Thomas, N. Sinha, J. Dauwels, M. Kaiser, T. Thesen, J. Ruths

Optimal control based seizure abatement using patient derived connectivity

in Frontiers in Neuroscience, 9(202):1, 2015

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P.N. Taylor, C.E. Han, J. Schoene-Bake, B. Weber, M. Kaiser

Structural connectivity changes in temporal lobe epilepsy: Spatial features contribute more than topological measures

in NeuroImage: Clinical, 8(C):322-328, 2015

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  title = {Structural connectivity changes in temporal lobe epilepsy: Spatial features contribute more than topological measures},
  author = {Taylor, Peter N. and Han, Cheol E. and Schoene-Bake, Jan-Christoph and Weber, Bernd and Kaiser, Marcus},
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B. Liu, S. Kong, S. Gao, P. Zuliani, E.M. Clarke

Towards personalized prostate cancer therapy using delta-reachability analysis

in Proceedings of the 18th International Conference on Hybrid Systems Computation and Control - HSCC '15, p.227-232, Seattle, Washington, 2015

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  title = {Towards personalized prostate cancer therapy using delta-reachability analysis},
  author = {Liu, Bing and Kong, Soonho and Gao, Sicun and Zuliani, Paolo and Clarke, Edmund M.},
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  doi = {10.1145/2728606.2728634},
  booktitle = {Proceedings of the 18th International Conference on Hybrid Systems Computation and Control - HSCC '15},
  pages = {227--232},
  address = {Seattle, Washington}
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C. Madsen, G. Misirli, M. Pocock, J. Hallinan, A. Wipat

SBOL Stack: The One-stop-shop for Storing and Publishing Synthetic Biology Designs

in 7th International Workshop on Bio-Design Automation, p.26-27, Seattle, US, 2015

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  title = {SBOL Stack: The One-stop-shop for Storing and Publishing Synthetic Biology Designs},
  author = {Madsen, Curtis and Misirli, Goksel and Pocock, Matthew and Hallinan, Jennifer and Wipat, Anil},
  year = 2015,
  booktitle = {7th International Workshop on Bio-Design Automation},
  pages = {26--27},
  address = {Seattle, US}
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Q. Wang, P. Zuliani, S. Kong, S. Gao, E.M. Clarke

SReach: A Probabilistic Bounded Delta-Reachability Analyzer for Stochastic Hybrid Systems

in Computational Methods in Systems Biology, Lecture Notes in Computer Science 9308, p.15-27, 2015

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  title = {SReach: A Probabilistic Bounded Delta-Reachability Analyzer for Stochastic Hybrid Systems},
  author = {Wang, Qinsi and Zuliani, Paolo and Kong, Soonho and Gao, Sicun and Clarke, Edmund M.},
  year = 2015,
  doi = {10.1007/978-3-319-23401-4_3},
  booktitle = {Computational Methods in Systems Biology},
  publisher = {Springer International Publishing},
  volume = {9308},
  series = {Lecture Notes in Computer Science},
  pages = {15--27}
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A. Goñi-Moreno, M. Amos

DiSCUS: A Simulation Platform for Conjugation Computing

in Unconventional Computation and Natural Computation, Lecture Notes in Computer Science 9252, p.181-191, 2015

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  title = {DiSCUS: A Simulation Platform for Conjugation Computing},
  author = {Goñi-Moreno, Angel and Amos, Martyn},
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  doi = {10.1007/978-3-319-21819-9_13},
  booktitle = {Unconventional Computation and Natural Computation},
  publisher = {Springer International Publishing},
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  series = {Lecture Notes in Computer Science},
  pages = {181--191}
}

B. Bartley, J. Beal, K. Clancy, G. Misirli, N. Roehner, E. Oberortner, M. Pocock, M. Bissell, C. Madsen, T. Nguyen, Z. Zhang, J.H. Gennari, C. Myers, A. Wipat, H. Sauro

Synthetic Biology Open Language (SBOL) Version 2.0.0

in Journal of Integrative Bioinformatics, 12(2):272, 2015

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  title = {Synthetic Biology Open Language (SBOL) Version 2.0.0},
  author = {Bartley, Bryan and Beal, Jacob and Clancy, Kevin and Misirli, Goksel and Roehner, Nicholas and Oberortner, Ernst and Pocock, Matthew and Bissell, Michael and Madsen, Curtis and Nguyen, Tramy and Zhang, Zhen and Gennari, John H and Myers, Chris and Wipat, Anil and Sauro, Herbert},
  year = 2015,
  doi = {10.2390/biecoll-jib-2015-272},
  journal = {Journal of Integrative Bioinformatics},
  volume = {12},
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C. Madsen, F. Shmarov, P. Zuliani

BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models

in Computational Methods in Systems Biology, Lecture Notes in Computer Science 9308, p.182-194, 2015

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  title = {BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models},
  author = {Madsen, Curtis and Shmarov, Fedor and Zuliani, Paolo},
  year = 2015,
  doi = {10.1007/978-3-319-23401-4_16},
  booktitle = {Computational Methods in Systems Biology},
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  series = {Lecture Notes in Computer Science},
  pages = {182--194}
}

M. Martínez-Ballesteros, J. Bacardit, A. Troncoso, J.C. Riquelme

Enhancing the scalability of a genetic algorithm to discover quantitative association rules in large-scale datasets

in Integrated Computer-Aided Engineering, 22(1):21-39, 2015

@ARTICLE{Martinez-Ballesteros2015,
  title = {Enhancing the scalability of a genetic algorithm to discover quantitative association rules in large-scale datasets},
  author = {Martínez-Ballesteros, María and Bacardit, Jaume and Troncoso, Alicia and Riquelme, José C},
  year = 2015,
  doi = {10.3233/ICA-140479},
  journal = {Integrated Computer-Aided Engineering},
  volume = {22},
  number = {1},
  pages = {21--39}
}

C. Myers, K. Clancy, G. Misirli, E. Oberortner, M. Pocock, J. Quinn, N. Roehner, H.M. Sauro

The Synthetic Biology Open Language

in Computational Methods in Synthetic Biology, Methods in Molecular Biology 1244, p.323-336, 2015

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  title = {The Synthetic Biology Open Language},
  author = {Myers, Chris and Clancy, Kevin and Misirli, Goksel and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline and Roehner, Nicholas and Sauro, Herbert M.},
  year = 2015,
  doi = {10.1007/978-1-4939-1878-2_16},
  booktitle = {Computational Methods in Synthetic Biology},
  publisher = {Springer New York},
  volume = {1244},
  series = {Methods in Molecular Biology},
  pages = {323--336}
}

F. Shmarov, P. Zuliani

ProbReach

in Proceedings of the 18th International Conference on Hybrid Systems Computation and Control - HSCC '15, p.134-139, Seattle, Washington, 2015

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  title = {ProbReach},
  author = {Shmarov, Fedor and Zuliani, Paolo},
  year = 2015,
  doi = {10.1145/2728606.2728625},
  booktitle = {Proceedings of the 18th International Conference on Hybrid Systems Computation and Control - HSCC '15},
  pages = {134--139},
  address = {Seattle, Washington}
}

S.O. Danso

Text Analytics to Predict Time and Cause of Death from Verbal Autopsies

PhD thesis, University of Leeds, 2015

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  title = {Text Analytics to Predict Time and Cause of Death from Verbal Autopsies},
  author = {Danso, Samuel Odei},
  year = 2015,
  school = {University of Leeds}
}

Y. Wang, F. Hutchings, M. Kaiser

Computational modeling of neurostimulation in brain diseases

in Computational Neurostimulation, Progress in Brain Research 222, p.191-228, 2015

@INCOLLECTION{Wang2015,
  title = {Computational modeling of neurostimulation in brain diseases},
  author = {Wang, Yujiang and Hutchings, Frances and Kaiser, Marcus},
  year = 2015,
  doi = {10.1016/bs.pbr.2015.06.012},
  booktitle = {Computational Neurostimulation},
  publisher = {Elsevier},
  volume = {222},
  series = {Progress in Brain Research},
  pages = {191--228}
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O. Gilfellon, G. Misirli, C. Madsen, J. Hallinan, P. Zuliani, A. Wipat

SynBad: An SVP Design Framework

in 7th International Workshop on Bio-Design Automation, p.49-50, Seattle, US, 2015

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  title = {SynBad: An SVP Design Framework},
  author = {Gilfellon, Owen and Misirli, Goksel and Madsen, Curtis and Hallinan, Jennifer and Zuliani, Paolo and Wipat, Anil},
  year = 2015,
  booktitle = {7th International Workshop on Bio-Design Automation},
  pages = {49--50},
  address = {Seattle, US}
}

2014

D. Klein, A. Rotarska-Jagiela, E. Genc, S. Sritharan, H. Mohr, F. Roux, C.E. Han, M. Kaiser, W. Singer, P.J. Uhlhaas

Adolescent Brain Maturation and Cortical Folding: Evidence for Reductions in Gyrification

in PLoS ONE, 9(1):e84914, January 2014

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  title = {Adolescent Brain Maturation and Cortical Folding: Evidence for Reductions in Gyrification},
  author = {Klein, Daniel and Rotarska-Jagiela, Anna and Genc, Erhan and Sritharan, Sharmili and Mohr, Harald and Roux, Frederic and Han, Cheol E. and Kaiser, Marcus and Singer, Wolf and Uhlhaas, Peter J.},
  year = 2014,
  doi = {10.1371/journal.pone.0084914},
  month = jan,
  journal = {PLoS ONE},
  volume = {9},
  number = {1},
  pages = {e84914}
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A. Garcia-Piquer, A. Fornells, J. Bacardit, A. Orriols-Puig, E. Golobardes

Large-Scale Experimental Evaluation of Cluster Representations for Multiobjective Evolutionary Clustering

in IEEE Transactions on Evolutionary Computation, 18(1):36-53, February 2014

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  title = {Large-Scale Experimental Evaluation of Cluster Representations for Multiobjective Evolutionary Clustering},
  author = {Garcia-Piquer, Alvaro and Fornells, Albert and Bacardit, Jaume and Orriols-Puig, Albert and Golobardes, Elisabet},
  year = 2014,
  doi = {10.1109/TEVC.2013.2281513},
  month = feb,
  journal = {IEEE Transactions on Evolutionary Computation},
  volume = {18},
  number = {1},
  pages = {36--53}
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R. Bauer, F. Zubler, A. Hauri, D.R. Muir, R.J. Douglas

Developmental Origin of Patchy Axonal Connectivity in the Neocortex: A Computational Model

in Cerebral Cortex, 24(2):487-500, February 2014

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  title = {Developmental Origin of Patchy Axonal Connectivity in the Neocortex: A Computational Model},
  author = {Bauer, R. and Zubler, F. and Hauri, A. and Muir, D. R. and Douglas, R. J.},
  year = 2014,
  doi = {10.1093/cercor/bhs327},
  month = feb,
  journal = {Cerebral Cortex},
  volume = {24},
  number = {2},
  pages = {487--500}
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P. Andras

Function Approximation Using Combined Unsupervised and Supervised Learning

in IEEE Transactions on Neural Networks and Learning Systems, 25(3):495-505, March 2014

@ARTICLE{Andras2014,
  title = {Function Approximation Using Combined Unsupervised and Supervised Learning},
  author = {Andras, Peter},
  year = 2014,
  doi = {10.1109/TNNLS.2013.2276044},
  month = mar,
  journal = {IEEE Transactions on Neural Networks and Learning Systems},
  volume = {25},
  number = {3},
  pages = {495--505}
}

M. Courtot, N. Juty, C. Knupfer, D. Waltemath, A. Zhukova, A. Drager, M. Dumontier, A. Finney, M. Golebiewski, J. Hastings, S. Hoops, S. Keating, D.B. Kell, S. Kerrien, J. Lawson, A. Lister, J. Lu, R. Machne, P. Mendes, M. Pocock, N. Rodriguez, A. Villeger, D.J. Wilkinson, S. Wimalaratne, C. Laibe, M. Hucka, N. Le Novere

Controlled vocabularies and semantics in systems biology

in Molecular Systems Biology, 7(1):543-543, April 2014

@ARTICLE{Courtot2014,
  title = {Controlled vocabularies and semantics in systems biology},
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  doi = {10.1038/msb.2011.77},
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  journal = {Molecular Systems Biology},
  volume = {7},
  number = {1},
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K.A. Koram, S. Amenga-Etego, K. Kayan, K. Osei-Kwakye, K.P. Asante, S. Owusu-Agyei, S. Danso, P. Bilson, D. Adu-Gyasi, E. Mahama, D.K. Dosoo

Biochemical and Hematologic Parameters for Children in the Middle Belt of Ghana

in The American Journal of Tropical Medicine and Hygiene, 90(4):767-773, April 2014

@ARTICLE{Koram2014,
  title = {Biochemical and Hematologic Parameters for Children in the Middle Belt of Ghana},
  author = {Koram, Kwadwo A. and Amenga-Etego, Stephen and Kayan, Kingsley and Osei-Kwakye, Kingsley and Asante, Kwaku P. and Owusu-Agyei, Seth and Danso, Samuel and Bilson, Philip and Adu-Gyasi, Dennis and Mahama, Emmanuel and Dosoo, David K.},
  year = 2014,
  doi = {10.4269/ajtmh.13-0098},
  month = apr,
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  volume = {90},
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}

DOI eprint code BibTeX

C. Winterhalter, P. Widera, N. Krasnogor

JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks

in Bioinformatics, 30(7):1029-1030, April 2014

@ARTICLE{Winterhalter2013,
  title = {JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks},
  author = {Winterhalter, C. and Widera, P. and Krasnogor, N.},
  year = 2014,
  doi = {10.1093/bioinformatics/btt732},
  month = apr,
  journal = {Bioinformatics},
  volume = {30},
  number = {7},
  pages = {1029--1030}
}

V.C. Epa, A.L. Hook, C. Chang, J. Yang, R. Langer, D.G. Anderson, P. Williams, M.C. Davies, M.R. Alexander, D.A. Winkler

Modelling and Prediction of Bacterial Attachment to Polymers

in Advanced Functional Materials, 24(14):2085-2093, April 2014

@ARTICLE{Epa2014,
  title = {Modelling and Prediction of Bacterial Attachment to Polymers},
  author = {Epa, V. C. and Hook, A. L. and Chang, C. and Yang, J. and Langer, R. and Anderson, D. G. and Williams, P. and Davies, M. C. and Alexander, M. R. and Winkler, D. A.},
  year = 2014,
  doi = {10.1002/adfm.201302877},
  month = apr,
  journal = {Advanced Functional Materials},
  volume = {24},
  number = {14},
  pages = {2085--2093}
}

J.S. Hallinan, O. Gilfellon, G. Misirli, A. Wipat

Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts

in 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, p.1-8, Honolulu, HI, USA, May 2014

@INPROCEEDINGS{Hallinan2014,
  title = {Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts},
  author = {Hallinan, J. S. and Gilfellon, O. and Misirli, G. and Wipat, A.},
  year = 2014,
  doi = {10.1109/CIBCB.2014.6845520},
  month = may,
  booktitle = {2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology},
  pages = {1--8},
  address = {Honolulu, HI, USA}
}

M. Galdzicki, K.P. Clancy, E. Oberortner, M. Pocock, J.Y. Quinn, C.A. Rodriguez, N. Roehner, M.L. Wilson, L. Adam, J.C. Anderson, B.A. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grünberg, J. Hallinan, N.J. Hillson, J.D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H.A. Plahar, E. Sirin, G. Stan, A. Villalobos, A. Wipat, J.H. Gennari, C.J. Myers, H.M. Sauro

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

in Nature Biotechnology, 32(6):545-550, June 2014

@ARTICLE{Galdzicki2014,
  title = {The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology},
  author = {Galdzicki, Michal and Clancy, Kevin P and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline Y and Rodriguez, Cesar A and Roehner, Nicholas and Wilson, Mandy L and Adam, Laura and Anderson, J Christopher and Bartley, Bryan A and Beal, Jacob and Chandran, Deepak and Chen, Joanna and Densmore, Douglas and Endy, Drew and Grünberg, Raik and Hallinan, Jennifer and Hillson, Nathan J and Johnson, Jeffrey D and Kuchinsky, Allan and Lux, Matthew and Misirli, Goksel and Peccoud, Jean and Plahar, Hector A and Sirin, Evren and Stan, Guy-Bart and Villalobos, Alan and Wipat, Anil and Gennari, John H and Myers, Chris J and Sauro, Herbert M},
  year = 2014,
  doi = {10.1038/nbt.2891},
  month = jun,
  journal = {Nature Biotechnology},
  volume = {32},
  number = {6},
  pages = {545--550}
}

J. Rusakovica, J. Hallinan, A. Wipat, P. Zuliani

Probabilistic Latent Semantic Analysis Applied to Whole Bacterial Genomes Identifies Common Genomic Features

in Journal of Integrative Bioinformatics, 11(2):243, June 2014

@ARTICLE{Rusakovica2014,
  title = {Probabilistic Latent Semantic Analysis Applied to Whole Bacterial Genomes Identifies Common Genomic Features},
  author = {Rusakovica, Julija and Hallinan, Jennifer and Wipat, Anil and Zuliani, Paolo},
  year = 2014,
  doi = {10.2390/biecoll-jib-2014-243},
  month = jun,
  journal = {Journal of Integrative Bioinformatics},
  volume = {11},
  number = {2},
  pages = {243}
}

A.L. Hook, C. Chang, D.J. Scurr, R. Langer, D.G. Anderson, P. Williams, M.C. Davies, M.R. Alexander

Thermally Switchable Polymers Achieve Controlled Escherichia coli Detachment

in Advanced Healthcare Materials, 3(7):1020-1025, July 2014

@ARTICLE{Hook2014,
  title = {Thermally Switchable Polymers Achieve Controlled Escherichia coli Detachment},
  author = {Hook, Andrew L. and Chang, Chien-Yi and Scurr, David J. and Langer, Robert and Anderson, Daniel G. and Williams, Paul and Davies, Martyn C. and Alexander, Morgan R.},
  year = 2014,
  doi = {10.1002/adhm.201300518},
  month = jul,
  journal = {Advanced Healthcare Materials},
  volume = {3},
  number = {7},
  pages = {1020--1025}
}

S. Tanaka, H. Fellermann, S. Rasmussen

Structure and selection in an autocatalytic binary polymer model

in EPL (Europhysics Letters), 107(2):28004, July 2014

@ARTICLE{Tanaka2014,
  title = {Structure and selection in an autocatalytic binary polymer model},
  author = {Tanaka, Shinpei and Fellermann, Harold and Rasmussen, Steen},
  year = 2014,
  doi = {10.1209/0295-5075/107/28004},
  month = jul,
  journal = {EPL (Europhysics Letters)},
  volume = {107},
  number = {2},
  pages = {28004}
}

L. Gram, S. Soremekun, A. ten Asbroek, A. Manu, M. O'Leary, Z. Hill, S. Danso, S. Amenga-Etego, S. Owusu-Agyei, B.R. Kirkwood

Socio-economic determinants and inequities in coverage and timeliness of early childhood immunisation in rural Ghana

in Tropical Medicine & International Health, 19(7):802-811, July 2014

@ARTICLE{Gram2014,
  title = {Socio-economic determinants and inequities in coverage and timeliness of early childhood immunisation in rural Ghana},
  author = {Gram, Lu and Soremekun, Seyi and ten Asbroek, Augustinus and Manu, Alexander and O'Leary, Maureen and Hill, Zelee and Danso, Samuel and Amenga-Etego, Seeba and Owusu-Agyei, Seth and Kirkwood, Betty R.},
  year = 2014,
  doi = {10.1111/tmi.12324},
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  volume = {19},
  number = {7},
  pages = {802--811}
}

I. Triguero, D. Peralta, J. Bacardit, S. Garcia, F. Herrera

A combined MapReduce-windowing two-level parallel scheme for evolutionary prototype generation

in 2014 IEEE Congress on Evolutionary Computation (CEC), p.3036-3043, Beijing, China, July 2014

@INPROCEEDINGS{Triguero2014,
  title = {A combined MapReduce-windowing two-level parallel scheme for evolutionary prototype generation},
  author = {Triguero, Isaac and Peralta, Daniel and Bacardit, Jaume and Garcia, Salvador and Herrera, Francisco},
  year = 2014,
  doi = {10.1109/CEC.2014.6900490},
  month = jul,
  booktitle = {2014 IEEE Congress on Evolutionary Computation (CEC)},
  pages = {3036--3043},
  address = {Beijing, China}
}

Y. Wang, M. Goodfellow, P.N. Taylor, G. Baier

Dynamic Mechanisms of Neocortical Focal Seizure Onset

in PLoS Computational Biology, 10(8):e1003787, August 2014

@ARTICLE{Wang2014,
  title = {Dynamic Mechanisms of Neocortical Focal Seizure Onset},
  author = {Wang, Yujiang and Goodfellow, Marc and Taylor, Peter Neal and Baier, Gerold},
  year = 2014,
  doi = {10.1371/journal.pcbi.1003787},
  month = aug,
  journal = {PLoS Computational Biology},
  volume = {10},
  number = {8},
  pages = {e1003787}
}

J. Blakes, O. Raz, U. Feige, J. Bacardit, P. Widera, T. Ben-Yehezkel, E. Shapiro, N. Krasnogor

Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly

in ACS Synthetic Biology, 3(8):529-542, August 2014

@ARTICLE{Blakes2014,
  title = {Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly},
  author = {Blakes, Jonathan and Raz, Ofir and Feige, Uriel and Bacardit, Jaume and Widera, Paweł and Ben-Yehezkel, Tuval and Shapiro, Ehud and Krasnogor, Natalio},
  year = 2014,
  doi = {10.1021/sb400161v},
  month = aug,
  journal = {ACS Synthetic Biology},
  volume = {3},
  number = {8},
  pages = {529--542}
}

H. Fellermann, L. Cardelli

Programming chemistry in DNA-addressable bioreactors

in Journal of The Royal Society Interface, 11(99):20130987-20130987, August 2014

@ARTICLE{Fellermann2014b,
  title = {Programming chemistry in DNA-addressable bioreactors},
  author = {Fellermann, H. and Cardelli, L.},
  year = 2014,
  doi = {10.1098/rsif.2013.0987},
  month = aug,
  journal = {Journal of The Royal Society Interface},
  volume = {11},
  number = {99},
  pages = {20130987--20130987}
}

D. Sanassy, H. Fellermann, N. Krasnogor, S. Konur, L.M. Mierla, M. Gheorghe, C. Ladroue, S. Kalvala

Modelling and Stochastic Simulation of Synthetic Biological Boolean Gates

in 2014 IEEE Intl Conf on High Performance Computing and Communications, 2014 IEEE 6th Intl Symp on Cyberspace Safety and Security, 2014 IEEE 11th Intl Conf on Embedded Software and Syst (HPCC,CSS,ICESS), p.404-408, Paris, France, August 2014

@INPROCEEDINGS{Sanassy2014a,
  title = {Modelling and Stochastic Simulation of Synthetic Biological Boolean Gates},
  author = {Sanassy, Daven and Fellermann, Harold and Krasnogor, Natalio and Konur, Savas and Mierla, Laurentiu M. and Gheorghe, Marian and Ladroue, Christophe and Kalvala, Sara},
  year = 2014,
  doi = {10.1109/HPCC.2014.68},
  month = aug,
  booktitle = {2014 IEEE Intl Conf on High Performance Computing and Communications, 2014 IEEE 6th Intl Symp on Cyberspace Safety and Security, 2014 IEEE 11th Intl Conf on Embedded Software and Syst (HPCC,CSS,ICESS)},
  pages = {404--408},
  address = {Paris, France}
}

B. Weobong, S. Soremekun, A.H. ten Asbroek, S. Amenga-Etego, S. Danso, S. Owusu-Agyei, M. Prince, B.R. Kirkwood

Prevalence and determinants of antenatal depression among pregnant women in a predominantly rural population in Ghana: The DON population-based study

in Journal of Affective Disorders, 165(C):1-7, August 2014

@ARTICLE{Weobong2014,
  title = {Prevalence and determinants of antenatal depression among pregnant women in a predominantly rural population in Ghana: The DON population-based study},
  author = {Weobong, Benedict and Soremekun, Seyi and ten Asbroek, Augustinus HA and Amenga-Etego, Seeba and Danso, Samuel and Owusu-Agyei, Seth and Prince, Martin and Kirkwood, Betty R.},
  year = 2014,
  doi = {10.1016/j.jad.2014.04.009},
  month = aug,
  journal = {Journal of Affective Disorders},
  volume = {165},
  number = {C},
  pages = {1--7}
}

J.S. Kim, M. Kaiser

From Caenorhabditis elegans to the human connectome: a specific modular organization increases metabolic, functional and developmental efficiency

in Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1653):20130529-20130529, September 2014

@ARTICLE{Kim2014,
  title = {From Caenorhabditis elegans to the human connectome: a specific modular organization increases metabolic, functional and developmental efficiency},
  author = {Kim, J. S. and Kaiser, M.},
  year = 2014,
  doi = {10.1098/rstb.2013.0529},
  month = sep,
  journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  volume = {369},
  number = {1653},
  pages = {20130529--20130529}
}

A. Best, K. James, C. Dalgliesh, E. Hong, M. Kheirolahi-Kouhestani, T. Curk, Y. Xu, M. Danilenko, R. Hussain, B. Keavney, A. Wipat, R. Klinck, I.G. Cowell, K. Cheong Lee, C.A. Austin, J.P. Venables, B. Chabot, M. Santibanez Koref, A. Tyson-Capper, D.J. Elliott

Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons

in Nature Communications, 5:4760, September 2014

@ARTICLE{Best2014,
  title = {Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons},
  author = {Best, Andrew and James, Katherine and Dalgliesh, Caroline and Hong, Elaine and Kheirolahi-Kouhestani, Mahsa and Curk, Tomaz and Xu, Yaobo and Danilenko, Marina and Hussain, Rafiq and Keavney, Bernard and Wipat, Anil and Klinck, Roscoe and Cowell, Ian G. and Cheong Lee, Ka and Austin, Caroline A. and Venables, Julian P. and Chabot, Benoit and Santibanez Koref, Mauro and Tyson-Capper, Alison and Elliott, David J.},
  year = 2014,
  doi = {10.1038/ncomms5760},
  month = sep,
  journal = {Nature Communications},
  volume = {5},
  pages = {4760}
}

A. Goñi-Moreno

On genetic logic circuits: forcing digital electronics standards?

in Memetic Computing, 6(3):149-155, September 2014

@ARTICLE{Goni-Moreno2014,
  title = {On genetic logic circuits: forcing digital electronics standards?},
  author = {Goñi-Moreno, Angel},
  year = 2014,
  doi = {10.1007/s12293-014-0136-8},
  month = sep,
  journal = {Memetic Computing},
  volume = {6},
  number = {3},
  pages = {149--155}
}

J. Bacardit, P. Widera, N. Lazzarini, N. Krasnogor

Hard Data Analytics Problems Make for Better Data Analysis Algorithms: Bioinformatics as an Example

in Big Data, 2(3):164-176, September 2014

@ARTICLE{Bacardit2014,
  title = {Hard Data Analytics Problems Make for Better Data Analysis Algorithms: Bioinformatics as an Example},
  author = {Bacardit, Jaume and Widera, Paweł and Lazzarini, Nicola and Krasnogor, Natalio},
  year = 2014,
  doi = {10.1089/big.2014.0023},
  month = sep,
  journal = {Big Data},
  volume = {2},
  number = {3},
  pages = {164--176}
}

G.A. Khoury, A. Liwo, F. Khatib, H. Zhou, G. Chopra, J. Bacardit, L.O. Bortot, R.A. Faccioli, X. Deng, Y. He, P. Krupa, J. Li, M.A. Mozolewska, A.K. Sieradzan, J. Smadbeck, T. Wirecki, S. Cooper, J. Flatten, K. Xu, D. Baker, J. Cheng, A.C.B. Delbem, C.A. Floudas, C. Keasar, M. Levitt, Z. Popović, H.A. Scheraga, J. Skolnick, S.N. Crivelli, F. Players

WeFold: A coopetition for protein structure prediction

in Proteins: Structure, Function, and Bioinformatics, 82(9):1850-1868, September 2014

@ARTICLE{Khoury2014,
  title = {WeFold: A coopetition for protein structure prediction},
  author = {Khoury, George A. and Liwo, Adam and Khatib, Firas and Zhou, Hongyi and Chopra, Gaurav and Bacardit, Jaume and Bortot, Leandro O. and Faccioli, Rodrigo A. and Deng, Xin and He, Yi and Krupa, Pawel and Li, Jilong and Mozolewska, Magdalena A. and Sieradzan, Adam K. and Smadbeck, James and Wirecki, Tomasz and Cooper, Seth and Flatten, Jeff and Xu, Kefan and Baker, David and Cheng, Jianlin and Delbem, Alexandre C. B. and Floudas, Christodoulos A. and Keasar, Chen and Levitt, Michael and Popović, Zoran and Scheraga, Harold A. and Skolnick, Jeffrey and Crivelli, Silvia N. and Players, Foldit},
  year = 2014,
  doi = {10.1002/prot.24538},
  month = sep,
  journal = {Proteins: Structure, Function, and Bioinformatics},
  volume = {82},
  number = {9},
  pages = {1850--1868}
}

M.-. Hutt, M. Kaiser, C.C. Hilgetag

Perspective: network-guided pattern formation of neural dynamics

in Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1653):20130522-20130522, September 2014

@ARTICLE{Hutt2014,
  title = {Perspective: network-guided pattern formation of neural dynamics},
  author = {Hutt, M. -t. and Kaiser, M. and Hilgetag, C. C.},
  year = 2014,
  doi = {10.1098/rstb.2013.0522},
  month = sep,
  journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  volume = {369},
  number = {1653},
  pages = {20130522--20130522}
}

N. Sinha, P.N. Taylor, J. Dauwels, J. Ruths

Development of optimal stimuli in a heterogeneous model of epileptic spike-wave oscillations

in 2014 IEEE International Conference on Systems, Man, and Cybernetics (SMC), p.3160-3165, San Diego, CA, USA, October 2014

@INPROCEEDINGS{Sinha2014,
  title = {Development of optimal stimuli in a heterogeneous model of epileptic spike-wave oscillations},
  author = {Sinha, Nishant and Taylor, Peter N. and Dauwels, Justin and Ruths, Justin},
  year = 2014,
  doi = {10.1109/SMC.2014.6974414},
  month = oct,
  booktitle = {2014 IEEE International Conference on Systems, Man, and Cybernetics (SMC)},
  pages = {3160--3165},
  address = {San Diego, CA, USA}
}

C.E. Han, L.R. Peraza, J. Taylor, M. Kaiser

Predicting age across human lifespan based on structural connectivity from diffusion tensor imaging

in 2014 IEEE Biomedical Circuits and Systems Conference (BioCAS) Proceedings, p.137-140, Lausanne, Switzerland, October 2014

@INPROCEEDINGS{Han2014,
  title = {Predicting age across human lifespan based on structural connectivity from diffusion tensor imaging},
  author = {Han, Cheol E. and Peraza, Luis R. and Taylor, John-Paul and Kaiser, Marcus},
  year = 2014,
  doi = {10.1109/BioCAS.2014.6981664},
  month = oct,
  booktitle = {2014 IEEE Biomedical Circuits and Systems Conference (BioCAS) Proceedings},
  pages = {137--140},
  address = {Lausanne, Switzerland}
}

D.J. Gibbs, J. Bacardit, A. Bachmair, M.J. Holdsworth

The eukaryotic N-end rule pathway: conserved mechanisms and diverse functions

in Trends in Cell Biology, 24(10):603-611, October 2014

@ARTICLE{Gibbs2014,
  title = {The eukaryotic N-end rule pathway: conserved mechanisms and diverse functions},
  author = {Gibbs, Daniel J. and Bacardit, Jaume and Bachmair, Andreas and Holdsworth, Michael J.},
  year = 2014,
  doi = {10.1016/j.tcb.2014.05.001},
  month = oct,
  journal = {Trends in Cell Biology},
  volume = {24},
  number = {10},
  pages = {603--611}
}

P.N. Taylor, M. Kaiser, J. Dauwels

Structural connectivity based whole brain modelling in epilepsy

in Journal of Neuroscience Methods, 236(C):51-57, October 2014

@ARTICLE{Taylor2014a,
  title = {Structural connectivity based whole brain modelling in epilepsy},
  author = {Taylor, Peter Neal and Kaiser, Marcus and Dauwels, Justin},
  year = 2014,
  doi = {10.1016/j.jneumeth.2014.08.010},
  month = oct,
  journal = {Journal of Neuroscience Methods},
  volume = {236},
  number = {C},
  pages = {51--57}
}

S. Konur, M. Gheorge, C. Dragomir, F. Ipate, N. Krasnogor

Conventional verification for unconventional computing: a genetic XOR gate example

in Fundamenta Informaticae, 134(1-2):97-110, November 2014

@ARTICLE{Konur2014,
  title = {Conventional verification for unconventional computing: a genetic XOR gate example},
  author = {Konur, Savas and Gheorge, Marian and Dragomir, Ciprian and Ipate, Florin and Krasnogor, Natalio},
  year = 2014,
  doi = {10.3233/FI-2014-1093},
  month = nov,
  journal = {Fundamenta Informaticae},
  volume = {134},
  number = {1-2},
  pages = {97--110}
}

DOI
I. Contreras, I. Arnaldo, N. Krasnogor, J.I. Hidalgo

Blind optimisation problem instance classification via enhanced universal similarity metric

in Memetic Computing, available online since November 2014

R. Bauer, M. Kaiser, E. Stoll

A Computational Model Incorporating Neural Stem Cell Dynamics Reproduces Glioma Incidence across the Lifespan in the Human Population

in PLoS ONE, 9(11):e111219, November 2014

@ARTICLE{Bauer2014a,
  title = {A Computational Model Incorporating Neural Stem Cell Dynamics Reproduces Glioma Incidence across the Lifespan in the Human Population},
  author = {Bauer, Roman and Kaiser, Marcus and Stoll, Elizabeth},
  year = 2014,
  doi = {10.1371/journal.pone.0111219},
  month = nov,
  journal = {PLoS ONE},
  volume = {9},
  number = {11},
  pages = {e111219}
}

J.C. Chaplin, N. Krasnogor, N.A. Russell

Photochromic molecular implementations of universal computation

in Biosystems, 126(C):12-26, December 2014

@ARTICLE{Chaplin2014,
  title = {Photochromic molecular implementations of universal computation},
  author = {Chaplin, Jack C. and Krasnogor, Natalio and Russell, Noah A.},
  year = 2014,
  doi = {10.1016/j.biosystems.2014.09.004},
  month = dec,
  journal = {Biosystems},
  volume = {126},
  number = {C},
  pages = {12--26}
}

C. Madsen, Z. Zhang, N. Roehner, C. Winstead, C. Myers

Stochastic Model Checking of Genetic Circuits

in ACM Journal on Emerging Technologies in Computing Systems, 11(3):1-21, December 2014

@ARTICLE{Madsen2014,
  title = {Stochastic Model Checking of Genetic Circuits},
  author = {Madsen, Curtis and Zhang, Zhen and Roehner, Nicholas and Winstead, Chris and Myers, Chris},
  year = 2014,
  doi = {10.1145/2644817},
  month = dec,
  journal = {ACM Journal on Emerging Technologies in Computing Systems},
  volume = {11},
  number = {3},
  pages = {1--21}
}

H. Fellermann, M. Hadorn, R.M. Füchslin, N. Krasnogor

Formalizing Modularization and Data Hiding in Synthetic Biology

in ACM Journal on Emerging Technologies in Computing Systems, 11(3):1-20, December 2014

@ARTICLE{Fellermann2014,
  title = {Formalizing Modularization and Data Hiding in Synthetic Biology},
  author = {Fellermann, Harold and Hadorn, Maik and Füchslin, Rudolf M. and Krasnogor, Natalio},
  year = 2014,
  doi = {10.1145/2667231},
  month = dec,
  journal = {ACM Journal on Emerging Technologies in Computing Systems},
  volume = {11},
  number = {3},
  pages = {1--20}
}

G. Misirli, J. Hallinan, A. Wipat

Composable Modular Models for Synthetic Biology

in ACM Journal on Emerging Technologies in Computing Systems, 11(3):1-19, December 2014

@ARTICLE{Misirli2014a,
  title = {Composable Modular Models for Synthetic Biology},
  author = {Misirli, Goksel and Hallinan, Jennifer and Wipat, Anil},
  year = 2014,
  doi = {10.1145/2631921},
  month = dec,
  journal = {ACM Journal on Emerging Technologies in Computing Systems},
  volume = {11},
  number = {3},
  pages = {1--19}
}

C.J. Myers, H. Sauro, A. Wipat

Introduction to the Special Issue on Computational Synthetic Biology

in ACM Journal on Emerging Technologies in Computing Systems, 11(3):1-5, December 2014

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R. Bauer, F. Zubler, S. Pfister, A. Hauri, M. Pfeiffer, D.R. Muir, R.J. Douglas

Developmental Self-Construction and -Configuration of Functional Neocortical Neuronal Networks

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M.M. Alkurashi, S.T. May, K. Kong, J. Bacardit, D. Haig, H.M. Elsheikha

Susceptibility to experimental infection of the invertebrate locusts ( Schistocerca gregaria ) with the apicomplexan parasite Neospora caninum

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P.N. Taylor, Y. Wang, M. Goodfellow, J. Dauwels, F. Moeller, U. Stephani, G. Baier

A Computational Study of Stimulus Driven Epileptic Seizure Abatement

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L.R. Peraza, M. Kaiser, M. Firbank, S. Graziadio, L. Bonanni, M. Onofrj, S.J. Colloby, A. Blamire, J. O'Brien, J. Taylor

fMRI resting state networks and their association with cognitive fluctuations in dementia with Lewy bodies

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B. Liu, S. Kong, S. Gao, P. Zuliani, E.M. Clarke

Parameter Synthesis for Cardiac Cell Hybrid Models Using δ-Decisions

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R. Gross, I. Fouxon, D. Lancet, O. Markovitch

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H. Fellermann, N. Krasnogor

Chemical Production and Molecular Computing in Addressable Reaction Compartments

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G. Misirli, J. Hallinan, R. Röttger, J. Baumbach, A. Wipat

BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species

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J. Blakes, J. Twycross, S. Konur, F.J. Romero-Campero, N. Krasnogor, M. Gheorghe

Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology

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S. Danso, E. Atwell, O. Johnson

A comparative study of machine learning methods for verbal autopsy text classification

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S. Danso, W. Lamb

Developing an automatic part-of-speech tagger for scottish gaelic

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J. Bacardit, X. Llorà

Large-scale data mining using genetics-based machine learning

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L. Hurt, A. ten Asbroek, S. Amenga-Etego, C. Zandoh, S. Danso, K. Edmond, C. Hurt, C. Tawiah, Z. Hill, J. Fenty, S. Owusu-Agyei, O.M. Campbell, B.R. Kirkwood

Effect of vitamin?A supplementation on cause-specific mortality in women of reproductive age in Ghana: a secondary analysis from the ObaapaVitA trial

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R. O'Dea, J.J. Crofts, M. Kaiser

Spreading dynamics on spatially constrained complex brain networks

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P. Andras, A. Andras

Type 2 diabetes: A side effect of the adaptation of neurons and fat cells to support increased cognitive performance

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H. Gong, P. Zuliani, E. M. Clarke

Model Checking a Synchronous Diabetes-Cancer Logical Network

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P.N. Taylor, M. Goodfellow, Y. Wang, G. Baier

Towards a large-scale model of patient-specific epileptic spike-wave discharges

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J. Sun, J.M. Garibaldi, N. Krasnogor, Q. Zhang

An Intelligent Multi-Restart Memetic Algorithm for Box Constrained Global Optimisation

in Evolutionary Computation, 21(1):107-147, March 2013

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G. Terrazas, N. Krasnogor

A genotype-phenotype-fitness assessment protocol for evolutionary self-assembly Wang tiles design

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P.N. Taylor, G. Baier, S.S. Cash, J. Dauwels, J. Slotine, Y. Wang

A model of stimulus induced epileptic spike-wave discharges

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A.L. Hook, C. Chang, J. Yang, S. Atkinson, R. Langer, D.G. Anderson, M.C. Davies, P. Williams, M.R. Alexander

Discovery of Novel Materials with Broad Resistance to Bacterial Attachment Using Combinatorial Polymer Microarrays

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M.A. Franco, N. Krasnogor, J. Bacardit

GAssist vs. BioHEL: critical assessment of two paradigms of genetics-based machine learning

in Soft Computing, 17(6):953-981, June 2013

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A. Goñi-Moreno, M. Amos, F. de la Cruz

Multicellular Computing Using Conjugation for Wiring

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D.A. Calian, J. Bacardit

Integrating memetic search into the BioHEL evolutionary learning system for large-scale datasets

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B.R. Kirkwood, A. Manu, A.H. ten Asbroek, S. Soremekun, B. Weobong, T. Gyan, S. Danso, S. Amenga-Etego, C. Tawiah-Agyemang, S. Owusu-Agyei, Z. Hill

Effect of the Newhints home-visits intervention on neonatal mortality rate and care practices in Ghana: a cluster randomised controlled trial

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I. Arnaldo, I. Contreras, D. Millán-Ruiz, J.I. Hidalgo, N. Krasnogor

Matching island topologies to problem structure in parallel evolutionary algorithms

in Soft Computing, 17(7):1209-1225, July 2013

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F. Zubler, A. Hauri, S. Pfister, R. Bauer, J.C. Anderson, A.M. Whatley, R.J. Douglas

Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects

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B.J.W. Dekkers, S. Pearce, R.P. van Bolderen-Veldkamp, A. Marshall, P. Widera, J. Gilbert, H.-. Drost, G.W. Bassel, K. Muller, J.R. King, A.T.A. Wood, I. Grosse, M. Quint, N. Krasnogor, G. Leubner-Metzger, M.J. Holdsworth, L. Bentsink

Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed Germination

in PLANT PHYSIOLOGY, 163(1):205-215, September 2013

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P. Zuliani, A. Platzer, E.M. Clarke

Bayesian statistical model checking with application to Stateflow/Simulink verification

in Formal Methods in System Design, 43(2):338-367, October 2013

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M.J. Bell, M. Collison, P. Lord

Can Inferred Provenance and Its Visualisation Be Used to Detect Erroneous Annotation? A Case Study Using UniProtKB

in PLoS ONE, 8(10):e75541, October 2013

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S. Pohl, G. Bhavsar, J. Hulme, A.E. Bloor, G. Misirli, M.W. Leckenby, D.S. Radford, W. Smith, A. Wipat, E.D. Williamson, C.R. Harwood, R.M. Cranenburgh

Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins

in PROTEOMICS, 13(22):3298-3308, November 2013

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L.T. Lui, X. Xue, C. Sui, A. Brown, D.I. Pritchard, N. Halliday, K. Winzer, S.M. Howdle, F. Fernandez-Trillo, N. Krasnogor, C. Alexander

Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes

in Nature Chemistry, 5(12):1058-1065, November 2013

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A.L. Swan, A. Mobasheri, D. Allaway, S. Liddell, J. Bacardit

Application of Machine Learning to Proteomics Data: Classification and Biomarker Identification in Postgenomics Biology

in OMICS: A Journal of Integrative Biology, 17(12):595-610, December 2013

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G. Terrazas, H. Zenil, N. Krasnogor

Exploring programmable self-assembly in non-DNA based molecular computing

in Natural Computing, 12(4):499-515, December 2013

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J.S. Hallinan

Computational Intelligence in the Design of Synthetic Microbial Genetic Systems

in Microbial Synthetic Biology, Methods in Microbiology 40, p.1-37, 2013

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C.R. Harwood, S. Pohl, W. Smith, A. Wipat

Bacillus subtilis

in Microbial Synthetic Biology, Methods in Microbiology 40, p.87-117, 2013

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}

M. Kaiser

The potential of the human connectome as a biomarker of brain disease

in Frontiers in Human Neuroscience, 7, 2013

@ARTICLE{Kaiser2013,
  title = {The potential of the human connectome as a biomarker of brain disease},
  author = {Kaiser, Marcus},
  year = 2013,
  doi = {10.3389/fnhum.2013.00484},
  journal = {Frontiers in Human Neuroscience},
  volume = {7}

X. Chan, C. Chang, K. Hong, K. Tee, W. Yin, K. Chan

Insights of biosurfactant producing Serratia marcescens strain W2.3 isolated from diseased tilapia fish: a draft genome analysis

in Gut Pathogens, 5(1):29, 2013

@ARTICLE{Chan2013,
  title = {Insights of biosurfactant producing Serratia marcescens strain W2.3 isolated from diseased tilapia fish: a draft genome analysis},
  author = {Chan, Xin and Chang, Chien and Hong, Kar and Tee, Kok and Yin, Wai and Chan, Kok},
  year = 2013,
  doi = {10.1186/1757-4749-5-29},
  journal = {Gut Pathogens},
  volume = {5},
  number = {1},
  pages = {29}
}

I.J. Bohr, E. Kenny, A. Blamire, J.T. O’Brien, A.J. Thomas, J. Richardson, M. Kaiser

Resting-State Functional Connectivity in Late-Life Depression: Higher Global Connectivity and More Long Distance Connections

in Frontiers in Psychiatry, 3, 2013

@ARTICLE{Bohr2013,
  title = {Resting-State Functional Connectivity in Late-Life Depression: Higher Global Connectivity and More Long Distance Connections},
  author = {Bohr, Iwo Jerzy and Kenny, Eva and Blamire, Andrew and O’Brien, John T. and Thomas, Alan J. and Richardson, Jonathan and Kaiser, Marcus},
  year = 2013,
  doi = {10.3389/fpsyt.2012.00116},
  journal = {Frontiers in Psychiatry},
  volume = {3}

A.L. Swan, K.L. Hillier, J.R. Smith, D. Allaway, S. Liddell, J. Bacardit, A. Mobasheri

Analysis of mass spectrometry data from the secretome of an explant model of articular cartilage exposed to pro-inflammatory and anti-inflammatory stimuli using machine learning

in BMC Musculoskeletal Disorders, 14(1):349, 2013

@ARTICLE{Swan2013a,
  title = {Analysis of mass spectrometry data from the secretome of an explant model of articular cartilage exposed to pro-inflammatory and anti-inflammatory stimuli using machine learning},
  author = {Swan, Anna L and Hillier, Kirsty L and Smith, Julia R and Allaway, David and Liddell, Susan and Bacardit, Jaume and Mobasheri, Ali},
  year = 2013,
  doi = {10.1186/1471-2474-14-349},
  journal = {BMC Musculoskeletal Disorders},
  volume = {14},
  number = {1},
  pages = {349}
}

G. Misirli, A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby, J. Hallinan

BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology

in Journal of Integrative Bioinformatics, 10(2):224, 2013

@ARTICLE{Misirli2013,
  title = {BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology},
  author = {Misirli, G. and Wipat, A. and Mullen, J. and James, K. and Pocock, M. and Smith, W. and Allenby, N. and Hallinan, J.},
  year = 2013,
  doi = {10.2390/biecoll-jib-2013-224},
  journal = {Journal of Integrative Bioinformatics},
  volume = {10},
  number = {2},
  pages = {224}
}

S. Danso, E. Atwell, O. Johnson

Linguistic and Statistically Derived Features for Cause of Death Prediction from Verbal Autopsy Text

in Language Processing and Knowledge in the Web, Lecture Notes in Computer Science 8105, p.47-60, 2013

@INCOLLECTION{Danso2013,
  title = {Linguistic and Statistically Derived Features for Cause of Death Prediction from Verbal Autopsy Text},
  author = {Danso, Samuel and Atwell, Eric and Johnson, Owen},
  year = 2013,
  doi = {10.1007/978-3-642-40722-2_5},
  booktitle = {Language Processing and Knowledge in the Web},
  publisher = {Springer Berlin Heidelberg},
  volume = {8105},
  series = {Lecture Notes in Computer Science},
  pages = {47--60}
}

M.S. Weyland, H. Fellermann, M. Hadorn, D. Sorek, D. Lancet, S. Rasmussen, R.M. F?chslin

The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers

in Computational and Mathematical Methods in Medicine, 2013:1-8, 2013

@ARTICLE{Weyland2013,
  title = {The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers},
  author = {Weyland, Mathias S. and Fellermann, Harold and Hadorn, Maik and Sorek, Daniel and Lancet, Doron and Rasmussen, Steen and F?chslin, Rudolf M.},
  year = 2013,
  doi = {10.1155/2013/467428},
  journal = {Computational and Mathematical Methods in Medicine},
  volume = {2013},
  pages = {1--8}
}

G. Terrazas, L.T. Lui, N. Krasnogor

Spatial Computation and Algorithmic Information content in Non-DNA based Molecular Self-Assembly

in Proceedings of the Spatial Computing Workshop (SCW 2013), p.85-90, Minessota, USA, 2013

@INPROCEEDINGS{Terrazas2013b,
  title = {Spatial Computation and Algorithmic Information content in Non-DNA based Molecular Self-Assembly},
  author = {Terrazas, German and Lui, Leong Ting and Krasnogor, Natalio},
  year = 2013,
  url = {http://www.spatial-computing.org/_media/scw13/corrected_prooceedings-workshop-9_spatial-computing.pdf},
  booktitle = {Proceedings of the Spatial Computing Workshop (SCW 2013)},
  pages = {85--90},
  address = {Minessota, USA}
}

2012

C. Städele, P. Andras, W. Stein

Simultaneous measurement of membrane potential changes in multiple pattern generating neurons using voltage sensitive dye imaging

in Journal of Neuroscience Methods, 203(1):78-88, January 2012

@ARTICLE{Stadele2012,
  title = {Simultaneous measurement of membrane potential changes in multiple pattern generating neurons using voltage sensitive dye imaging},
  author = {Städele, Carola and Andras, Peter and Stein, Wolfgang},
  year = 2012,
  doi = {10.1016/j.jneumeth.2011.09.015},
  month = jan,
  journal = {Journal of Neuroscience Methods},
  volume = {203},
  number = {1},
  pages = {78--88}
}

S. Nakjang, D.A. Ndeh, A. Wipat, D.N. Bolam, R.P. Hirt

A Novel Extracellular Metallopeptidase Domain Shared by Animal Host-Associated Mutualistic and Pathogenic Microbes

in PLoS ONE, 7(1):e30287, January 2012

@ARTICLE{Nakjang2012,
  title = {A Novel Extracellular Metallopeptidase Domain Shared by Animal Host-Associated Mutualistic and Pathogenic Microbes},
  author = {Nakjang, Sirintra and Ndeh, Didier A. and Wipat, Anil and Bolam, David N. and Hirt, Robert P.},
  year = 2012,
  doi = {10.1371/journal.pone.0030287},
  month = jan,
  journal = {PLoS ONE},
  volume = {7},
  number = {1},
  pages = {e30287}
}

DOI
A.L. Hook, C. Chang, J. Yang, D.J. Scurr, R. Langer, D.G. Anderson, S. Atkinson, P. Williams, M.C. Davies, M.R. Alexander

Polymer Microarrays for High Throughput Discovery of Biomaterials

in Journal of Visualized Experiments, available online since January 2012

J. Marcelino, M. Kaiser

Critical paths in a metapopulation model of H1N1: Efficiently delaying influenza spreading through flight cancellation

in PLoS Currents, 4:e4f8c9a2e1fca8, April 2012

@ARTICLE{Marcelino2012,
  title = {Critical paths in a metapopulation model of H1N1: Efficiently delaying influenza spreading through flight cancellation},
  author = {Marcelino, Jose and Kaiser, Marcus},
  year = 2012,
  doi = {10.1371/4f8c9a2e1fca8},
  month = apr,
  journal = {PLoS Currents},
  volume = {4},
  pages = {e4f8c9a2e1fca8}
}

DOI slides data BibTeX

M.A. Franco, N. Krasnogor, J. Bacardit

Analysing BioHEL using challenging boolean functions

in Evolutionary Intelligence, 5(2):87-102, June 2012

@ARTICLE{Franco2012,
  title = {Analysing BioHEL using challenging boolean functions},
  author = {Franco, María A. and Krasnogor, Natalio and Bacardit, Jaume},
  year = 2012,
  doi = {10.1007/s12065-012-0080-9},
  month = jun,
  journal = {Evolutionary Intelligence},
  volume = {5},
  number = {2},
  pages = {87--102}
}

M.R. Brust, D. Turgut, C.H.C. Ribeiro, M. Kaiser

Is the clustering coefficient a measure for fault tolerance in wireless sensor networks?

in 2012 IEEE International Conference on Communications (ICC), p.183-187, Ottawa, ON, Canada, June 2012

@INPROCEEDINGS{Brust2012,
  title = {Is the clustering coefficient a measure for fault tolerance in wireless sensor networks?},
  author = {Brust, Matthias R. and Turgut, Damla and Ribeiro, Carlos H. C. and Kaiser, Marcus},
  year = 2012,
  doi = {10.1109/ICC.2012.6364474},
  month = jun,
  booktitle = {2012 IEEE International Conference on Communications (ICC)},
  pages = {183--187},
  address = {Ottawa, ON, Canada}
}

S. Yu, N. Hammerla, J. Yan, P. Andras

A statistical aimbot detection method for online FPS games

in The 2012 International Joint Conference on Neural Networks (IJCNN), p.1-8, Brisbane, Australia, June 2012

@INPROCEEDINGS{Yu2012,
  title = {A statistical aimbot detection method for online FPS games},
  author = {Yu, Su-Yang and Hammerla, Nils and Yan, Jeff and Andras, Peter},
  year = 2012,
  doi = {10.1109/IJCNN.2012.6252489},
  month = jun,
  booktitle = {The 2012 International Joint Conference on Neural Networks (IJCNN)},
  pages = {1--8},
  address = {Brisbane, Australia}
}

A. Pakhira, P. Andras

Using network analysis metrics to discover functionally important methods in large-scale software systems

in 2012 3rd International Workshop on Emerging Trends in Software Metrics (WETSoM), p.70-76, Zurich, Switzerland, June 2012

@INPROCEEDINGS{Pakhira2012,
  title = {Using network analysis metrics to discover functionally important methods in large-scale software systems},
  author = {Pakhira, Anjan and Andras, Peter},
  year = 2012,
  doi = {10.1109/WETSoM.2012.6226996},
  month = jun,
  booktitle = {2012 3rd International Workshop on Emerging Trends in Software Metrics (WETSoM)},
  pages = {70--76},
  address = {Zurich, Switzerland}
}

J. Weile, K. James, J. Hallinan, S.J. Cockell, P. Lord, A. Wipat, D.J. Wilkinson

Bayesian integration of networks without gold standards

in Bioinformatics, 28(11):1495-1500, June 2012

@ARTICLE{Weile2012,
  title = {Bayesian integration of networks without gold standards},
  author = {Weile, J. and James, K. and Hallinan, J. and Cockell, S. J. and Lord, P. and Wipat, A. and Wilkinson, D. J.},
  year = 2012,
  doi = {10.1093/bioinformatics/bts154},
  month = jun,
  journal = {Bioinformatics},
  volume = {28},
  number = {11},
  pages = {1495--1500}
}

DOI data BibTeX

E. Glaab, J. Bacardit, J.M. Garibaldi, N. Krasnogor

Using Rule-Based Machine Learning for Candidate Disease Gene Prioritization and Sample Classification of Cancer Gene Expression Data

in PLoS ONE, 7(7):e39932, July 2012

@ARTICLE{Glaab2012,
  title = {Using Rule-Based Machine Learning for Candidate Disease Gene Prioritization and Sample Classification of Cancer Gene Expression Data},
  author = {Glaab, Enrico and Bacardit, Jaume and Garibaldi, Jonathan M. and Krasnogor, Natalio},
  year = 2012,
  doi = {10.1371/journal.pone.0039932},
  month = jul,
  journal = {PLoS ONE},
  volume = {7},
  number = {7},
  pages = {e39932}
}

J.C. Chaplin, N.A. Russell, N. Krasnogor

Implementing conventional logic unconventionally: Photochromic molecular populations as registers and logic gates

in Biosystems, 109(1):35-51, July 2012

@ARTICLE{Chaplin2012,
  title = {Implementing conventional logic unconventionally: Photochromic molecular populations as registers and logic gates},
  author = {Chaplin, J. C. and Russell, N. A. and Krasnogor, N.},
  year = 2012,
  doi = {10.1016/j.biosystems.2011.12.005},
  month = jul,
  journal = {Biosystems},
  volume = {109},
  number = {1},
  pages = {35--51}
}

A. Goñi-Moreno, M. Amos

Continuous computation in engineered gene circuits

in Biosystems, 109(1):52-56, July 2012

@ARTICLE{Goni-Moreno2012a,
  title = {Continuous computation in engineered gene circuits},
  author = {Goñi-Moreno, Angel and Amos, Martyn},
  year = 2012,
  doi = {10.1016/j.biosystems.2012.02.001},
  month = jul,
  journal = {Biosystems},
  volume = {109},
  number = {1},
  pages = {52--56}
}

C.H. Comin, J.L.B. Batista, M.P. Viana, L.D.F. Costa, B.A.N. Travençolo, M. Kaiser

Structure And Dynamics: The Transition From Nonequilibrium To Equilibrium In Integrate-and-fire Dynamics

in International Journal of Bifurcation and Chaos, 22(07):1250174, July 2012

@ARTICLE{Comin2012,
  title = {Structure And Dynamics: The Transition From Nonequilibrium To Equilibrium In Integrate-and-fire Dynamics},
  author = {Comin, Cesar H. and Batista, João L. B. and Viana, Matheus P. and Costa, Luciano Da F. and Travençolo, Bruno A. N. and Kaiser, Marcus},
  year = 2012,
  doi = {10.1142/S021812741250174X},
  month = jul,
  journal = {International Journal of Bifurcation and Chaos},
  volume = {22},
  number = {07},
  pages = {1250174}
}

A.L. Hook, C. Chang, J. Yang, J. Luckett, A. Cockayne, S. Atkinson, Y. Mei, R. Bayston, D.J. Irvine, R. Langer, D.G. Anderson, P. Williams, M.C. Davies, M.R. Alexander

Combinatorial discovery of polymers resistant to bacterial attachment

in Nature Biotechnology, 30(9):868-875, August 2012

@ARTICLE{Hook2012,
  title = {Combinatorial discovery of polymers resistant to bacterial attachment},
  author = {Hook, Andrew L and Chang, Chien-Yi and Yang, Jing and Luckett, Jeni and Cockayne, Alan and Atkinson, Steve and Mei, Ying and Bayston, Roger and Irvine, Derek J and Langer, Robert and Anderson, Daniel G and Williams, Paul and Davies, Martyn C and Alexander, Morgan R},
  year = 2012,
  doi = {10.1038/nbt.2316},
  month = aug,
  journal = {Nature Biotechnology},
  volume = {30},
  number = {9},
  pages = {868--875}
}

C. Chang, C. Koh, C. Sam, X. Chan, W.F. Yin, K.G. Chan

Unusual Long-Chain N-Acyl Homoserine Lactone Production by and Presence of Quorum Quenching Activity in Bacterial Isolates from Diseased Tilapia Fish

in PLoS ONE, 7(8):e44034, August 2012

@ARTICLE{Chang2012,
  title = {Unusual Long-Chain N-Acyl Homoserine Lactone Production by and Presence of Quorum Quenching Activity in Bacterial Isolates from Diseased Tilapia Fish},
  author = {Chang, Chien-Yi and Koh, Chong-Lek and Sam, Choon-Kook and Chan, Xin-Yue and Yin, Wai Fong and Chan, Kok Gan},
  year = 2012,
  doi = {10.1371/journal.pone.0044034},
  month = aug,
  journal = {PLoS ONE},
  volume = {7},
  number = {8},
  pages = {e44034}
}

E. Glaab, A. Baudot, N. Krasnogor, R. Schneider, A. Valencia

EnrichNet: network-based gene set enrichment analysis

in Bioinformatics, 28(18):i451-i457, September 2012

@ARTICLE{Glaab2012a,
  title = {EnrichNet: network-based gene set enrichment analysis},
  author = {Glaab, E. and Baudot, A. and Krasnogor, N. and Schneider, R. and Valencia, A.},
  year = 2012,
  doi = {10.1093/bioinformatics/bts389},
  month = sep,
  journal = {Bioinformatics},
  volume = {28},
  number = {18},
  pages = {i451--i457}
}

M.J. Bell, C.S. Gillespie, D. Swan, P. Lord

An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB

in Bioinformatics, 28(18):i562-i568, September 2012

@ARTICLE{Bell2012,
  title = {An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB},
  author = {Bell, M. J. and Gillespie, C. S. and Swan, D. and Lord, P.},
  year = 2012,
  doi = {10.1093/bioinformatics/bts372},
  month = sep,
  journal = {Bioinformatics},
  volume = {28},
  number = {18},
  pages = {i562--i568}
}

D. Henriques, J.G. Martins, P. Zuliani, A. Platzer, E.M. Clarke

Statistical Model Checking for Markov Decision Processes

in 2012 Ninth International Conference on Quantitative Evaluation of Systems, p.84-93, London, United Kingdom, September 2012

@INPROCEEDINGS{Henriques2012,
  title = {Statistical Model Checking for Markov Decision Processes},
  author = {Henriques, David and Martins, Joao G. and Zuliani, Paolo and Platzer, Andre and Clarke, Edmund M.},
  year = 2012,
  doi = {10.1109/QEST.2012.19},
  month = sep,
  booktitle = {2012 Ninth International Conference on Quantitative Evaluation of Systems},
  pages = {84--93},
  address = {London, United Kingdom}
}

DOI eprint slides BibTeX

J. Bacardit, P. Widera, A. Marquez-Chamorro, F. Divina, J.S. Aguilar-Ruiz, N. Krasnogor

Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features

in Bioinformatics, 28(19):2441-2448, October 2012

@ARTICLE{Bacardit2012,
  title = {Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features},
  author = {Bacardit, J. and Widera, P. and Marquez-Chamorro, A. and Divina, F. and Aguilar-Ruiz, J. S. and Krasnogor, N.},
  year = 2012,
  doi = {10.1093/bioinformatics/bts472},
  month = oct,
  journal = {Bioinformatics},
  volume = {28},
  number = {19},
  pages = {2441--2448}
}

O. Markovitch, D. Sorek, L.T. Lui, D. Lancet, N. Krasnogor

Is There an Optimal Level of Open-Endedness in Prebiotic Evolution?

in Origins of Life and Evolution of Biospheres, 42(5):469-474, October 2012

@ARTICLE{Markovitch2012,
  title = {Is There an Optimal Level of Open-Endedness in Prebiotic Evolution?},
  author = {Markovitch, Omer and Sorek, Daniel and Lui, Leong Ting and Lancet, Doron and Krasnogor, Natalio},
  year = 2012,
  doi = {10.1007/s11084-012-9309-y},
  month = oct,
  journal = {Origins of Life and Evolution of Biospheres},
  volume = {42},
  number = {5},
  pages = {469--474}
}

K. Zawadzki, C. Feenders, M.P. Viana, M. Kaiser, L.d.F. Costa

Morphological Homogeneity of Neurons: Searching for Outlier Neuronal Cells

in Neuroinformatics, 10(4):379-389, October 2012

@ARTICLE{Zawadzki2012,
  title = {Morphological Homogeneity of Neurons: Searching for Outlier Neuronal Cells},
  author = {Zawadzki, Krissia and Feenders, Christoph and Viana, Matheus P. and Kaiser, Marcus and Costa, Luciano da F.},
  year = 2012,
  doi = {10.1007/s12021-012-9150-5},
  month = oct,
  journal = {Neuroinformatics},
  volume = {10},
  number = {4},
  pages = {379--389}
}

P. Andras

A Bayesian Interpretation of the Particle Swarm Optimization and Its Kernel Extension

in PLoS ONE, 7(11):e48710, November 2012

@ARTICLE{Andras2012,
  title = {A Bayesian Interpretation of the Particle Swarm Optimization and Its Kernel Extension},
  author = {Andras, Peter},
  year = 2012,
  doi = {10.1371/journal.pone.0048710},
  month = nov,
  journal = {PLoS ONE},
  volume = {7},
  number = {11},
  pages = {e48710}
}

H.P. Fainberg, K. Bodley, J. Bacardit, D. Li, F. Wessely, N.P. Mongan, M.E. Symonds, L. Clarke, A. Mostyn

Reduced Neonatal Mortality in Meishan Piglets: A Role for Hepatic Fatty Acids?

in PLoS ONE, 7(11):e49101, November 2012

@ARTICLE{Fainberg2012,
  title = {Reduced Neonatal Mortality in Meishan Piglets: A Role for Hepatic Fatty Acids?},
  author = {Fainberg, Hernan P. and Bodley, Katherine and Bacardit, Jaume and Li, Dongfang and Wessely, Frank and Mongan, Nigel P. and Symonds, Michael E. and Clarke, Lynne and Mostyn, Alison},
  year = 2012,
  doi = {10.1371/journal.pone.0049101},
  month = nov,
  journal = {PLoS ONE},
  volume = {7},
  number = {11},
  pages = {e49101}
}

P. Lord, S. Cockell, R. Stevens

Three Steps to Heaven: Semantic Publishing in a Real World Workflow

in Future Internet, 4(4):1004-1015, November 2012

@ARTICLE{Lord2012,
  title = {Three Steps to Heaven: Semantic Publishing in a Real World Workflow},
  author = {Lord, Phillip and Cockell, Simon and Stevens, Robert},
  year = 2012,
  doi = {10.3390/fi4041004},
  month = nov,
  journal = {Future Internet},
  volume = {4},
  number = {4},
  pages = {1004--1015}
}

M. Collison, R.P. Hirt, A. Wipat, S. Nakjang, P. Sanseau, J.R. Brown

Data mining the human gut microbiota for therapeutic targets

in Briefings in Bioinformatics, 13(6):751-768, November 2012

@ARTICLE{Collison2012,
  title = {Data mining the human gut microbiota for therapeutic targets},
  author = {Collison, M. and Hirt, R. P. and Wipat, A. and Nakjang, S. and Sanseau, P. and Brown, J. R.},
  year = 2012,
  doi = {10.1093/bib/bbs002},
  month = nov,
  journal = {Briefings in Bioinformatics},
  volume = {13},
  number = {6},
  pages = {751--768}
}

M. Hadorn, E. Boenzli, K.T. Sorensen, H. Fellermann, P. Eggenberger Hotz, M.M. Hanczyc

Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets

in Proceedings of the National Academy of Sciences, 109(50):20320-20325, December 2012

@ARTICLE{Hadorn2012,
  title = {Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets},
  author = {Hadorn, M. and Boenzli, E. and Sorensen, K. T. and Fellermann, H. and Eggenberger Hotz, P. and Hanczyc, M. M.},
  year = 2012,
  doi = {10.1073/pnas.1214386109},
  month = dec,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {109},
  number = {50},
  pages = {20320--20325}
}

P. Zuliani, C. Baier, E.M. Clarke

Rare-event verification for stochastic hybrid systems

in Proceedings of the 15th ACM international conference on Hybrid Systems: Computation and Control - HSCC '12, p.217, Beijing, China, 2012

@INPROCEEDINGS{Zuliani2012,
  title = {Rare-event verification for stochastic hybrid systems},
  author = {Zuliani, Paolo and Baier, Christel and Clarke, Edmund M.},
  year = 2012,
  doi = {10.1145/2185632.2185665},
  booktitle = {Proceedings of the 15th ACM international conference on Hybrid Systems: Computation and Control - HSCC '12},
  pages = {217},
  address = {Beijing, China}
}

H. Gong, P. Zuliani, A. Komuravelli, J.R. Faeder, E.M. Clarke

Computational Modeling and Verification of Signaling Pathways in Cancer

in Algebraic and Numeric Biology, Lecture Notes in Computer Science 6479, p.117-135, 2012

@INCOLLECTION{Gong2012,
  title = {Computational Modeling and Verification of Signaling Pathways in Cancer},
  author = {Gong, Haijun and Zuliani, Paolo and Komuravelli, Anvesh and Faeder, James R. and Clarke, Edmund M.},
  year = 2012,
  doi = {10.1007/978-3-642-28067-2_7},
  booktitle = {Algebraic and Numeric Biology},
  publisher = {Springer Berlin Heidelberg},
  volume = {6479},
  series = {Lecture Notes in Computer Science},
  pages = {117--135}
}

S. Yu, N. Hammerla, J. Yan, P. Andras

Aimbot Detection in Online FPS Games Using a Heuristic Method Based on Distribution Comparison Matrix

in Neural Information Processing, Lecture Notes in Computer Science 7667, p.654-661, 2012

@INCOLLECTION{Yu2012a,
  title = {Aimbot Detection in Online FPS Games Using a Heuristic Method Based on Distribution Comparison Matrix},
  author = {Yu, Su-Yang and Hammerla, Nils and Yan, Jeff and Andras, Peter},
  year = 2012,
  doi = {10.1007/978-3-642-34500-5_77},
  booktitle = {Neural Information Processing},
  publisher = {Springer Berlin Heidelberg},
  volume = {7667},
  series = {Lecture Notes in Computer Science},
  pages = {654--661}
}

A. Goñi-Moreno, M. Amos

A reconfigurable NAND/NOR genetic logic gate

in BMC Systems Biology, 6(1):126, 2012

@ARTICLE{Goni-Moreno2012,
  title = {A reconfigurable NAND/NOR genetic logic gate},
  author = {Goñi-Moreno, Angel and Amos, Martyn},
  year = 2012,
  doi = {10.1186/1752-0509-6-126},
  journal = {BMC Systems Biology},
  volume = {6},
  number = {1},
  pages = {126}
}

E.M. Clarke, W. Klieber, M. Nováček, P. Zuliani

Model Checking and the State Explosion Problem

in Tools for Practical Software Verification, Lecture Notes in Computer Science 7682, p.1-30, 2012

@INCOLLECTION{Clarke2012,
  title = {Model Checking and the State Explosion Problem},
  author = {Clarke, Edmund M. and Klieber, William and Nováček, Miloš and Zuliani, Paolo},
  year = 2012,
  doi = {10.1007/978-3-642-35746-6_1},
  booktitle = {Tools for Practical Software Verification},
  publisher = {Springer Berlin Heidelberg},
  volume = {7682},
  series = {Lecture Notes in Computer Science},
  pages = {1--30}
}

M. Galdzicki, M.L. Wilson, C.A. Rodriguez, M.R. Pocock, E. Oberortner, L. Adam, A. Adler, J.C. Anderson, J. Beal, Y. Cai, D. Chandran, D. Densmore, O.A. Drory, D. Endy, J.H. Gennari, R. Grünberg, T.S. Ham, N.J. Hillson, J.D. Johnson, A. Kuchinsky, M.W. Lux, C. Madsen, G. Misirli, C.J. Myers, C. Olguin, J. Peccoud, H. Plahar, D. Platt, N. Roehner, E. Sirin, T.F. Smith, G. Stan, et al.

Synthetic Biology Open Language (SBOL) Version 1.1.0

The BioBricks Foundation technical report, BBF RFC \#87, 2012

@TECHREPORT{Galdzicki2012,
  title = {Synthetic Biology Open Language (SBOL) Version 1.1.0},
  author = {Galdzicki, Michal and Wilson, Mandy L. and Rodriguez, Cesar A. and Pocock, Matthew R. and Oberortner, Ernst and Adam, Laura and Adler, Aaron and Anderson, J. Christopher and Beal, Jacob and Cai, Yizhi and Chandran, Deepak and Densmore, Douglas and Drory, Omri A. and Endy, Drew and Gennari, John H. and Grünberg, Raik and Ham, Timothy S. and Hillson, Nathan J. and Johnson, Jeffrey D. and Kuchinsky, Allan and Lux, Matthew W. and Madsen, Curtis and Misirli, Goksel and Myers, Chris J. and Olguin, Carlos and Peccoud, Jean and Plahar, Hector and Platt, Darren and Roehner, Nicholas and Sirin, Evren and Smith, Trevor F. and Stan, Guy-Bart and Villalobos, Alan and Wipat, Anil and Sauro, Herbert M.},
  year = 2012,
  doi = {1721.1/73909},
  number = {BBF RFC \#87},
  institution = {The BioBricks Foundation}
}

G. Terrazas, N. Krasnogor

Genotype-Fitness Correlation Analysis for Evolutionary Design of Self-assembly Wang Tiles

in Nature Inspired Cooperative Strategies for Optimization (NICSO 2011), Studies in Computational Intelligence 387, p.73-84, 2012

@INCOLLECTION{Terrazas2012,
  title = {Genotype-Fitness Correlation Analysis for Evolutionary Design of Self-assembly Wang Tiles},
  author = {Terrazas, Germán and Krasnogor, Natalio},
  year = 2012,
  doi = {10.1007/978-3-642-24094-2_5},
  booktitle = {Nature Inspired Cooperative Strategies for Optimization (NICSO 2011)},
  publisher = {Springer Berlin Heidelberg},
  volume = {387},
  series = {Studies in Computational Intelligence},
  pages = {73--84}
}

K. James, A. Wipat, J. Hallinan

Is newer better?—evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae

in Integrative Biology, 4(7):715, 2012

@ARTICLE{James2012,
  title = {Is newer better?—evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae},
  author = {James, Katherine and Wipat, Anil and Hallinan, Jennifer},
  year = 2012,
  doi = {10.1039/c2ib00123c},
  journal = {Integrative Biology},
  volume = {4},
  number = {7},
  pages = {715}
}

K. Edmond, L. Hurt, J. Fenty, S. Amenga-Etego, C. Zandoh, C. Hurt, S. Danso, C. Tawiah, Z. Hill, A.H.A. ten Asbroek, S. Owusu-Agyei, O. Campbell, B.R. Kirkwood

Effect of vitamin A supplementation in women of reproductive age on cause-specific early and late infant mortality in rural Ghana: ObaapaVitA double-blind, cluster-randomised, placebo-controlled trial

in BMJ Open, 2(1):e000658, 2012

@ARTICLE{Edmond2012,
  title = {Effect of vitamin A supplementation in women of reproductive age on cause-specific early and late infant mortality in rural Ghana: ObaapaVitA double-blind, cluster-randomised, placebo-controlled trial},
  author = {Edmond, Karen and Hurt, Lisa and Fenty, Justin and Amenga-Etego, Seeba and Zandoh, Charles and Hurt, Chris and Danso, Samuel and Tawiah, Charlotte and Hill, Zelee and ten Asbroek, Augustinus H A and Owusu-Agyei, Seth and Campbell, Oona and Kirkwood, Betty R},
  year = 2012,
  doi = {10.1136/bmjopen-2011-000658},
  journal = {BMJ Open},
  volume = {2},
  number = {1},
  pages = {e000658}
}

DOI slides code BibTeX

M.A. Franco, N. Krasnogor, J. Bacardit

Post-processing operators for decision lists

in Proceedings of the fourteenth international conference on Genetic and evolutionary computation conference - GECCO '12, p.847, Philadelphia, Pennsylvania, USA, 2012

@INPROCEEDINGS{Franco2012a,
  title = {Post-processing operators for decision lists},
  author = {Franco, Maria A. and Krasnogor, Natalio and Bacardit, Jaume},
  year = 2012,
  doi = {10.1145/2330163.2330281},
  booktitle = {Proceedings of the fourteenth international conference on Genetic and evolutionary computation conference - GECCO '12},
  pages = {847},
  address = {Philadelphia, Pennsylvania, USA}
}

2011

S. Varier, M. Kaiser

Neural Development Features: Spatio-Temporal Development of the Caenorhabditis elegans Neuronal Network

in PLoS Computational Biology, 7(1):e1001044, January 2011

@ARTICLE{Varier2011a,
  title = {Neural Development Features: Spatio-Temporal Development of the Caenorhabditis elegans Neuronal Network},
  author = {Varier, Sreedevi and Kaiser, Marcus},
  year = 2011,
  doi = {10.1371/journal.pcbi.1001044},
  month = jan,
  journal = {PLoS Computational Biology},
  volume = {7},
  number = {1},
  pages = {e1001044}
}

S. Atkinson, R.J. Goldstone, G.W.P. Joshua, C. Chang, H.L. Patrick, M. Cámara, B.W. Wren, P. Williams

Biofilm Development on Caenorhabditis elegans by Yersinia Is Facilitated by Quorum Sensing-Dependent Repression of Type III Secretion

in PLoS Pathogens, 7(1):e1001250, January 2011

@ARTICLE{Atkinson2011,
  title = {Biofilm Development on Caenorhabditis elegans by Yersinia Is Facilitated by Quorum Sensing-Dependent Repression of Type III Secretion},
  author = {Atkinson, Steve and Goldstone, Robert J. and Joshua, George W. P. and Chang, Chien-Yi and Patrick, Hannah L. and Cámara, Miguel and Wren, Brendan W. and Williams, Paul},
  year = 2011,
  doi = {10.1371/journal.ppat.1001250},
  month = jan,
  journal = {PLoS Pathogens},
  volume = {7},
  number = {1},
  pages = {e1001250}
}

DOI
M. Hucka, C. Laibe, N. Juty, W. Liebermeister, S. Keating, C. Lloyd, C. Knuepfer, G. Misirli, M. Schulz, D. Waltemath, M. Taschuk, N. Swainston, N. Le Novère, A. Lister, F. Bergmann, R. Henkel, F. Krause, S. Hoops

SBML Level 3 Package Proposal: Annotation

in Nature Precedings, available online since January 2011

W. Stein, C. Städele, P. Andras

Single-sweep voltage-sensitive dye imaging of interacting identified neurons

in Journal of Neuroscience Methods, 194(2):224-234, January 2011

@ARTICLE{Stein2011a,
  title = {Single-sweep voltage-sensitive dye imaging of interacting identified neurons},
  author = {Stein, Wolfgang and Städele, Carola and Andras, Peter},
  year = 2011,
  doi = {10.1016/j.jneumeth.2010.10.007},
  month = jan,
  journal = {Journal of Neuroscience Methods},
  volume = {194},
  number = {2},
  pages = {224--234}
}

Y. Wang, A. Komuravelli, P. Zuliani, E.M. Clarke

Analog circuit verification by statistical model checking

in 16th Asia and South Pacific Design Automation Conference (ASP-DAC 2011), p.1-6, Yokohama, Japan, January 2011

@INPROCEEDINGS{Wang2011,
  title = {Analog circuit verification by statistical model checking},
  author = {Wang, Ying-Chih and Komuravelli, Anvesh and Zuliani, Paolo and Clarke, Edmund M.},
  year = 2011,
  doi = {10.1109/ASPDAC.2011.5722168},
  month = jan,
  booktitle = {16th Asia and South Pacific Design Automation Conference (ASP-DAC 2011)},
  pages = {1--6},
  address = {Yokohama, Japan}
}

C. Echtermeyer, L. da Fontoura Costa, F.A. Rodrigues, M. Kaiser

Automatic Network Fingerprinting through Single-Node Motifs

in PLoS ONE, 6(1):e15765, January 2011

@ARTICLE{Echtermeyer2011,
  title = {Automatic Network Fingerprinting through Single-Node Motifs},
  author = {Echtermeyer, Christoph and da Fontoura Costa, Luciano and Rodrigues, Francisco A. and Kaiser, Marcus},
  year = 2011,
  doi = {10.1371/journal.pone.0015765},
  month = jan,
  journal = {PLoS ONE},
  volume = {6},
  number = {1},
  pages = {e15765}
}

URL eprint code BibTeX

P. Widera, N. Krasnogor

Protein Models Comparator: Scalable Bioinformatics Computing on the Google App Engine Platform

in Computing Research Repository, arXiv:1102.4293v2, February 2011

@ARTICLE{Widera2011,
  title = {Protein Models Comparator: Scalable Bioinformatics Computing on the Google App Engine Platform},
  author = {Widera, Paweł and Krasnogor, Natalio},
  year = 2011,
  url = {http://arxiv.org/abs/1102.4293},
  month = feb,
  journal = {Computing Research Repository},
  volume = {arXiv:1102.4293v2}

DOI
W. Stein, C. Städele, P. Andras

Optical Imaging of Neurons in the Crab Stomatogastric Ganglion with Voltage-sensitive Dyes

in Journal of Visualized Experiments, available online since March 2011

A. Goñi-Moreno, M. Redondo-Nieto, F. Arroyo, J. Castellanos

Biocircuit design through engineering bacterial logic gates

in Natural Computing, 10(1):119-127, March 2011

@ARTICLE{Goni-Moreno2011a,
  title = {Biocircuit design through engineering bacterial logic gates},
  author = {Goñi-Moreno, Angel and Redondo-Nieto, Miguel and Arroyo, Fernando and Castellanos, Juan},
  year = 2011,
  doi = {10.1007/s11047-010-9184-2},
  month = mar,
  journal = {Natural Computing},
  volume = {10},
  number = {1},
  pages = {119--127}
}

G. Misirli, J.S. Hallinan, T. Yu, J.R. Lawson, S.M. Wimalaratne, M.T. Cooling, A. Wipat

Model annotation for synthetic biology: automating model to nucleotide sequence conversion

in Bioinformatics, 27(7):973-979, April 2011

@ARTICLE{Misirli2011,
  title = {Model annotation for synthetic biology: automating model to nucleotide sequence conversion},
  author = {Misirli, G. and Hallinan, J. S. and Yu, T. and Lawson, J. R. and Wimalaratne, S. M. and Cooling, M. T. and Wipat, A.},
  year = 2011,
  doi = {10.1093/bioinformatics/btr048},
  month = apr,
  journal = {Bioinformatics},
  volume = {27},
  number = {7},
  pages = {973--979}
}

S.G. Addinall, E. Holstein, C. Lawless, M. Yu, K. Chapman, A.P. Banks, H. Ngo, L. Maringele, M. Taschuk, A. Young, A. Ciesiolka, A.L. Lister, A. Wipat, D.J. Wilkinson, D. Lydall

Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects

in PLoS Genetics, 7(4):e1001362, April 2011

@ARTICLE{Addinall2011,
  title = {Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects},
  author = {Addinall, Stephen Gregory and Holstein, Eva-Maria and Lawless, Conor and Yu, Min and Chapman, Kaye and Banks, A. Peter and Ngo, Hien-Ping and Maringele, Laura and Taschuk, Morgan and Young, Alexander and Ciesiolka, Adam and Lister, Allyson Lurena and Wipat, Anil and Wilkinson, Darren James and Lydall, David},
  year = 2011,
  doi = {10.1371/journal.pgen.1001362},
  month = apr,
  journal = {PLoS Genetics},
  volume = {7},
  number = {4},
  pages = {e1001362}
}

K.T. Lythgow, G. Hudson, P. Andras, P.F. Chinnery

A critical analysis of the combined usage of protein localization prediction methods: Increasing the number of independent data sets can reduce the accuracy of predicted mitochondrial localization

in Mitochondrion, 11(3):444-449, May 2011

@ARTICLE{Lythgow2011,
  title = {A critical analysis of the combined usage of protein localization prediction methods: Increasing the number of independent data sets can reduce the accuracy of predicted mitochondrial localization},
  author = {Lythgow, Kieren T. and Hudson, Gavin and Andras, Peter and Chinnery, Patrick F.},
  year = 2011,
  doi = {10.1016/j.mito.2010.12.016},
  month = may,
  journal = {Mitochondrion},
  volume = {11},
  number = {3},
  pages = {444--449}
}

J. Weile, M. Pocock, S.J. Cockell, P. Lord, J.M. Dewar, E.-. Holstein, D. Wilkinson, D. Lydall, J. Hallinan, A. Wipat

Customizable views on semantically integrated networks for systems biology

in Bioinformatics, 27(9):1299-1306, May 2011

@ARTICLE{Weile2011,
  title = {Customizable views on semantically integrated networks for systems biology},
  author = {Weile, J. and Pocock, M. and Cockell, S. J. and Lord, P. and Dewar, J. M. and Holstein, E. -m. and Wilkinson, D. and Lydall, D. and Hallinan, J. and Wipat, A.},
  year = 2011,
  doi = {10.1093/bioinformatics/btr134},
  month = may,
  journal = {Bioinformatics},
  volume = {27},
  number = {9},
  pages = {1299--1306}
}

M. Porcar, A. Danchin, V. de Lorenzo, V.A. dos Santos, N. Krasnogor, S. Rasmussen, A. Moya

The ten grand challenges of synthetic life

in Systems and Synthetic Biology, 5(1-2):1-9, June 2011

@ARTICLE{Porcar2011,
  title = {The ten grand challenges of synthetic life},
  author = {Porcar, Manuel and Danchin, Antoine and de Lorenzo, Victor and dos Santos, Vitor A. and Krasnogor, Natalio and Rasmussen, Steen and Moya, Andrés},
  year = 2011,
  doi = {10.1007/s11693-011-9084-5},
  month = jun,
  journal = {Systems and Synthetic Biology},
  volume = {5},
  number = {1-2},
  pages = {1--9}
}

P. Andras

Research: metrics, quality, and management implications

in Research Evaluation, 20(2):90-106, June 2011

@ARTICLE{Andras2011,
  title = {Research: metrics, quality, and management implications},
  author = {Andras, Peter},
  year = 2011,
  doi = {10.3152/095820211X12941371876265},
  month = jun,
  journal = {Research Evaluation},
  volume = {20},
  number = {2},
  pages = {90--106}
}

G.W. Bassel, H. Lan, E. Glaab, D.J. Gibbs, T. Gerjets, N. Krasnogor, A.J. Bonner, M.J. Holdsworth, N.J. Provart

Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions

in Proceedings of the National Academy of Sciences, 108(23):9709-9714, June 2011

@ARTICLE{Bassel2011a,
  title = {Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions},
  author = {Bassel, G. W. and Lan, H. and Glaab, E. and Gibbs, D. J. and Gerjets, T. and Krasnogor, N. and Bonner, A. J. and Holdsworth, M. J. and Provart, N. J.},
  year = 2011,
  doi = {10.1073/pnas.1100958108},
  month = jun,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {108},
  number = {23},
  pages = {9709--9714}
}

H.O. Habashy, D.G. Powe, E. Glaab, G. Ball, I. Spiteri, N. Krasnogor, J.M. Garibaldi, E.A. Rakha, A.R. Green, C. Caldas, I.O. Ellis

RERG (Ras-like, oestrogen-regulated, growth-inhibitor) expression in breast cancer: a marker of ER-positive luminal-like subtype

in Breast Cancer Research and Treatment, 128(2):315-326, July 2011

@ARTICLE{Habashy2011,
  title = {RERG (Ras-like, oestrogen-regulated, growth-inhibitor) expression in breast cancer: a marker of ER-positive luminal-like subtype},
  author = {Habashy, Hany Onsy and Powe, Desmond G. and Glaab, Enrico and Ball, Graham and Spiteri, Inmaculada and Krasnogor, Natalio and Garibaldi, Jonathan M. and Rakha, Emad A. and Green, Andrew R. and Caldas, C. and Ellis, Ian O.},
  year = 2011,
  doi = {10.1007/s10549-010-1073-y},
  month = jul,
  journal = {Breast Cancer Research and Treatment},
  volume = {128},
  number = {2},
  pages = {315--326}
}

M. Kaiser

A tutorial in connectome analysis: Topological and spatial features of brain networks

in NeuroImage, 57(3):892-907, August 2011

@ARTICLE{Kaiser2011,
  title = {A tutorial in connectome analysis: Topological and spatial features of brain networks},
  author = {Kaiser, Marcus},
  year = 2011,
  doi = {10.1016/j.neuroimage.2011.05.025},
  month = aug,
  journal = {NeuroImage},
  volume = {57},
  number = {3},
  pages = {892--907}
}

H.-. Chang, C. Lawless, S.G. Addinall, S. Oexle, M. Taschuk, A. Wipat, D.J. Wilkinson, D. Lydall, B.J. Andrews

Genome-Wide Analysis to Identify Pathways Affecting Telomere-Initiated Senescence in Budding Yeast

in G3: Genes|Genomes|Genetics, 1(3):197-208, August 2011

@ARTICLE{Chang2011a,
  title = {Genome-Wide Analysis to Identify Pathways Affecting Telomere-Initiated Senescence in Budding Yeast},
  author = {Chang, H. -y. and Lawless, C. and Addinall, S. G. and Oexle, S. and Taschuk, M. and Wipat, A. and Wilkinson, D. J. and Lydall, D. and Andrews, B. J.},
  year = 2011,
  doi = {10.1534/g3.111.000216},
  month = aug,
  journal = {G3&#58; Genes|Genomes|Genetics},
  volume = {1},
  number = {3},
  pages = {197--208}
}

S.C. Weatherhead, P.M. Farr, D. Jamieson, J.S. Hallinan, J.J. Lloyd, A. Wipat, N.J. Reynolds

Keratinocyte Apoptosis in Epidermal Remodeling and Clearance of Psoriasis Induced by UV Radiation

in Journal of Investigative Dermatology, 131(9):1916-1926, September 2011

@ARTICLE{Weatherhead2011,
  title = {Keratinocyte Apoptosis in Epidermal Remodeling and Clearance of Psoriasis Induced by UV Radiation},
  author = {Weatherhead, Sophie C and Farr, Peter M and Jamieson, David and Hallinan, Jennifer S and Lloyd, James J and Wipat, Anil and Reynolds, Nick J},
  year = 2011,
  doi = {10.1038/jid.2011.134},
  month = sep,
  journal = {Journal of Investigative Dermatology},
  volume = {131},
  number = {9},
  pages = {1916--1926}
}

A. Goñi-Moreno, M. Amos

Model for a population-based microbial oscillator

in Biosystems, 105(3):286-294, September 2011

@ARTICLE{Goni-Moreno2011,
  title = {Model for a population-based microbial oscillator},
  author = {Goñi-Moreno, Angel and Amos, Martyn},
  year = 2011,
  doi = {10.1016/j.biosystems.2011.05.011},
  month = sep,
  journal = {Biosystems},
  volume = {105},
  number = {3},
  pages = {286--294}
}

G.W. Bassel, E. Glaab, J. Marquez, M.J. Holdsworth, J. Bacardit

Functional Network Construction in Arabidopsis Using Rule-Based Machine Learning on Large-Scale Data Sets

in THE PLANT CELL ONLINE, 23(9):3101-3116, September 2011

@ARTICLE{Bassel2011,
  title = {Functional Network Construction in Arabidopsis Using Rule-Based Machine Learning on Large-Scale Data Sets},
  author = {Bassel, G. W. and Glaab, E. and Marquez, J. and Holdsworth, M. J. and Bacardit, J.},
  year = 2011,
  doi = {10.1105/tpc.111.088153},
  month = sep,
  journal = {THE PLANT CELL ONLINE},
  volume = {23},
  number = {9},
  pages = {3101--3116}
}

L.K.J. Stadler, T. Hoffmann, D.C. Tomlinson, Q. Song, T. Lee, M. Busby, Y. Nyathi, E. Gendra, C. Tiede, K. Flanagan, S.J. Cockell, A. Wipat, C. Harwood, S.D. Wagner, M.A. Knowles, J.J. Davis, N. Keegan, P. Ko Ferrigno

Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant

in Protein Engineering Design and Selection, 24(9):751-763, September 2011

@ARTICLE{Stadler2011,
  title = {Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant},
  author = {Stadler, L. K. J. and Hoffmann, T. and Tomlinson, D. C. and Song, Q. and Lee, T. and Busby, M. and Nyathi, Y. and Gendra, E. and Tiede, C. and Flanagan, K. and Cockell, S. J. and Wipat, A. and Harwood, C. and Wagner, S. D. and Knowles, M. A. and Davis, J. J. and Keegan, N. and Ko Ferrigno, P.},
  year = 2011,
  doi = {10.1093/protein/gzr019},
  month = sep,
  journal = {Protein Engineering Design and Selection},
  volume = {24},
  number = {9},
  pages = {751--763}
}

H. Fellermann, S. Rasmussen

On the Growth Rate of Non-Enzymatic Molecular Replicators

in Entropy, 13(12):1882-1903, October 2011

@ARTICLE{Fellermann2011,
  title = {On the Growth Rate of Non-Enzymatic Molecular Replicators},
  author = {Fellermann, Harold and Rasmussen, Steen},
  year = 2011,
  doi = {10.3390/e13101882},
  month = oct,
  journal = {Entropy},
  volume = {13},
  number = {12},
  pages = {1882--1903}
}

T.A. Quinn, S. Granite, M.A. Allessie, C. Antzelevitch, C. Bollensdorff, G. Bub, R.A. Burton, E. Cerbai, P.S. Chen, M. Delmar, D. DiFrancesco, Y.E. Earm, I.R. Efimov, M. Egger, E. Entcheva, M. Fink, R. Fischmeister, M.R. Franz, A. Garny, W.R. Giles, T. Hannes, S.E. Harding, P.J. Hunter, G. Iribe, J. Jalife, C.R. Johnson, R.S. Kass, I. Kodama, G. Koren, P. Lord, V.S. Markhasin, S. Matsuoka, et al.

Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): Standardised reporting for model reproducibility, interoperability, and data sharing

in Progress in Biophysics and Molecular Biology, 107(1):4-10, October 2011

@ARTICLE{Quinn2011,
  title = {Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): Standardised reporting for model reproducibility, interoperability, and data sharing},
  author = {Quinn, T. A. and Granite, S. and Allessie, M. A. and Antzelevitch, C. and Bollensdorff, C. and Bub, G. and Burton, R. A.b. and Cerbai, E. and Chen, P. S. and Delmar, M. and DiFrancesco, D. and Earm, Y. E. and Efimov, I. R. and Egger, M. and Entcheva, E. and Fink, M. and Fischmeister, R. and Franz, M. R. and Garny, A. and Giles, W. R. and Hannes, T. and Harding, S. E. and Hunter, P. J. and Iribe, G. and Jalife, J. and Johnson, C. R. and Kass, R. S. and Kodama, I. and Koren, G. and Lord, P. and Markhasin, V. S. and Matsuoka, S. and McCulloch, A. D. and Mirams, G. R. and Morley, G. E. and Nattel, S. and Noble, D. and Olesen, S. P. and Panfilov, A. V. and Trayanova, N. A. and Ravens, U. and Richard, S. and Rosenbaum, D. S. and Rudy, Y. and Sachs, F. and Sachse, F. B. and Saint, D. A. and Schotten, U. and Solovyova, O. and Taggart, P. and Tung, L. and Varró, A. and Volders, P. G. and Wang, K. and Weiss, J. N. and Wettwer, E. and White, E. and Wilders, R. and Winslow, R. L. and Kohl, P.},
  year = 2011,
  doi = {10.1016/j.pbiomolbio.2011.07.001},
  month = oct,
  journal = {Progress in Biophysics and Molecular Biology},
  volume = {107},
  number = {1},
  pages = {4--10}
}

F. Dupeux, J. Santiago, K. Betz, J. Twycross, S. Park, L. Rodriguez, M. Gonzalez-Guzman, M.R. Jensen, N. Krasnogor, M. Blackledge, M. Holdsworth, S.R. Cutler, P.L. Rodriguez, J.A. Márquez

A thermodynamic switch modulates abscisic acid receptor sensitivity

in The EMBO Journal, 30(20):4171-4184, October 2011

@ARTICLE{Dupeux2011,
  title = {A thermodynamic switch modulates abscisic acid receptor sensitivity},
  author = {Dupeux, Florine and Santiago, Julia and Betz, Katja and Twycross, Jamie and Park, Sang-Youl and Rodriguez, Lesia and Gonzalez-Guzman, Miguel and Jensen, Malene Ringkjøbing and Krasnogor, Natalio and Blackledge, Martin and Holdsworth, Michael and Cutler, Sean R and Rodriguez, Pedro L and Márquez, José Antonio},
  year = 2011,
  doi = {10.1038/emboj.2011.294},
  month = oct,
  journal = {The EMBO Journal},
  volume = {30},
  number = {20},
  pages = {4171--4184}
}

S. Varier, M. Kaiser, R. Forsyth

Establishing, versus Maintaining, Brain Function: A Neuro-computational Model of Cortical Reorganization after Injury to the Immature Brain

in Journal of the International Neuropsychological Society, 17(06):1030-1038, November 2011

@ARTICLE{Varier2011,
  title = {Establishing, versus Maintaining, Brain Function: A Neuro-computational Model of Cortical Reorganization after Injury to the Immature Brain},
  author = {Varier, Sreedevi and Kaiser, Marcus and Forsyth, Rob},
  year = 2011,
  doi = {10.1017/S1355617711000993},
  month = nov,
  journal = {Journal of the International Neuropsychological Society},
  volume = {17},
  number = {06},
  pages = {1030--1038}
}

C.-. Chang, L. Hobley, R. Till, M. Capeness, M. Kanna, W. Burtt, P. Jagtap, S.-. Aizawa, R.E. Sockett

The Bdellovibrio bacteriovorus twin-arginine transport system has roles in predatory and prey-independent growth

in Microbiology, 157(11):3079-3093, November 2011

@ARTICLE{Chang2011,
  title = {The Bdellovibrio bacteriovorus twin-arginine transport system has roles in predatory and prey-independent growth},
  author = {Chang, C. -y. and Hobley, L. and Till, R. and Capeness, M. and Kanna, M. and Burtt, W. and Jagtap, P. and Aizawa, S. -i. and Sockett, R. E.},
  year = 2011,
  doi = {10.1099/mic.0.052449-0},
  month = nov,
  journal = {Microbiology},
  volume = {157},
  number = {11},
  pages = {3079--3093}
}

H. Gong, P. Zuliani, Q. Wang, E.M. Clarke

Formal analysis for logical models of pancreatic cancer

in IEEE Conference on Decision and Control and European Control Conference, p.4855-4860, Orlando, FL, USA, December 2011

@INPROCEEDINGS{Gong2011,
  title = {Formal analysis for logical models of pancreatic cancer},
  author = {Gong, Haijun and Zuliani, Paolo and Wang, Qinsi and Clarke, Edmund M.},
  year = 2011,
  doi = {10.1109/CDC.2011.6161052},
  month = dec,
  booktitle = {IEEE Conference on Decision and Control and European Control Conference},
  pages = {4855--4860},
  address = {Orlando, FL, USA}
}

J. Blakes, J. Twycross, F.J. Romero-Campero, N. Krasnogor

The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology

in Bioinformatics, 27(23):3323-3324, December 2011

@ARTICLE{Blakes2011,
  title = {The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology},
  author = {Blakes, J. and Twycross, J. and Romero-Campero, F. J. and Krasnogor, N.},
  year = 2011,
  doi = {10.1093/bioinformatics/btr571},
  month = dec,
  journal = {Bioinformatics},
  volume = {27},
  number = {23},
  pages = {3323--3324}
}

C. Echtermeyer, C.E. Han, A. Rotarska-Jagiela, H. Mohr, P.J. Uhlhaas, M. Kaiser

Integrating Temporal and Spatial Scales: Human Structural Network Motifs Across Age and Region of Interest Size

in Frontiers in Neuroinformatics, 5, 2011

@ARTICLE{Echtermeyer2011a,
  title = {Integrating Temporal and Spatial Scales: Human Structural Network Motifs Across Age and Region of Interest Size},
  author = {Echtermeyer, Christoph and Han, Cheol E. and Rotarska-Jagiela, Anna and Mohr, Harald and Uhlhaas, Peter J. and Kaiser, Marcus},
  year = 2011,
  doi = {10.3389/fninf.2011.00010},
  journal = {Frontiers in Neuroinformatics},
  volume = {5}

J.S. Hallinan, K. James, A. Wipat

Network Approaches to the Functional Analysis of Microbial Proteins

in Advances in Microbial Physiology, 59, p.101-133, 2011

@INCOLLECTION{Hallinan2011,
  title = {Network Approaches to the Functional Analysis of Microbial Proteins},
  author = {Hallinan, J. S. and James, K. and Wipat, A.},
  year = 2011,
  doi = {10.1016/B978-0-12-387661-4.00005-7},
  booktitle = {Advances in Microbial Physiology},
  pages = {101--133}
}

DOI slides BibTeX

M.A. Franco, N. Krasnogor, J. Bacardit

Modelling the initialisation stage of the ALKR representation for discrete domains and GABIL encoding

in Proceedings of the 13th annual conference on Genetic and evolutionary computation - GECCO '11, p.1291, Dublin, Ireland, 2011

Best Paper Award in GBML track

@INPROCEEDINGS{Franco2011,
  title = {Modelling the initialisation stage of the ALKR representation for discrete domains and GABIL encoding},
  author = {Franco, Maria A. and Krasnogor, Natalio and Bacardit, Jaume},
  year = 2011,
  doi = {10.1145/2001576.2001750},
  note = {Best Paper Award in GBML track},
  booktitle = {Proceedings of the 13th annual conference on Genetic and evolutionary computation - GECCO '11},
  pages = {1291},
  address = {Dublin, Ireland}
}

H. Gong, P. Zuliani, E.M. Clarke, T.D. Pham, X. Zhou, H. Tanaka, M. Oyama-Higa, X. Jiang, C. Sun, J. Kowalski, X. Jia

Model Checking of a Diabetes-Cancer Model

in 2011 International Symposium On Computational Models For Life Sciences (CMLS-11), p.234-243, Toyama City, (Japan), 2011

@INPROCEEDINGS{Gong2011a,
  title = {Model Checking of a Diabetes-Cancer Model},
  author = {Gong, Haijun and Zuliani, Paolo and Clarke, Edmund M. and Pham, Tuan D. and Zhou, Xiaobo and Tanaka, Hiroshi and Oyama-Higa, Mayumi and Jiang, Xiaoyi and Sun, Changming and Kowalski, Jeanne and Jia, Xiuping},
  year = 2011,
  doi = {10.1063/1.3596647},
  booktitle = {2011 International Symposium On Computational Models For Life Sciences (CMLS-11)},
  pages = {234--243},
  address = {Toyama City, (Japan)}
}

H.L.S. Younes, E.M. Clarke, P. Zuliani

Statistical Verification of Probabilistic Properties with Unbounded Until

in Formal Methods: Foundations and Applications, Lecture Notes in Computer Science 6527, p.144-160, 2011

@INCOLLECTION{Younes2011,
  title = {Statistical Verification of Probabilistic Properties with Unbounded Until},
  author = {Younes, Håkan L. S. and Clarke, Edmund M. and Zuliani, Paolo},
  year = 2011,
  doi = {10.1007/978-3-642-19829-8_10},
  booktitle = {Formal Methods: Foundations and Applications},
  publisher = {Springer Berlin Heidelberg},
  volume = {6527},
  series = {Lecture Notes in Computer Science},
  pages = {144--160}
}

R.A.J. Woolley, J. Stirling, A. Radocea, N. Krasnogor, P. Moriarty

Automated probe microscopy via evolutionary optimization at the atomic scale

in Applied Physics Letters, 98(25):253104, 2011

@ARTICLE{Woolley2011,
  title = {Automated probe microscopy via evolutionary optimization at the atomic scale},
  author = {Woolley, Richard A. J. and Stirling, Julian and Radocea, Adrian and Krasnogor, Natalio and Moriarty, Philip},
  year = 2011,
  doi = {10.1063/1.3600662},
  journal = {Applied Physics Letters},
  volume = {98},
  number = {25},
  pages = {253104}
}

E.M. Clarke, P. Zuliani

Statistical Model Checking for Cyber-Physical Systems

in Automated Technology for Verification and Analysis, Lecture Notes in Computer Science 6996, p.1-12, 2011

@INCOLLECTION{Clarke2011,
  title = {Statistical Model Checking for Cyber-Physical Systems},
  author = {Clarke, Edmund M. and Zuliani, Paolo},
  year = 2011,
  doi = {10.1007/978-3-642-24372-1_1},
  booktitle = {Automated Technology for Verification and Analysis},
  publisher = {Springer Berlin Heidelberg},
  volume = {6996},
  series = {Lecture Notes in Computer Science},
  pages = {1--12}
}

M. Kaiser, S. Varier

Evolution and development of Brain Networks: From Caenorhabditis elegans to Homo sapiens

in Network: Computation in Neural Systems, 22(1-4):143-147, 2011

@ARTICLE{Kaiser2011a,
  title = {Evolution and development of Brain Networks: From Caenorhabditis elegans to Homo sapiens},
  author = {Kaiser, Marcus and Varier, Sreedevi},
  year = 2011,
  journal = {Network: Computation in Neural Systems},
  volume = {22},
  number = {1-4},
  pages = {143--147}
}

2010

A.K. Roopun, J.D. Simonotto, M.L. Pierce, A. Jenkins, C. Nicholson, I.S. Schofield, R.G. Whittaker, M. Kaiser, M.A. Whittington, R.D. Traub, M.O. Cunningham

A nonsynaptic mechanism underlying interictal discharges in human epileptic neocortex

in Proceedings of the National Academy of Sciences, 107(1):338-343, January 2010

@ARTICLE{Roopun2010,
  title = {A nonsynaptic mechanism underlying interictal discharges in human epileptic neocortex},
  author = {Roopun, A. K. and Simonotto, J. D. and Pierce, M. L. and Jenkins, A. and Nicholson, C. and Schofield, I. S. and Whittaker, R. G. and Kaiser, M. and Whittington, M. A. and Traub, R. D. and Cunningham, M. O.},
  year = 2010,
  doi = {10.1073/pnas.0912652107},
  month = jan,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {107},
  number = {1},
  pages = {338--343}
}

A.L. Lister, R.S. Datta, O. Hofmann, R. Krause, M. Kuhn, B. Roth, R. Schneider

Live Coverage of Scientific Conferences Using Web Technologies

in PLoS Computational Biology, 6(1):e1000563, January 2010

@ARTICLE{Lister2010a,
  title = {Live Coverage of Scientific Conferences Using Web Technologies},
  author = {Lister, Allyson L. and Datta, Ruchira S. and Hofmann, Oliver and Krause, Roland and Kuhn, Michael and Roth, Bettina and Schneider, Reinhard},
  year = 2010,
  doi = {10.1371/journal.pcbi.1000563},
  month = jan,
  journal = {PLoS Computational Biology},
  volume = {6},
  number = {1},
  pages = {e1000563}
}

C. Lambert, C. Chang, M.J. Capeness, R.E. Sockett

The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio

in PLoS ONE, 5(1):e8599, January 2010

@ARTICLE{Lambert2010,
  title = {The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio},
  author = {Lambert, Carey and Chang, Chien-Yi and Capeness, Michael J. and Sockett, R. Elizabeth},
  year = 2010,
  doi = {10.1371/journal.pone.0008599},
  month = jan,
  journal = {PLoS ONE},
  volume = {5},
  number = {1},
  pages = {e8599}
}

A.L. Lister, R.S. Datta, O. Hofmann, R. Krause, M. Kuhn, B. Roth, R. Schneider

Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009

in PLoS Computational Biology, 6(1):e1000640, January 2010

@ARTICLE{Lister2010,
  title = {Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009},
  author = {Lister, Allyson L. and Datta, Ruchira S. and Hofmann, Oliver and Krause, Roland and Kuhn, Michael and Roth, Bettina and Schneider, Reinhard},
  year = 2010,
  doi = {10.1371/journal.pcbi.1000640},
  month = jan,
  journal = {PLoS Computational Biology},
  volume = {6},
  number = {1},
  pages = {e1000640}
}

H. Cao, F.J. Romero-Campero, S. Heeb, M. Cámara, N. Krasnogor

Evolving cell models for systems and synthetic biology

in Systems and Synthetic Biology, 4(1):55-84, March 2010

@ARTICLE{Cao2010,
  title = {Evolving cell models for systems and synthetic biology},
  author = {Cao, Hongqing and Romero-Campero, Francisco J. and Heeb, Stephan and Cámara, Miguel and Krasnogor, Natalio},
  year = 2010,
  doi = {10.1007/s11693-009-9050-7},
  month = mar,
  journal = {Systems and Synthetic Biology},
  volume = {4},
  number = {1},
  pages = {55--84}
}

R.E. Smith, M.K. Jiang, J. Bacardit, M. Stout, N. Krasnogor, J.D. Hirst

A learning classifier system with mutual-information-based fitness

in Evolutionary Intelligence, 3(1):31-50, March 2010

@ARTICLE{Smith2010,
  title = {A learning classifier system with mutual-information-based fitness},
  author = {Smith, Robert Elliott and Jiang, Max Kun and Bacardit, Jaume and Stout, Michael and Krasnogor, Natalio and Hirst, Jonathan D.},
  year = 2010,
  doi = {10.1007/s12065-010-0037-9},
  month = mar,
  journal = {Evolutionary Intelligence},
  volume = {3},
  number = {1},
  pages = {31--50}
}

DOI eprint data BibTeX

P. Widera, J.M. Garibaldi, N. Krasnogor

GP challenge: evolving energy function for protein structure prediction

in Genetic Programming and Evolvable Machines, 11(1):61-88, March 2010

@ARTICLE{Widera2010,
  title = {GP challenge: evolving energy function for protein structure prediction},
  author = {Widera, Paweł and Garibaldi, Jonathan M. and Krasnogor, Natalio},
  year = 2010,
  doi = {10.1007/s10710-009-9087-0},
  month = mar,
  journal = {Genetic Programming and Evolvable Machines},
  volume = {11},
  number = {1},
  pages = {61--88}
}

M.T. Cooling, V. Rouilly, G. Misirli, J. Lawson, T. Yu, J. Hallinan, A. Wipat

Standard virtual biological parts: a repository of modular modeling components for synthetic biology

in Bioinformatics, 26(7):925-931, April 2010

@ARTICLE{Cooling2010,
  title = {Standard virtual biological parts: a repository of modular modeling components for synthetic biology},
  author = {Cooling, M. T. and Rouilly, V. and Misirli, G. and Lawson, J. and Yu, T. and Hallinan, J. and Wipat, A.},
  year = 2010,
  doi = {10.1093/bioinformatics/btq063},
  month = apr,
  journal = {Bioinformatics},
  volume = {26},
  number = {7},
  pages = {925--931}
}

E. Glaab, A. Baudot, N. Krasnogor, A. Valencia

TopoGSA: network topological gene set analysis

in Bioinformatics, 26(9):1271-1272, May 2010

@ARTICLE{Glaab2010a,
  title = {TopoGSA: network topological gene set analysis},
  author = {Glaab, E. and Baudot, A. and Krasnogor, N. and Valencia, A.},
  year = 2010,
  doi = {10.1093/bioinformatics/btq131},
  month = may,
  journal = {Bioinformatics},
  volume = {26},
  number = {9},
  pages = {1271--1272}
}

W. Stein, P. Andras

Light-induced effects of a fluorescent voltage-sensitive dye on neuronal activity in the crab stomatogastric ganglion

in Journal of Neuroscience Methods, 188(2):290-294, May 2010

@ARTICLE{Stein2010,
  title = {Light-induced effects of a fluorescent voltage-sensitive dye on neuronal activity in the crab stomatogastric ganglion},
  author = {Stein, Wolfgang and Andras, Peter},
  year = 2010,
  doi = {10.1016/j.jneumeth.2010.03.003},
  month = may,
  journal = {Journal of Neuroscience Methods},
  volume = {188},
  number = {2},
  pages = {290--294}
}

B.R. Kirkwood, L. Hurt, S. Amenga-Etego, C. Tawiah, C. Zandoh, S. Danso, C. Hurt, K. Edmond, Z. Hill, G. ten Asbroek, J. Fenty, S. Owusu-Agyei, O. Campbell, P. Arthur

Effect of vitamin A supplementation in women of reproductive age on maternal survival in Ghana (ObaapaVitA): a cluster-randomised, placebo-controlled trial

in The Lancet, 375(9726):1640-1649, May 2010

@ARTICLE{Kirkwood2010,
  title = {Effect of vitamin A supplementation in women of reproductive age on maternal survival in Ghana (ObaapaVitA): a cluster-randomised, placebo-controlled trial},
  author = {Kirkwood, Betty R and Hurt, Lisa and Amenga-Etego, Seeba and Tawiah, Charlotte and Zandoh, Charles and Danso, Samuel and Hurt, Chris and Edmond, Karen and Hill, Zelee and ten Asbroek, Guus and Fenty, Justin and Owusu-Agyei, Seth and Campbell, Oona and Arthur, Paul},
  year = 2010,
  doi = {10.1016/S0140-6736(10)60311-X},
  month = may,
  journal = {The Lancet},
  volume = {375},
  number = {9726},
  pages = {1640--1649}
}

M. Gheorghe, V. Manca, F.J. Romero-Campero

Deterministic and stochastic P systems for modelling cellular processes

in Natural Computing, 9(2):457-473, June 2010

@ARTICLE{Gheorghe2010,
  title = {Deterministic and stochastic P systems for modelling cellular processes},
  author = {Gheorghe, Marian and Manca, Vincenzo and Romero-Campero, Francisco J.},
  year = 2010,
  doi = {10.1007/s11047-009-9158-4},
  month = jun,
  journal = {Natural Computing},
  volume = {9},
  number = {2},
  pages = {457--473}
}

A.A. Shah, G. Folino, N. Krasnogor

Toward High-Throughput, Multicriteria Protein-Structure Comparison and Analysis

in IEEE Transactions on NanoBioscience, 9(2):144-155, June 2010

@ARTICLE{Shah2010,
  title = {Toward High-Throughput, Multicriteria Protein-Structure Comparison and Analysis},
  author = {Shah, Azhar Ali and Folino, Gianluigi and Krasnogor, Natalio},
  year = 2010,
  doi = {10.1109/TNB.2010.2043851},
  month = jun,
  journal = {IEEE Transactions on NanoBioscience},
  volume = {9},
  number = {2},
  pages = {144--155}
}

G. Terrazas, D. Landa-Silva, N. Krasnogor

Towards the Design of Heuristics by Means of Self-Assembly

in Electronic Proceedings in Theoretical Computer Science, 26:135-146, June 2010

@ARTICLE{Terrazas2010a,
  title = {Towards the Design of Heuristics by Means of Self-Assembly},
  author = {Terrazas, German and Landa-Silva, Dario and Krasnogor, Natalio},
  year = 2010,
  doi = {10.4204/EPTCS.26.13},
  month = jun,
  journal = {Electronic Proceedings in Theoretical Computer Science},
  volume = {26},
  pages = {135--146}
}

G. Terrazas, N. Krasnogor

Grammatical rules for the automated construction of heuristics

in IEEE Congress on Evolutionary Computation, p.1-8, Barcelona, Spain, July 2010

@INPROCEEDINGS{Terrazas2010,
  title = {Grammatical rules for the automated construction of heuristics},
  author = {Terrazas, German and Krasnogor, Natalio},
  year = 2010,
  doi = {10.1109/CEC.2010.5586192},
  month = jul,
  booktitle = {IEEE Congress on Evolutionary Computation},
  pages = {1--8},
  address = {Barcelona, Spain}
}

J.S. Hallinan, G. Misirli, A. Wipat

Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits

in 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology, p.768-774, Buenos Aires, August 2010

@INPROCEEDINGS{Hallinan2010,
  title = {Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits},
  author = {Hallinan, J S and Misirli, G and Wipat, A},
  year = 2010,
  doi = {10.1109/IEMBS.2010.5626353},
  month = aug,
  booktitle = {2010 Annual International Conference of the IEEE Engineering in Medicine and Biology},
  pages = {768--774},
  address = {Buenos Aires}
}

D. Gilbert, A. Jaramillo, N. Krasnogor, V. de Lorenzo

Synthetic biology gains momentum in Europe

in Systems and Synthetic Biology, 4(3):145-147, September 2010

@ARTICLE{Gilbert2010,
  title = {Synthetic biology gains momentum in Europe},
  author = {Gilbert, David and Jaramillo, Alfonso and Krasnogor, Natalio and de Lorenzo, Victor},
  year = 2010,
  doi = {10.1007/s11693-010-9065-0},
  month = sep,
  journal = {Systems and Synthetic Biology},
  volume = {4},
  number = {3},
  pages = {145--147}
}

B.R. Kirkwood, L. Hurt, S. Amenga-Etego, C. Tawiah, C. Zandoh, S. Danso, C. Hurt, K. Edmond, Z. Hill, G. Ten Asbroek, J. Fenty, S. Owusu-Agyei, O. Campbell, P. Arthur

Effect of Vitamin A Supplementation in Women of Reproductive Age on Maternal Survival in Ghana (ObaapaVita): A Cluster-Randomized, Placebo-Controlled Trial

in Obstetrical & Gynecological Survey, 65(9):552-554, September 2010

@ARTICLE{Kirkwood2010b,
  title = {Effect of Vitamin A Supplementation in Women of Reproductive Age on Maternal Survival in Ghana (ObaapaVita): A Cluster-Randomized, Placebo-Controlled Trial},
  author = {Kirkwood, Betty R. and Hurt, Lisa and Amenga-Etego, Seeba and Tawiah, Charlotte and Zandoh, Charles and Danso, Samuel and Hurt, Chris and Edmond, Karen and Hill, Zelee and Ten Asbroek, Guus and Fenty, Justin and Owusu-Agyei, Seth and Campbell, Oona and Arthur, Paul},
  year = 2010,
  doi = {10.1097/OGX.0b013e3182021d40},
  month = sep,
  journal = {Obstetrical & Gynecological Survey},
  volume = {65},
  number = {9},
  pages = {552--554}
}

P. Lord, R. Stevens

Adding a Little Reality to Building Ontologies for Biology

in PLoS ONE, 5(9):e12258, September 2010

@ARTICLE{Lord2010,
  title = {Adding a Little Reality to Building Ontologies for Biology},
  author = {Lord, Phillip and Stevens, Robert},
  year = 2010,
  doi = {10.1371/journal.pone.0012258},
  month = sep,
  journal = {PLoS ONE},
  volume = {5},
  number = {9},
  pages = {e12258}
}

J. Smaldon, F.J. Romero-Campero, F. Fernández Trillo, M. Gheorghe, C. Alexander, N. Krasnogor

A computational study of liposome logic: towards cellular computing from the bottom up

in Systems and Synthetic Biology, 4(3):157-179, September 2010

@ARTICLE{Smaldon2010,
  title = {A computational study of liposome logic: towards cellular computing from the bottom up},
  author = {Smaldon, James and Romero-Campero, Francisco J. and Fernández Trillo, Francisco and Gheorghe, Marian and Alexander, Cameron and Krasnogor, Natalio},
  year = 2010,
  doi = {10.1007/s11693-010-9060-5},
  month = sep,
  journal = {Systems and Synthetic Biology},
  volume = {4},
  number = {3},
  pages = {157--179}
}

B.R. Kirkwood, A. Manu, C. Tawiah-Agyemang, G. ten Asbroek, T. Gyan, B. Weobong, R.E. Lewandowski, S. Soremekun, S. Danso, C. Pitt, K. Hanson, S. Owusu-Agyei, Z. Hill

NEWHINTS cluster randomised trial to evaluate the impact on neonatal mortality in rural Ghana of routine home visits to provide a package of essential newborn care interventions in the third trimester of pregnancy and the first week of life: trial protocol

in Trials, 11(1), December 2010

@ARTICLE{Kirkwood2010a,
  title = {NEWHINTS cluster randomised trial to evaluate the impact on neonatal mortality in rural Ghana of routine home visits to provide a package of essential newborn care interventions in the third trimester of pregnancy and the first week of life: trial protocol},
  author = {Kirkwood, Betty R and Manu, Alexander and Tawiah-Agyemang, Charlotte and ten Asbroek, Guus and Gyan, Thomas and Weobong, Benedict and Lewandowski, R Eric and Soremekun, Seyi and Danso, Samuel and Pitt, Catherine and Hanson, Kara and Owusu-Agyei, Seth and Hill, Zelee},
  year = 2010,
  doi = {10.1186/1745-6215-11-58},
  month = dec,
  journal = {Trials},
  volume = {11},
  number = {1}

P. Widera, J. Bacardit, N. Krasnogor, C. García-Martínez, M. Lozano

Evolutionary symbolic discovery for bioinformatics, systems and synthetic biology

in Proceedings of the 12th annual conference comp on Genetic and evolutionary computation - GECCO '10, p.1991, Portland, Oregon, USA, 2010

@INPROCEEDINGS{Widera2010a,
  title = {Evolutionary symbolic discovery for bioinformatics, systems and synthetic biology},
  author = {Widera, Paweł and Bacardit, Jaume and Krasnogor, Natalio and García-Martínez, Carlos and Lozano, Manuel},
  year = 2010,
  doi = {10.1145/1830761.1830842},
  booktitle = {Proceedings of the 12th annual conference comp on Genetic and evolutionary computation - GECCO '10},
  pages = {1991},
  address = {Portland, Oregon, USA}
}

P. Zuliani, A. Platzer, E.M. Clarke

Bayesian statistical model checking with application to Simulink/Stateflow verification

in Proceedings of the 13th ACM international conference on Hybrid systems: computation and control - HSCC '10, p.243, Stockholm, Sweden, 2010

@INPROCEEDINGS{Zuliani2010,
  title = {Bayesian statistical model checking with application to Simulink/Stateflow verification},
  author = {Zuliani, Paolo and Platzer, André and Clarke, Edmund M.},
  year = 2010,
  doi = {10.1145/1755952.1755987},
  booktitle = {Proceedings of the 13th ACM international conference on Hybrid systems: computation and control - HSCC '10},
  pages = {243},
  address = {Stockholm, Sweden}
}

URL code BibTeX

E. Glaab, J.M. Garibaldi, N. Krasnogor

vrmlgen: An R Package for 3D Data Visualization on the Web

in Journal of Statistical Software, 36(8):1-18, 2010

@ARTICLE{Glaab2010b,
  title = {vrmlgen: An R Package for 3D Data Visualization on the Web},
  author = {Glaab, Enrico and Garibaldi, Jonathan Mark and Krasnogor, Natalio},
  year = 2010,
  url = {http://www.jstatsoft.org/v36/i08/},
  journal = {Journal of Statistical Software},
  volume = {36},
  number = {8},
  pages = {1--18}
}

E. Glaab, A. Baudot, N. Krasnogor, A. Valencia

Extending pathways and processes using molecular interaction networks to analyse cancer genome data

in BMC Bioinformatics, 11(1):597, 2010

@ARTICLE{Glaab2010,
  title = {Extending pathways and processes using molecular interaction networks to analyse cancer genome data},
  author = {Glaab, Enrico and Baudot, Anaïs and Krasnogor, Natalio and Valencia, Alfonso},
  year = 2010,
  doi = {10.1186/1471-2105-11-597},
  journal = {BMC Bioinformatics},
  volume = {11},
  number = {1},
  pages = {597}
}

DOI eprint slides BibTeX

M.A. Franco, N. Krasnogor, J. Bacardit

Speeding up the evaluation of evolutionary learning systems using GPGPUs

in Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10, p.1039, Portland, Oregon, USA, 2010

Best Paper Award in the GBML track

@INPROCEEDINGS{Franco2010,
  title = {Speeding up the evaluation of evolutionary learning systems using GPGPUs},
  author = {Franco, María A. and Krasnogor, Natalio and Bacardit, Jaume},
  year = 2010,
  doi = {10.1145/1830483.1830672},
  note = {Best Paper Award in the GBML track},
  booktitle = {Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10},
  pages = {1039},
  address = {Portland, Oregon, USA}
}

G. Pasparakis, N. Krasnogor, L. Cronin, B.G. Davis, C. Alexander

Controlled polymer synthesis—from biomimicry towards synthetic biology

in Chem. Soc. Rev., 39(1):286-300, 2010

@ARTICLE{Pasparakis2010,
  title = {Controlled polymer synthesis—from biomimicry towards synthetic biology},
  author = {Pasparakis, George and Krasnogor, Natalio and Cronin, Leroy and Davis, Benjamin G. and Alexander, Cameron},
  year = 2010,
  doi = {10.1039/B809333B},
  journal = {Chem. Soc. Rev.},
  volume = {39},
  number = {1},
  pages = {286--300}
}

DOI
M. Kaiser

Optimal hierarchical modular topologies for producing limited sustained activation of neural networks

in Frontiers in Neuroinformatics, available online since 2010

J. Bacardit, W. Browne, J. Drugowitsch, E. Bernadó-Mansilla, M.V. Butz

Learning Classifier Systems

Lecture Notes in Computer Science 6471, Springer Berlin Heidelberg, 2010

@BOOK{Bacardit2010,
  title = {Learning Classifier Systems},
  author = {Bacardit, Jaume and Browne, Will and Drugowitsch, Jan and Bernadó-Mansilla, Ester and Butz, Martin V.},
  year = 2010,
  doi = {10.1007/978-3-642-17508-4},
  publisher = {Springer Berlin Heidelberg},
  volume = {6471},
  series = {Lecture Notes in Computer Science}
}

H. Gong, P. Zuliani, A. Komuravelli, J.R. Faeder, E.M. Clarke

Analysis and verification of the HMGB1 signaling pathway

in BMC Bioinformatics, 11(Suppl 7):S10, 2010

@ARTICLE{Gong2010,
  title = {Analysis and verification of the HMGB1 signaling pathway},
  author = {Gong, Haijun and Zuliani, Paolo and Komuravelli, Anvesh and Faeder, James R and Clarke, Edmund M},
  year = 2010,
  doi = {10.1186/1471-2105-11-S7-S10},
  journal = {BMC Bioinformatics},
  volume = {11},
  number = {Suppl 7},
  pages = {S10}
}

DOI slides BibTeX

M.A. Franco, N. Krasnogor, J. Bacardit

Analysing bioHEL using challenging boolean functions

in Proceedings of the 12th annual conference comp on Genetic and evolutionary computation - GECCO '10, p.1855, Portland, Oregon, USA, 2010

@INPROCEEDINGS{Franco2010a,
  title = {Analysing bioHEL using challenging boolean functions},
  author = {Franco, Maria A. and Krasnogor, Natalio and Bacardit, Jaume},
  year = 2010,
  doi = {10.1145/1830761.1830817},
  booktitle = {Proceedings of the 12th annual conference comp on Genetic and evolutionary computation - GECCO '10},
  pages = {1855},
  address = {Portland, Oregon, USA}
}

P. Lord

An evolutionary approach to Function

in Journal of Biomedical Semantics, 1(Suppl 1):S4, 2010

@ARTICLE{Lord2010a,
  title = {An evolutionary approach to Function},
  author = {Lord, Phillip},
  year = 2010,
  doi = {10.1186/2041-1480-1-S1-S4},
  journal = {Journal of Biomedical Semantics},
  volume = {1},
  number = {Suppl 1},
  pages = {S4}
}

C. García-Martínez, C. Lima, J. Twycross, N. Krasnogor, M. Lozano

P system model optimisation by means of evolutionary based search algorithms

in Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10, p.187, Portland, Oregon, USA, 2010

@INPROCEEDINGS{Garcia-Martinez2010,
  title = {P system model optimisation by means of evolutionary based search algorithms},
  author = {García-Martínez, Carlos and Lima, Claudio and Twycross, Jamie and Krasnogor, Natalio and Lozano, Manuel},
  year = 2010,
  doi = {10.1145/1830483.1830517},
  booktitle = {Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10},
  pages = {187},
  address = {Portland, Oregon, USA}
}

J. Twycross, L.R. Band, M.J. Bennett, J.R. King, N. Krasnogor

Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study

in BMC Systems Biology, 4(1):34, 2010

@ARTICLE{Twycross2010,
  title = {Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study},
  author = {Twycross, Jamie and Band, Leah R and Bennett, Malcolm J and King, John R and Krasnogor, Natalio},
  year = 2010,
  doi = {10.1186/1752-0509-4-34},
  journal = {BMC Systems Biology},
  volume = {4},
  number = {1},
  pages = {34}
}

M. Kaiser

Hierarchy and dynamics of neural networks

in Frontiers in Neuroinformatics, 4, 2010

@ARTICLE{Kaiser2010a,
  title = {Hierarchy and dynamics of neural networks},
  author = {Kaiser, Marcus},
  year = 2010,
  doi = {10.3389/fninf.2010.00112},
  journal = {Frontiers in Neuroinformatics},
  volume = {4}

G. Terrazas, D. Landa-Silva, N. Krasnogor

Discovering Beneficial Cooperative Structures for the Automated Construction of Heuristics

in Nature Inspired Cooperative Strategies for Optimization (NICSO 2010), Studies in Computational Intelligence 284, p.89-100, 2010

@INCOLLECTION{Terrazas2010b,
  title = {Discovering Beneficial Cooperative Structures for the Automated Construction of Heuristics},
  author = {Terrazas, Germán and Landa-Silva, Dario and Krasnogor, Natalio},
  year = 2010,
  doi = {10.1007/978-3-642-12538-6_8},
  booktitle = {Nature Inspired Cooperative Strategies for Optimization (NICSO 2010)},
  publisher = {Springer Berlin Heidelberg},
  volume = {284},
  series = {Studies in Computational Intelligence},
  pages = {89--100}
}

A.R. Jones, A.L. Lister

Managing Experimental Data Using FuGE

in Proteome Bioinformatics, Methods in Molecular Biology 604, p.333-343, 2010

@INCOLLECTION{Jones2010,
  title = {Managing Experimental Data Using FuGE},
  author = {Jones, Andrew R. and Lister, Allyson L.},
  year = 2010,
  doi = {10.1007/978-1-60761-444-9_23},
  booktitle = {Proteome Bioinformatics},
  publisher = {Humana Press},
  volume = {604},
  series = {Methods in Molecular Biology},
  pages = {333--343}
}

2009

J. Hinks, J. Bush, P. Andras, J. Garratt, G. Pigott, A. Kennedy, T. Pless-Mulloli

Views on chemical safety information and influences on chemical disposal behaviour in the UK

in Science of The Total Environment, 407(4):1299-1306, February 2009

@ARTICLE{Hinks2009,
  title = {Views on chemical safety information and influences on chemical disposal behaviour in the UK},
  author = {Hinks, J. and Bush, J. and Andras, P. and Garratt, J. and Pigott, G. and Kennedy, A. and Pless-Mulloli, T.},
  year = 2009,
  doi = {10.1016/j.scitotenv.2008.10.056},
  month = feb,
  journal = {Science of The Total Environment},
  volume = {407},
  number = {4},
  pages = {1299--1306}
}

M. Stout, J. Bacardit, J.D. Hirst, R.E. Smith, N. Krasnogor

Prediction of topological contacts in proteins using learning classifier systems

in Soft Computing, 13(3):245-258, February 2009

@ARTICLE{Stout2009,
  title = {Prediction of topological contacts in proteins using learning classifier systems},
  author = {Stout, Michael and Bacardit, Jaume and Hirst, Jonathan D. and Smith, Robert E. and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1007/s00500-008-0318-8},
  month = feb,
  journal = {Soft Computing},
  volume = {13},
  number = {3},
  pages = {245--258}
}

J. Alcalá-Fdez, L. Sánchez, S. García, M.J. del Jesus, S. Ventura, J.M. Garrell, J. Otero, C. Romero, J. Bacardit, V.M. Rivas, J.C. Fernández, F. Herrera

KEEL: a software tool to assess evolutionary algorithms for data mining problems

in Soft Computing, 13(3):307-318, February 2009

@ARTICLE{Alcala-Fdez2009,
  title = {KEEL: a software tool to assess evolutionary algorithms for data mining problems},
  author = {Alcalá-Fdez, J. and Sánchez, L. and García, S. and del Jesus, M. J. and Ventura, S. and Garrell, J. M. and Otero, J. and Romero, C. and Bacardit, J. and Rivas, V. M. and Fernández, J. C. and Herrera, F.},
  year = 2009,
  doi = {10.1007/s00500-008-0323-y},
  month = feb,
  journal = {Soft Computing},
  volume = {13},
  number = {3},
  pages = {307--318}
}

J. Bacardit, E.K. Burke, N. Krasnogor

Improving the scalability of rule-based evolutionary learning

in Memetic Computing, 1(1):55-67, March 2009

@ARTICLE{Bacardit2009,
  title = {Improving the scalability of rule-based evolutionary learning},
  author = {Bacardit, Jaume and Burke, Edmund K. and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1007/s12293-008-0005-4},
  month = mar,
  journal = {Memetic Computing},
  volume = {1},
  number = {1},
  pages = {55--67}
}

L. Fiaschi, J.M. Garibaldi, N. Krasnogora

A framework for the application of decision trees to the analysis of SNPs data

in 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, p.106-113, Nashville, TN, USA, March 2009

@INPROCEEDINGS{Fiaschi2009,
  title = {A framework for the application of decision trees to the analysis of SNPs data},
  author = {Fiaschi, Linda and Garibaldi, Jonathan M. and Krasnogora, Natalio},
  year = 2009,
  doi = {10.1109/CIBCB.2009.4925715},
  month = mar,
  booktitle = {2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology},
  pages = {106--113},
  address = {Nashville, TN, USA}
}

P. Andras, B.G. Charlton

Why are top universities losing their lead? An economics modelling-based approach

in Science and Public Policy, 36(4):317-330, May 2009

@ARTICLE{Andras2009a,
  title = {Why are top universities losing their lead? An economics modelling-based approach},
  author = {Andras, Peter and Charlton, Bruce G},
  year = 2009,
  doi = {10.3152/030234209X436563},
  month = may,
  journal = {Science and Public Policy},
  volume = {36},
  number = {4},
  pages = {317--330}
}

P. Widera, J.M. Garibaldi, N. Krasnogor

Evolutionary design of the energy function for protein structure prediction

in 2009 IEEE Congress on Evolutionary Computation, p.1305-1312, Trondheim, Norway, May 2009

@INPROCEEDINGS{Widera2009,
  title = {Evolutionary design of the energy function for protein structure prediction},
  author = {Widera, Pawel and Garibaldi, Jonathan M. and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1109/CEC.2009.4983095},
  month = may,
  booktitle = {2009 IEEE Congress on Evolutionary Computation},
  pages = {1305--1312},
  address = {Trondheim, Norway}
}

R.M. F?chslin, H. Fellermann, A. Eriksson, H. Ziock

Coarse graining and scaling in dissipative particle dynamics

in The Journal of Chemical Physics, 130(21):214102, June 2009

@ARTICLE{Fuchslin2009,
  title = {Coarse graining and scaling in dissipative particle dynamics},
  author = {F?chslin, Rudolf M. and Fellermann, Harold and Eriksson, Anders and Ziock, Hans-Joachim},
  year = 2009,
  doi = {10.1063/1.3143976},
  month = jun,
  journal = {The Journal of Chemical Physics},
  volume = {130},
  number = {21},
  pages = {214102}
}

F.J. Romero-Campero, J. Twycross, M. Cámara, M. Bennett, M. Gheorghe, N. Krasnogor

Modular Assembly Of Cell Systems Biology Models Using P Systems

in International Journal of Foundations of Computer Science, 20(03):427-442, June 2009

@ARTICLE{Romero-Campero2009,
  title = {Modular Assembly Of Cell Systems Biology Models Using P Systems},
  author = {Romero-Campero, Francisco J. and Twycross, Jamie and Cámara, Miguel and Bennett, Malcolm and Gheorghe, Marian and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1142/S0129054109006668},
  month = jun,
  journal = {International Journal of Foundations of Computer Science},
  volume = {20},
  number = {03},
  pages = {427--442}
}

A.R. Jones, A.L. Lister, L. Hermida, P. Wilkinson, M. Eisenacher, K. Belhajjame, F. Gibson, P. Lord, M. Pocock, H. Rosenfelder, J. Santoyo-Lopez, A. Wipat, N.W. Paton

Modeling and Managing Experimental Data Using FuGE

in OMICS: A Journal of Integrative Biology, 13(3):239-251, June 2009

@ARTICLE{Jones2009,
  title = {Modeling and Managing Experimental Data Using FuGE},
  author = {Jones, Andrew R. and Lister, Allyson L. and Hermida, Leandro and Wilkinson, Peter and Eisenacher, Martin and Belhajjame, Khalid and Gibson, Frank and Lord, Phil and Pocock, Matthew and Rosenfelder, Heiko and Santoyo-Lopez, Javier and Wipat, Anil and Paton, Norman W.},
  year = 2009,
  doi = {10.1089/omi.2008.0080},
  month = jun,
  journal = {OMICS: A Journal of Integrative Biology},
  volume = {13},
  number = {3},
  pages = {239--251}
}

N.Q. Huy, O.Y. Soon, L.M. Hiot, N. Krasnogor

Adaptive Cellular Memetic Algorithms

in Evolutionary Computation, 17(2):231-256, June 2009

@ARTICLE{Huy2009,
  title = {Adaptive Cellular Memetic Algorithms},
  author = {Huy, Nguyen Quang and Soon, Ong Yew and Hiot, Lim Meng and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1162/evco.2009.17.2.231},
  month = jun,
  journal = {Evolutionary Computation},
  volume = {17},
  number = {2},
  pages = {231--256}
}

B.G. Charlton, P. Andras

The Sleep Elaboration–Awake Pruning (SEAP) theory of memory: Long term memories grow in complexity during sleep and undergo selection while awake. Clinical, psychopharmacological and creative implications

in Medical Hypotheses, 73(1):1-4, July 2009

@ARTICLE{Charlton2009,
  title = {The Sleep Elaboration–Awake Pruning (SEAP) theory of memory: Long term memories grow in complexity during sleep and undergo selection while awake. Clinical, psychopharmacological and creative implications},
  author = {Charlton, Bruce G. and Andras, Peter},
  year = 2009,
  doi = {10.1016/j.mehy.2009.03.005},
  month = jul,
  journal = {Medical Hypotheses},
  volume = {73},
  number = {1},
  pages = {1--4}
}

L.d.F. Costa, F.A. Rodrigues, C.C. Hilgetag, M. Kaiser

Beyond the average: Detecting global singular nodes from local features in complex networks

in EPL (Europhysics Letters), 87(1):18008, July 2009

@ARTICLE{Costa2009,
  title = {Beyond the average: Detecting global singular nodes from local features in complex networks},
  author = {Costa, L. da F. and Rodrigues, F. A. and Hilgetag, C. C. and Kaiser, M.},
  year = 2009,
  doi = {10.1209/0295-5075/87/18008},
  month = jul,
  journal = {EPL (Europhysics Letters)},
  volume = {87},
  number = {1},
  pages = {18008}
}

L. Li, J.M. Garibaldi, N. Krasnogor

Automated self-assembly programming paradigm: The impact of network topology

in International Journal of Intelligent Systems, 24(7):793-817, July 2009

@ARTICLE{Li2009,
  title = {Automated self-assembly programming paradigm: The impact of network topology},
  author = {Li, Lin and Garibaldi, Jonathan M and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1002/int.20361},
  month = jul,
  journal = {International Journal of Intelligent Systems},
  volume = {24},
  number = {7},
  pages = {793--817}
}

C. Pesquita, D. Faria, A.O. Falcão, P. Lord, F.M. Couto

Semantic Similarity in Biomedical Ontologies

in PLoS Computational Biology, 5(7):e1000443, July 2009

@ARTICLE{Pesquita2009,
  title = {Semantic Similarity in Biomedical Ontologies},
  author = {Pesquita, Catia and Faria, Daniel and Falcão, André O. and Lord, Phillip and Couto, Francisco M.},
  year = 2009,
  doi = {10.1371/journal.pcbi.1000443},
  month = jul,
  journal = {PLoS Computational Biology},
  volume = {5},
  number = {7},
  pages = {e1000443}
}

G. Folino, A.A. Shah, N. Kransnogor

On the storage, management and analysis of (multi) similarity for large scale protein structure datasets in the grid

in 2009 22nd IEEE International Symposium on Computer-Based Medical Systems, p.1-8, Albuquerque, NM, USA, August 2009

@INPROCEEDINGS{Folino2009,
  title = {On the storage, management and analysis of (multi) similarity for large scale protein structure datasets in the grid},
  author = {Folino, Gianluigi and Shah, Azhar Ali and Kransnogor, Natalio},
  year = 2009,
  doi = {10.1109/CBMS.2009.5255328},
  month = aug,
  booktitle = {2009 22nd IEEE International Symposium on Computer-Based Medical Systems},
  pages = {1--8},
  address = {Albuquerque, NM, USA}
}

J. Marcelino, M. Kaiser

Reducing inﬂuenza spreading over the airline network

in PLoS Currents, 1:RRN1005, August 2009

@ARTICLE{Marcelino2009,
  title = {Reducing inﬂuenza spreading over the airline network},
  author = {Marcelino, Jose and Kaiser, Marcus},
  year = 2009,
  doi = {10.1371/currents.RRN1005},
  month = aug,
  journal = {PLoS Currents},
  volume = {1},
  pages = {RRN1005}
}

A. Moya, N. Krasnogor, J. Peretó, A. Latorre

Goethe's dream. Challenges and opportunities for synthetic biology

in EMBO reports, 10(S1):S28-S32, August 2009

@ARTICLE{Moya2009,
  title = {Goethe's dream. Challenges and opportunities for synthetic biology},
  author = {Moya, Andrés and Krasnogor, Natalio and Peretó, Juli and Latorre, Amparo},
  year = 2009,
  doi = {10.1038/embor.2009.120},
  month = aug,
  journal = {EMBO reports},
  volume = {10},
  number = {S1},
  pages = {S28--S32}
}

J. Bacardit, N. Krasnogor

Performance and Efficiency of Memetic Pittsburgh Learning Classifier Systems

in Evolutionary Computation, 17(3):307-342, September 2009

@ARTICLE{Bacardit2009c,
  title = {Performance and Efficiency of Memetic Pittsburgh Learning Classifier Systems},
  author = {Bacardit, Jaume and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1162/evco.2009.17.3.307},
  month = sep,
  journal = {Evolutionary Computation},
  volume = {17},
  number = {3},
  pages = {307--342}
}

P. Zuliani

Reasoning about faulty quantum programs

in Acta Informatica, 46(6):403-432, October 2009

@ARTICLE{Zuliani2009,
  title = {Reasoning about faulty quantum programs},
  author = {Zuliani, Paolo},
  year = 2009,
  doi = {10.1007/s00236-009-0100-0},
  month = oct,
  journal = {Acta Informatica},
  volume = {46},
  number = {6},
  pages = {403--432}
}

A.L. Lister, M. Pocock, M. Taschuk, A. Wipat

Saint: a lightweight integration environment for model annotation

in Bioinformatics, 25(22):3026-3027, November 2009

@ARTICLE{Lister2009a,
  title = {Saint: a lightweight integration environment for model annotation},
  author = {Lister, A. L. and Pocock, M. and Taschuk, M. and Wipat, A.},
  year = 2009,
  doi = {10.1093/bioinformatics/btp523},
  month = nov,
  journal = {Bioinformatics},
  volume = {25},
  number = {22},
  pages = {3026--3027}
}

P. Ribeiro, J. Simonotto, M. Kaiser, F. Silva

Parallel calculation of multi-electrode array correlation networks

in Journal of Neuroscience Methods, 184(2):357-364, November 2009

@ARTICLE{Ribeiro2009,
  title = {Parallel calculation of multi-electrode array correlation networks},
  author = {Ribeiro, Pedro and Simonotto, Jennifer and Kaiser, Marcus and Silva, Fernando},
  year = 2009,
  doi = {10.1016/j.jneumeth.2009.08.001},
  month = nov,
  journal = {Journal of Neuroscience Methods},
  volume = {184},
  number = {2},
  pages = {357--364}
}

P. Andras

Molecular neuroimaging – A proposal for a novel approach to high resolution recording of neural activity in nervous systems

in Medical Hypotheses, 73(6):876-882, December 2009

@ARTICLE{Andras2009,
  title = {Molecular neuroimaging – A proposal for a novel approach to high resolution recording of neural activity in nervous systems},
  author = {Andras, Peter},
  year = 2009,
  doi = {10.1016/j.mehy.2009.06.056},
  month = dec,
  journal = {Medical Hypotheses},
  volume = {73},
  number = {6},
  pages = {876--882}
}

M. Kaiser, C.C. Hilgetag, A. van Ooyen

A Simple Rule for Axon Outgrowth and Synaptic Competition Generates Realistic Connection Lengths and Filling Fractions

in Cerebral Cortex, 19(12):3001-3010, December 2009

@ARTICLE{Kaiser2009,
  title = {A Simple Rule for Axon Outgrowth and Synaptic Competition Generates Realistic Connection Lengths and Filling Fractions},
  author = {Kaiser, M. and Hilgetag, C. C. and van Ooyen, A.},
  year = 2009,
  doi = {10.1093/cercor/bhp071},
  month = dec,
  journal = {Cerebral Cortex},
  volume = {19},
  number = {12},
  pages = {3001--3010}
}

P. Ribeiro, F. Silva, M. Kaiser

Strategies for Network Motifs Discovery

in 2009 Fifth IEEE International Conference on e-Science, p.80-87, Oxford, United Kingdom, December 2009

@INPROCEEDINGS{Ribeiro2009a,
  title = {Strategies for Network Motifs Discovery},
  author = {Ribeiro, Pedro and Silva, Fernando and Kaiser, Marcus},
  year = 2009,
  doi = {10.1109/e-Science.2009.20},
  month = dec,
  booktitle = {2009 Fifth IEEE International Conference on e-Science},
  pages = {80--87},
  address = {Oxford, United Kingdom}
}

A. Lister, V. Charoensawan, S. De, K. James, S.C. Janga, J. Huppert

Interfacing systems biology and synthetic biology

in Genome Biology, 10(6):309, 2009

@ARTICLE{Lister2009,
  title = {Interfacing systems biology and synthetic biology},
  author = {Lister, Allyson and Charoensawan, Varodom and De, Subhajyoti and James, Katherine and Janga, Sarath Chandra and Huppert, Julian},
  year = 2009,
  doi = {10.1186/gb-2009-10-6-309},
  journal = {Genome Biology},
  volume = {10},
  number = {6},
  pages = {309}
}

F.J. Romero-Campero, J. Twycross, H. Cao, J. Blakes, N. Krasnogor

A Multiscale Modeling Framework Based on P Systems

in Membrane Computing, Lecture Notes in Computer Science 5391, p.63-77, 2009

@INCOLLECTION{Romero-Campero2009a,
  title = {A Multiscale Modeling Framework Based on P Systems},
  author = {Romero-Campero, Francisco José and Twycross, Jamie and Cao, Hongqing and Blakes, Jonathan and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1007/978-3-540-95885-7_5},
  booktitle = {Membrane Computing},
  publisher = {Springer Berlin Heidelberg},
  volume = {5391},
  series = {Lecture Notes in Computer Science},
  pages = {63--77}
}

S.K. Jha, E.M. Clarke, C.J. Langmead, A. Legay, A. Platzer, P. Zuliani

A Bayesian Approach to Model Checking Biological Systems

in Computational Methods in Systems Biology, Lecture Notes in Computer Science 5688, p.218-234, 2009

@INCOLLECTION{Jha2009,
  title = {A Bayesian Approach to Model Checking Biological Systems},
  author = {Jha, Sumit K. and Clarke, Edmund M. and Langmead, Christopher J. and Legay, Axel and Platzer, André and Zuliani, Paolo},
  year = 2009,
  doi = {10.1007/978-3-642-03845-7_15},
  booktitle = {Computational Methods in Systems Biology},
  publisher = {Springer Berlin Heidelberg},
  volume = {5688},
  series = {Lecture Notes in Computer Science},
  pages = {218--234}
}

F.J. Romero-Campero, N. Krasnogor

An Approach to the Engineering of Cellular Models Based on P Systems

in Mathematical Theory and Computational Practice, Lecture Notes in Computer Science 5635, p.430-436, 2009

@INCOLLECTION{Romero-Campero2009b,
  title = {An Approach to the Engineering of Cellular Models Based on P Systems},
  author = {Romero-Campero, Francisco J. and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1007/978-3-642-03073-4_44},
  booktitle = {Mathematical Theory and Computational Practice},
  publisher = {Springer Berlin Heidelberg},
  volume = {5635},
  series = {Lecture Notes in Computer Science},
  pages = {430--436}
}

K. James, A. Wipat, J. Hallinan

Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes

in Data Integration in the Life Sciences, Lecture Notes in Computer Science 5647, p.31-46, 2009

@INCOLLECTION{James2009,
  title = {Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes},
  author = {James, Katherine and Wipat, Anil and Hallinan, Jennifer},
  year = 2009,
  doi = {10.1007/978-3-642-02879-3_4},
  booktitle = {Data Integration in the Life Sciences},
  publisher = {Springer Berlin Heidelberg},
  volume = {5647},
  series = {Lecture Notes in Computer Science},
  pages = {31--46}
}

E. Glaab, J.M. Garibaldi, N. Krasnogor

ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

in BMC Bioinformatics, 10(1):358, 2009

@ARTICLE{Glaab2009,
  title = {ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization},
  author = {Glaab, Enrico and Garibaldi, Jonathan M and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1186/1471-2105-10-358},
  journal = {BMC Bioinformatics},
  volume = {10},
  number = {1},
  pages = {358}
}

G. Pasparakis, M. Vamvakaki, N. Krasnogor, C. Alexander

Diol–boronic acid complexes integrated by responsive polymers—a route to chemical sensing and logic operations

in Soft Matter, 5(20):3839, 2009

@ARTICLE{Pasparakis2009,
  title = {Diol–boronic acid complexes integrated by responsive polymers—a route to chemical sensing and logic operations},
  author = {Pasparakis, George and Vamvakaki, Maria and Krasnogor, Natalio and Alexander, Cameron},
  year = 2009,
  doi = {10.1039/b911341j},
  journal = {Soft Matter},
  volume = {5},
  number = {20},
  pages = {3839}
}

J. Smaldon, N. Krasnogor, C. Alexander, M. Gheorghe

Liposome logic

in Proceedings of the 11th Annual conference on Genetic and evolutionary computation - GECCO '09, p.161, Montreal, Québec, Canada, 2009

@INPROCEEDINGS{Smaldon2009,
  title = {Liposome logic},
  author = {Smaldon, James and Krasnogor, Natalio and Alexander, Cameron and Gheorghe, Marian},
  year = 2009,
  doi = {10.1145/1569901.1569924},
  booktitle = {Proceedings of the 11th Annual conference on Genetic and evolutionary computation - GECCO '09},
  pages = {161},
  address = {Montreal, Québec, Canada}
}

R. Stevens, P. Lord

Application of Ontologies in Bioinformatics

in Handbook on Ontologies, p.735-756, 2009

@INCOLLECTION{Stevens2009,
  title = {Application of Ontologies in Bioinformatics},
  author = {Stevens, Robert and Lord, Phillip},
  year = 2009,
  doi = {10.1007/978-3-540-92673-3_33},
  booktitle = {Handbook on Ontologies},
  publisher = {Springer Berlin Heidelberg},
  pages = {735--756}
}

N. Krasnogor, M.B. Melián-Batista, J.A.M. Pérez, J.M. Moreno-Vega, D.A. Pelta

Nature Inspired Cooperative Strategies for Optimization (NICSO 2008)

Studies in Computational Intelligence 236, Springer Berlin Heidelberg, 2009

@BOOK{Krasnogor2009,
  title = {Nature Inspired Cooperative Strategies for Optimization (NICSO 2008)},
  author = {Krasnogor, Natalio and Melián-Batista, María Belén and Pérez, José Andrés Moreno and Moreno-Vega, J. Marcos and Pelta, David Alejandro},
  year = 2009,
  doi = {10.1007/978-3-642-03211-0},
  publisher = {Springer Berlin Heidelberg},
  volume = {236},
  series = {Studies in Computational Intelligence}
}

J. Bacardit, N. Krasnogor

A mixed discrete-continuous attribute list representation for large scale classification domains

in Proceedings of the 11th Annual conference on Genetic and evolutionary computation - GECCO '09, p.1155, Montreal, Québec, Canada, 2009

@INPROCEEDINGS{Bacardit2009b,
  title = {A mixed discrete-continuous attribute list representation for large scale classification domains},
  author = {Bacardit, Jaume and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1145/1569901.1570057},
  booktitle = {Proceedings of the 11th Annual conference on Genetic and evolutionary computation - GECCO '09},
  pages = {1155},
  address = {Montreal, Québec, Canada}
}

J. Bacardit, M. Stout, J.D. Hirst, A. Valencia, R.E. Smith, N. Krasnogor

Automated Alphabet Reduction for Protein Datasets

in BMC Bioinformatics, 10(1):6, 2009

@ARTICLE{Bacardit2009a,
  title = {Automated Alphabet Reduction for Protein Datasets},
  author = {Bacardit, Jaume and Stout, Michael and Hirst, Jonathan D and Valencia, Alfonso and Smith, Robert E and Krasnogor, Natalio},
  year = 2009,
  doi = {10.1186/1471-2105-10-6},
  journal = {BMC Bioinformatics},
  volume = {10},
  number = {1},
  pages = {6}
}

2008

B.G. Charlton, P. Andras

Stimulating revolutionary science with mega-cash prizes

in Medical Hypotheses, 70(4):709-713, January 2008

@ARTICLE{Charlton2008a,
  title = {Stimulating revolutionary science with mega-cash prizes},
  author = {Charlton, Bruce G. and Andras, Peter},
  year = 2008,
  doi = {10.1016/j.mehy.2008.01.001},
  month = jan,
  journal = {Medical Hypotheses},
  volume = {70},
  number = {4},
  pages = {709--713}
}

N. Krasnogor, A. Shah, D. Barthel, P. Lukasiak, J. Blazewicz

Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review

in Current Bioinformatics, 3(1):10-31, January 2008

@ARTICLE{Krasnogor2008b,
  title = {Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review},
  author = {Krasnogor, Natalio and Shah, Azhar and Barthel, Daniel and Lukasiak, Piotr and Blazewicz, Jacek},
  year = 2008,
  doi = {10.2174/157489308783329850},
  month = jan,
  journal = {Current Bioinformatics},
  volume = {3},
  number = {1},
  pages = {10--31}
}

B.G. Charlton, P. Andras

‘Down-shifting’ among top UK scientists? – The decline of ‘revolutionary science’ and the rise of ‘normal science’ in the UK compared with the USA

in Medical Hypotheses, 70(3):465-472, January 2008

@ARTICLE{Charlton2008,
  title = {‘Down-shifting’ among top UK scientists? – The decline of ‘revolutionary science’ and the rise of ‘normal science’ in the UK compared with the USA},
  author = {Charlton, Bruce G. and Andras, Peter},
  year = 2008,
  doi = {10.1016/j.mehy.2007.12.004},
  month = jan,
  journal = {Medical Hypotheses},
  volume = {70},
  number = {3},
  pages = {465--472}
}

M. Gheorghe, N. Krasnogor, M. Camara

P systems applications to systems biology

in Biosystems, 91(3):435-437, March 2008

@ARTICLE{Gheorghe2008,
  title = {P systems applications to systems biology},
  author = {Gheorghe, Marian and Krasnogor, Natalio and Camara, Miguel},
  year = 2008,
  doi = {10.1016/j.biosystems.2007.07.002},
  month = mar,
  journal = {Biosystems},
  volume = {91},
  number = {3},
  pages = {435--437}
}

N. Krasnogor, J. Smith

Memetic Algorithms: The Polynomial Local Search Complexity Theory Perspective

in Journal of Mathematical Modelling and Algorithms, 7(1):3-24, March 2008

@ARTICLE{Krasnogor2008,
  title = {Memetic Algorithms: The Polynomial Local Search Complexity Theory Perspective},
  author = {Krasnogor, Natalio and Smith, Jim},
  year = 2008,
  doi = {10.1007/s10852-007-9070-9},
  month = mar,
  journal = {Journal of Mathematical Modelling and Algorithms},
  volume = {7},
  number = {1},
  pages = {3--24}
}

M. Stout, J. Bacardit, J.D. Hirst, N. Krasnogor

Prediction of recursive convex hull class assignments for protein residues

in Bioinformatics, 24(7):916-923, April 2008

@ARTICLE{Stout2008,
  title = {Prediction of recursive convex hull class assignments for protein residues},
  author = {Stout, M. and Bacardit, J. and Hirst, J. D. and Krasnogor, N.},
  year = 2008,
  doi = {10.1093/bioinformatics/btn050},
  month = apr,
  journal = {Bioinformatics},
  volume = {24},
  number = {7},
  pages = {916--923}
}

S. Fitch, T. Jackson, P. Andras, C. Robson

Unsupervised segmentation of cell nuclei using geometric models

in 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, p.728-731, Paris, France, May 2008

@INPROCEEDINGS{Fitch2008,
  title = {Unsupervised segmentation of cell nuclei using geometric models},
  author = {Fitch, Shaun and Jackson, Trevor and Andras, Peter and Robson, Craig},
  year = 2008,
  doi = {10.1109/ISBI.2008.4541099},
  month = may,
  booktitle = {2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro},
  pages = {728--731},
  address = {Paris, France}
}

D. Field, G. Garrity, T. Gray, N. Morrison, J. Selengut, P. Sterk, T. Tatusova, N. Thomson, M.J. Allen, S.V. Angiuoli, M. Ashburner, N. Axelrod, S. Baldauf, S. Ballard, J. Boore, G. Cochrane, J. Cole, P. Dawyndt, P. De Vos, C. dePamphilis, R. Edwards, N. Faruque, R. Feldman, J. Gilbert, P. Gilna, F.O. Glöckner, P. Goldstein, R. Guralnick, D. Haft, D. Hancock, H. Hermjakob, C. Hertz-Fowler, et al.

The minimum information about a genome sequence (MIGS) specification

in Nature Biotechnology, 26(5):541-547, May 2008

@ARTICLE{Field2008a,
  title = {The minimum information about a genome sequence (MIGS) specification},
  author = {Field, Dawn and Garrity, George and Gray, Tanya and Morrison, Norman and Selengut, Jeremy and Sterk, Peter and Tatusova, Tatiana and Thomson, Nicholas and Allen, Michael J and Angiuoli, Samuel V and Ashburner, Michael and Axelrod, Nelson and Baldauf, Sandra and Ballard, Stuart and Boore, Jeffrey and Cochrane, Guy and Cole, James and Dawyndt, Peter and De Vos, Paul and dePamphilis, Claude and Edwards, Robert and Faruque, Nadeem and Feldman, Robert and Gilbert, Jack and Gilna, Paul and Glöckner, Frank Oliver and Goldstein, Philip and Guralnick, Robert and Haft, Dan and Hancock, David and Hermjakob, Henning and Hertz-Fowler, Christiane and Hugenholtz, Phil and Joint, Ian and Kagan, Leonid and Kane, Matthew and Kennedy, Jessie and Kowalchuk, George and Kottmann, Renzo and Kolker, Eugene and Kravitz, Saul and Kyrpides, Nikos and Leebens-Mack, Jim and Lewis, Suzanna E and Li, Kelvin and Lister, Allyson L and Lord, Phillip and Maltsev, Natalia and Markowitz, Victor and Martiny, Jennifer and Methe, Barbara and Mizrachi, Ilene and Moxon, Richard and Nelson, Karen and Parkhill, Julian and Proctor, Lita and White, Owen and Sansone, Susanna-Assunta and Spiers, Andrew and Stevens, Robert and Swift, Paul and Taylor, Chris and Tateno, Yoshio and Tett, Adrian and Turner, Sarah and Ussery, David and Vaughan, Bob and Ward, Naomi and Whetzel, Trish and San Gil, Ingio and Wilson, Gareth and Wipat, Anil},
  year = 2008,
  doi = {10.1038/nbt1360},
  month = may,
  journal = {Nature Biotechnology},
  volume = {26},
  number = {5},
  pages = {541--547}
}

D. Field, F.O. Glöckner, G.M. Garrity, T. Gray, P. Sterk, G. Cochrane, R. Vaughan, E. Kolker, R. Kottmann, N. Kyrpides, S. Angiuoli, P. Dawyndt, R. Guralnick, P. Goldstein, N. Hall, L. Hirschman, S. Kravitz, A.L. Lister, V. Markowitz, N. Thomson, T. Whetzel

Meeting Report: The Fourth Genomic Standards Consortium (GSC) Workshop

in OMICS: A Journal of Integrative Biology, 12(2):101-108, June 2008

@ARTICLE{Field2008,
  title = {Meeting Report: The Fourth Genomic Standards Consortium (GSC) Workshop},
  author = {Field, Dawn and Glöckner, Frank Oliver and Garrity, George M. and Gray, Tanya and Sterk, Peter and Cochrane, Guy and Vaughan, Robert and Kolker, Eugene and Kottmann, Renzo and Kyrpides, Nikos and Angiuoli, Sam and Dawyndt, Peter and Guralnick, Robert and Goldstein, Philip and Hall, Neil and Hirschman, Lynette and Kravitz, Saul and Lister, Allyson L. and Markowitz, Victor and Thomson, Nick and Whetzel, Trish},
  year = 2008,
  doi = {10.1089/omi.2008.0014},
  month = jun,
  journal = {OMICS: A Journal of Integrative Biology},
  volume = {12},
  number = {2},
  pages = {101--108}
}

P. Andras

Uncertainty in iterated cooperation games

in 2008 IEEE Congress on Evolutionary Computation (IEEE World Congress on Computational Intelligence), p.593-599, Hong Kong, China, June 2008

@INPROCEEDINGS{Andras2008,
  title = {Uncertainty in iterated cooperation games},
  author = {Andras, Peter},
  year = 2008,
  doi = {10.1109/CEC.2008.4630856},
  month = jun,
  booktitle = {2008 IEEE Congress on Evolutionary Computation (IEEE World Congress on Computational Intelligence)},
  pages = {593--599},
  address = {Hong Kong, China}
}

M. Oakley, D. Barthel, Y. Bykov, J. Garibaldi, E. Burke, N. Krasnogor, J. Hirst

Search Strategies in Structural Bioinformatics

in Current Protein & Peptide Science, 9(3):260-274, June 2008

@ARTICLE{Oakley2008,
  title = {Search Strategies in Structural Bioinformatics},
  author = {Oakley, Mark and Barthel, Daniel and Bykov, Yuri and Garibaldi, Jonathan and Burke, Edmund and Krasnogor, Natalio and Hirst, Jonathan},
  year = 2008,
  doi = {10.2174/138920308784534032},
  month = jun,
  journal = {Current Protein & Peptide Science},
  volume = {9},
  number = {3},
  pages = {260--274}
}

S. Sansone, P. Rocca-Serra, M. Brandizi, A. Brazma, D. Field, J. Fostel, A.G. Garrow, J. Gilbert, F. Goodsaid, N. Hardy, P. Jones, A. Lister, M. Miller, N. Morrison, T. Rayner, N. Sklyar, C. Taylor, W. Tong, G. Warner, S. Wiemann

The First RSBI (ISA-TAB) Workshop: “Can a Simple Format Work for Complex Studies?”

in OMICS: A Journal of Integrative Biology, 12(2):143-149, June 2008

@ARTICLE{Sansone2008,
  title = {The First RSBI (ISA-TAB) Workshop: “Can a Simple Format Work for Complex Studies?”},
  author = {Sansone, Susanna-Assunta and Rocca-Serra, Philippe and Brandizi, Marco and Brazma, Alvis and Field, Dawn and Fostel, Jennifer and Garrow, Andrew G. and Gilbert, Jack and Goodsaid, Federico and Hardy, Nigel and Jones, Phil and Lister, Allyson and Miller, Michael and Morrison, Norman and Rayner, Tim and Sklyar, Nataliya and Taylor, Chris and Tong, Weida and Warner, Guy and Wiemann, Stefan},
  year = 2008,
  doi = {10.1089/omi.2008.0019},
  month = jun,
  journal = {OMICS: A Journal of Integrative Biology},
  volume = {12},
  number = {2},
  pages = {143--149}
}

S. Atkinson, C. Chang, H.L. Patrick, C.M.F. Buckley, Y. Wang, R.E. Sockett, M. Cámara, P. Williams

Functional interplay between the Yersinia pseudotuberculosis YpsRI and YtbRI quorum sensing systems modulates swimming motility by controlling expression of flhDC and fliA

in Molecular Microbiology, 69(1):137-151, July 2008

@ARTICLE{Atkinson2008,
  title = {Functional interplay between the Yersinia pseudotuberculosis YpsRI and YtbRI quorum sensing systems modulates swimming motility by controlling expression of flhDC and fliA },
  author = {Atkinson, Steve and Chang, Chien-Yi and Patrick, Hannah L. and Buckley, Catherine M. F. and Wang, Yao and Sockett, R. Elizabeth and Cámara, Miguel and Williams, Paul},
  year = 2008,
  doi = {10.1111/j.1365-2958.2008.06268.x},
  month = jul,
  journal = {Molecular Microbiology},
  volume = {69},
  number = {1},
  pages = {137--151}
}

C.F. Taylor, D. Field, S. Sansone, J. Aerts, R. Apweiler, M. Ashburner, C.A. Ball, P. Binz, M. Bogue, T. Booth, A. Brazma, R.R. Brinkman, A. Michael Clark, E.W. Deutsch, O. Fiehn, J. Fostel, P. Ghazal, F. Gibson, T. Gray, G. Grimes, J.M. Hancock, N.W. Hardy, H. Hermjakob, R.K. Julian, M. Kane, C. Kettner, C. Kinsinger, E. Kolker, M. Kuiper, N.L. Novère, J. Leebens-Mack, S.E. Lewis, et al.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

in Nature Biotechnology, 26(8):889-896, August 2008

@ARTICLE{Taylor2008,
  title = {Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project},
  author = {Taylor, Chris F and Field, Dawn and Sansone, Susanna-Assunta and Aerts, Jan and Apweiler, Rolf and Ashburner, Michael and Ball, Catherine A and Binz, Pierre-Alain and Bogue, Molly and Booth, Tim and Brazma, Alvis and Brinkman, Ryan R and Michael Clark, Adam and Deutsch, Eric W and Fiehn, Oliver and Fostel, Jennifer and Ghazal, Peter and Gibson, Frank and Gray, Tanya and Grimes, Graeme and Hancock, John M and Hardy, Nigel W and Hermjakob, Henning and Julian, Randall K and Kane, Matthew and Kettner, Carsten and Kinsinger, Christopher and Kolker, Eugene and Kuiper, Martin and Novère, Nicolas Le and Leebens-Mack, Jim and Lewis, Suzanna E and Lord, Phillip and Mallon, Ann-Marie and Marthandan, Nishanth and Masuya, Hiroshi and McNally, Ruth and Mehrle, Alexander and Morrison, Norman and Orchard, Sandra and Quackenbush, John and Reecy, James M and Robertson, Donald G and Rocca-Serra, Philippe and Rodriguez, Henry and Rosenfelder, Heiko and Santoyo-Lopez, Javier and Scheuermann, Richard H and Schober, Daniel and Smith, Barry and Snape, Jason and Stoeckert, Christian J and Tipton, Keith and Sterk, Peter and Untergasser, Andreas and Vandesompele, Jo and Wiemann, Stefan},
  year = 2008,
  doi = {10.1038/nbt.1411},
  month = aug,
  journal = {Nature Biotechnology},
  volume = {26},
  number = {8},
  pages = {889--896}
}

M. Kaiser

Mean clustering coefficients: the role of isolated nodes and leafs on clustering measures for small-world networks

in New Journal of Physics, 10(8):083042, August 2008

@ARTICLE{Kaiser2008,
  title = {Mean clustering coefficients: the role of isolated nodes and leafs on clustering measures for small-world networks},
  author = {Kaiser, Marcus},
  year = 2008,
  doi = {10.1088/1367-2630/10/8/083042},
  month = aug,
  journal = {New Journal of Physics},
  volume = {10},
  number = {8},
  pages = {083042}
}

F. Gibson, L. Anderson, G. Babnigg, M. Baker, M. Berth, P. Binz, A. Borthwick, P. Cash, B.W. Day, D.B. Friedman, D. Garland, H.B. Gutstein, C. Hoogland, N.A. Jones, A. Khan, J. Klose, A.I. Lamond, P.F. Lemkin, K.S. Lilley, J. Minden, N.J. Morris, N.W. Paton, M.R. Pisano, J.E. Prime, T. Rabilloud, D.A. Stead, C.F. Taylor, H. Voshol, A. Wipat, A.R. Jones

Guidelines for reporting the use of gel electrophoresis in proteomics

in Nature Biotechnology, 26(8):863-864, August 2008

@ARTICLE{Gibson2008,
  title = {Guidelines for reporting the use of gel electrophoresis in proteomics},
  author = {Gibson, Frank and Anderson, Leigh and Babnigg, Gyorgy and Baker, Mark and Berth, Matthias and Binz, Pierre-Alain and Borthwick, Andy and Cash, Phil and Day, Billy W and Friedman, David B and Garland, Donita and Gutstein, Howard B and Hoogland, Christine and Jones, Neil A and Khan, Alamgir and Klose, Joachim and Lamond, Angus I and Lemkin, Peter F and Lilley, Kathryn S and Minden, Jonathan and Morris, Nicholas J and Paton, Norman W and Pisano, Michael R and Prime, John E and Rabilloud, Thierry and Stead, David A and Taylor, Chris F and Voshol, Hans and Wipat, Anil and Jones, Andrew R},
  year = 2008,
  doi = {10.1038/nbt0808-863},
  month = aug,
  journal = {Nature Biotechnology},
  volume = {26},
  number = {8},
  pages = {863--864}
}

K.M. Edmond, M.A. Quigley, C. Zandoh, S. Danso, C. Hurt, S.O. Agyei, B.R. Kirkwood

Aetiology of stillbirths and neonatal deaths in rural Ghana: implications for health programming in developing countries

in Paediatric and Perinatal Epidemiology, 22(5):430-437, September 2008

@ARTICLE{Edmond2008,
  title = {Aetiology of stillbirths and neonatal deaths in rural Ghana: implications for health programming in developing countries},
  author = {Edmond, Karen M. and Quigley, Maria A. and Zandoh, Charles and Danso, Samuel and Hurt, Chris and Agyei, Seth Owusu and Kirkwood, Betty R.},
  year = 2008,
  doi = {10.1111/j.1365-3016.2008.00961.x},
  month = sep,
  journal = {Paediatric and Perinatal Epidemiology},
  volume = {22},
  number = {5},
  pages = {430--437}
}

K.M. Edmond, M.A. Quigley, C. Zandoh, S. Danso, C. Hurt, S.O. Agyei, B.R. Kirkwood

Diagnostic accuracy of verbal autopsies in ascertaining the causes of stillbirths and neonatal deaths in rural Ghana

in Paediatric and Perinatal Epidemiology, 22(5):417-429, September 2008

@ARTICLE{Edmond2008a,
  title = {Diagnostic accuracy of verbal autopsies in ascertaining the causes of stillbirths and neonatal deaths in rural Ghana},
  author = {Edmond, Karen M. and Quigley, Maria A. and Zandoh, Charles and Danso, Samuel and Hurt, Chris and Agyei, Seth Owusu and Kirkwood, Betty R.},
  year = 2008,
  doi = {10.1111/j.1365-3016.2008.00962.x},
  month = sep,
  journal = {Paediatric and Perinatal Epidemiology},
  volume = {22},
  number = {5},
  pages = {417--429}
}

A.A. Shah, D. Barthel, G. Folino, N. Krasnogor

Performance Evaluation of Protein Structure Comparison Algorithms Under Integrated Resource Management Environment for MPI Jobs

in 2008 IEEE International Symposium on Parallel and Distributed Processing with Applications, p.817-822, Sydney, Australia, December 2008

@INPROCEEDINGS{Shah2008,
  title = {Performance Evaluation of Protein Structure Comparison Algorithms Under Integrated Resource Management Environment for MPI Jobs},
  author = {Shah, Azhar A. and Barthel, Daniel and Folino, Gianluigi and Krasnogor, Natalio},
  year = 2008,
  doi = {10.1109/ISPA.2008.41},
  month = dec,
  booktitle = {2008 IEEE International Symposium on Parallel and Distributed Processing with Applications},
  pages = {817--822},
  address = {Sydney, Australia}
}

A.K. Roopun

Temporal interactions between cortical rhythms

in frontiers in Neuroscience, 2(2):145-154, December 2008

@ARTICLE{Roopun2008a,
  title = {Temporal interactions between cortical rhythms},
  author = {Roopun, Anita K},
  year = 2008,
  doi = {10.3389/neuro.01.034.2008},
  month = dec,
  journal = {frontiers in Neuroscience},
  volume = {2},
  number = {2},
  pages = {145--154}
}

S.G. Addinall, M. Downey, M. Yu, M.K. Zubko, J. Dewar, A. Leake, J. Hallinan, O. Shaw, K. James, D.J. Wilkinson, A. Wipat, D. Durocher, D. Lydall

A Genomewide Suppressor and Enhancer Analysis of cdc13-1 Reveals Varied Cellular Processes Influencing Telomere Capping in Saccharomyces cerevisiae

in Genetics, 180(4):2251-2266, December 2008

@ARTICLE{Addinall2008,
  title = {A Genomewide Suppressor and Enhancer Analysis of cdc13-1 Reveals Varied Cellular Processes Influencing Telomere Capping in Saccharomyces cerevisiae},
  author = {Addinall, S G and Downey, M and Yu, M and Zubko, M K and Dewar, J and Leake, A and Hallinan, J and Shaw, O and James, K and Wilkinson, D J and Wipat, A and Durocher, D and Lydall, D},
  year = 2008,
  doi = {10.1534/genetics.108.092577},
  month = dec,
  journal = {Genetics},
  volume = {180},
  number = {4},
  pages = {2251--2266}
}

J. Bacardit, N. Krasnogor

Fast rule representation for continuous attributes in genetics-based machine learning

in Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, p.1421, Atlanta, GA, USA, 2008

@INPROCEEDINGS{Bacardit2008,
  title = {Fast rule representation for continuous attributes in genetics-based machine learning},
  author = {Bacardit, Jaume and Krasnogor, Natalio},
  year = 2008,
  doi = {10.1145/1389095.1389369},
  booktitle = {Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08},
  pages = {1421},
  address = {Atlanta, GA, USA}
}

F.J. Romero-Campero, H. Cao, M. Camara, N. Krasnogor

Structure and parameter estimation for cell systems biology models

in Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, p.331, Atlanta, GA, USA, 2008

@INPROCEEDINGS{Romero-Campero2008,
  title = {Structure and parameter estimation for cell systems biology models},
  author = {Romero-Campero, Francisco J. and Cao, Hongqing and Camara, Miguel and Krasnogor, Natalio},
  year = 2008,
  doi = {10.1145/1389095.1389153},
  booktitle = {Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08},
  pages = {331},
  address = {Atlanta, GA, USA}
}

J. Smaldon, J. Blakes, N. Krasnogor, D. Lancet

A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics

in Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, p.249, Atlanta, GA, USA, 2008

@INPROCEEDINGS{Smaldon2008,
  title = {A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics},
  author = {Smaldon, James and Blakes, Jonathan and Krasnogor, Natalio and Lancet, Doron},
  year = 2008,
  doi = {10.1145/1389095.1389134},
  booktitle = {Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08},
  pages = {249},
  address = {Atlanta, GA, USA}
}

A.K. Roopun

concatenation underlies interactions between gamma and beta rhythms in neocortex

in Frontiers in Cellular Neuroscience, 2, 2008

@ARTICLE{Roopun2008,
  title = {concatenation underlies interactions between gamma and beta rhythms in neocortex},
  author = {Roopun, Anita K.},
  year = 2008,
  doi = {10.3389/neuro.03.001.2008},
  journal = {Frontiers in Cellular Neuroscience},
  volume = {2}

M. Tabacman, N. Krasnogor, J. Bacardit, I. Loiseau

Learning classifier systems for optimisation problems

in Proceedings of the 2008 GECCO conference companion on Genetic and evolutionary computation - GECCO '08, p.2039, Atlanta, GA, USA, 2008

@INPROCEEDINGS{Tabacman2008,
  title = {Learning classifier systems for optimisation problems},
  author = {Tabacman, Maximiliano and Krasnogor, Natalio and Bacardit, Jaume and Loiseau, Irene},
  year = 2008,
  doi = {10.1145/1388969.1389018},
  booktitle = {Proceedings of the 2008 GECCO conference companion on Genetic and evolutionary computation - GECCO '08},
  pages = {2039},
  address = {Atlanta, GA, USA}
}

J. Bacardit, E. Bernadó-Mansilla, M.V. Butz

Learning Classifier Systems: Looking Back and Glimpsing Ahead

in Learning Classifier Systems, Lecture Notes in Computer Science 4998, p.1-21, 2008

@INCOLLECTION{Bacardit2008d,
  title = {Learning Classifier Systems: Looking Back and Glimpsing Ahead},
  author = {Bacardit, Jaume and Bernadó-Mansilla, Ester and Butz, Martin V.},
  year = 2008,
  doi = {10.1007/978-3-540-88138-4_1},
  booktitle = {Learning Classifier Systems},
  publisher = {Springer Berlin Heidelberg},
  volume = {4998},
  series = {Lecture Notes in Computer Science},
  pages = {1--21}
}

J. Bacardit, M. Stout, J.D. Hirst, N. Krasnogor

Data Mining in Proteomics with Learning Classifier Systems

in Learning Classifier Systems in Data Mining, Studies in Computational Intelligence 125, p.17-46, 2008

@INCOLLECTION{Bacardit2008a,
  title = {Data Mining in Proteomics with Learning Classifier Systems},
  author = {Bacardit, Jaume and Stout, Michael and Hirst, Jonathan D. and Krasnogor, Natalio},
  year = 2008,
  doi = {10.1007/978-3-540-78979-6_2},
  booktitle = {Learning Classifier Systems in Data Mining},
  publisher = {Springer Berlin Heidelberg},
  volume = {125},
  series = {Studies in Computational Intelligence},
  pages = {17--46}
}

C. Lambert, L. Hobley, C. Chang, A. Fenton, M. Capeness, L. Sockett

A Predatory Patchwork: Membrane and Surface Structures of Bdellovibrio bacteriovorus

in Advances in Microbial Physiology, 54, p.313-361, 2008

@INCOLLECTION{Lambert2008,
  title = {A Predatory Patchwork: Membrane and Surface Structures of Bdellovibrio bacteriovorus},
  author = {Lambert, Carey and Hobley, Laura and Chang, Chien-Yi and Fenton, Andrew and Capeness, Michael and Sockett, Liz},
  year = 2008,
  doi = {10.1016/S0065-2911(08)00005-2},
  booktitle = {Advances in Microbial Physiology},
  pages = {313--361}
}

N. Krasnogor, G. Nicosia, M. Pavone, D. Pelta

Nature Inspired Cooperative Strategies for Optimization (NICSO 2007)

Studies in Computational Intelligence 129, Springer Berlin Heidelberg, 2008

@BOOK{Krasnogor2008a,
  title = {Nature Inspired Cooperative Strategies for Optimization (NICSO 2007)},
  author = {Krasnogor, Natalio and Nicosia, Giuseppe and Pavone, Mario and Pelta, David},
  year = 2008,
  doi = {10.1007/978-3-540-78987-1},
  publisher = {Springer Berlin Heidelberg},
  volume = {129},
  series = {Studies in Computational Intelligence}
}

C.C. Hilgetag, M. Kaiser

Organization and Function of Complex Cortical Networks

in Lectures in Supercomputational Neurosciences, p.107-133, 2008

@INCOLLECTION{Hilgetag2008,
  title = {Organization and Function of Complex Cortical Networks},
  author = {Hilgetag, Claus C. and Kaiser, Marcus},
  year = 2008,
  doi = {10.1007/978-3-540-73159-7_4},
  booktitle = {Lectures in Supercomputational Neurosciences},
  publisher = {Springer Berlin Heidelberg},
  pages = {107--133}
}

A. Greenall, G. Lei, D.C. Swan, K. James, L. Wang, H. Peters, A. Wipat, D.J. Wilkinson, D. Lydall

A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection

in Genome Biology, 9(10):R146, 2008

@ARTICLE{Greenall2008,
  title = {A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection},
  author = {Greenall, Amanda and Lei, Guiyuan and Swan, Daniel C and James, Katherine and Wang, Liming and Peters, Heiko and Wipat, Anil and Wilkinson, Darren J and Lydall, David},
  year = 2008,
  doi = {10.1186/gb-2008-9-10-r146},
  journal = {Genome Biology},
  volume = {9},
  number = {10},
  pages = {R146}
}

J. Bacardit, E. Bernadó-Mansilla, M.V. Butz, T. Kovacs, X. Llorà, K. Takadama

Learning Classifier Systems

Lecture Notes in Computer Science 4998, Springer Berlin Heidelberg, 2008

@BOOK{Bacardit2008c,
  title = {Learning Classifier Systems},
  author = {Bacardit, Jaume and Bernadó-Mansilla, Ester and Butz, Martin V. and Kovacs, Tim and Llorà, Xavier and Takadama, Keiki},
  year = 2008,
  doi = {10.1007/978-3-540-88138-4},
  publisher = {Springer Berlin Heidelberg},
  volume = {4998},
  series = {Lecture Notes in Computer Science}
}

J. Bacardit, N. Krasnogor

Empirical Evaluation of Ensemble Techniques for a Pittsburgh Learning Classifier System

in Learning Classifier Systems, Lecture Notes in Computer Science 4998, p.255-268, 2008

@INCOLLECTION{Bacardit2008b,
  title = {Empirical Evaluation of Ensemble Techniques for a Pittsburgh Learning Classifier System},
  author = {Bacardit, Jaume and Krasnogor, Natalio},
  year = 2008,
  doi = {10.1007/978-3-540-88138-4_15},
  booktitle = {Learning Classifier Systems},
  publisher = {Springer Berlin Heidelberg},
  volume = {4998},
  series = {Lecture Notes in Computer Science},
  pages = {255--268}
}

2007

L.J. Steggles, R. Banks, O. Shaw, A. Wipat

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach

in Bioinformatics, 23(3):336-343, February 2007

@ARTICLE{Steggles2007,
  title = {Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach},
  author = {Steggles, L. J. and Banks, R. and Shaw, O. and Wipat, A.},
  year = 2007,
  doi = {10.1093/bioinformatics/btl596},
  month = feb,
  journal = {Bioinformatics},
  volume = {23},
  number = {3},
  pages = {336--343}
}

Y. Ong, N. Krasnogor, H. Ishibuchi

Special Issue on Memetic Algorithms

in IEEE Transactions on Systems, Man and Cybernetics, Part B (Cybernetics), 37(1):2-5, February 2007

@ARTICLE{Ong2007,
  title = {Special Issue on Memetic Algorithms},
  author = {Ong, Yew-Soon and Krasnogor, Natalio and Ishibuchi, Hisao},
  year = 2007,
  doi = {10.1109/TSMCB.2006.883274},
  month = feb,
  journal = {IEEE Transactions on Systems, Man and Cybernetics, Part B (Cybernetics)},
  volume = {37},
  number = {1},
  pages = {2--5}
}

F. Bernardini, M. Gheorghe, N. Krasnogor

Quorum sensing P systems

in Theoretical Computer Science, 371(1-2):20-33, February 2007

@ARTICLE{Bernardini2007,
  title = {Quorum sensing P systems},
  author = {Bernardini, Francesco and Gheorghe, Marian and Krasnogor, Natalio},
  year = 2007,
  doi = {10.1016/j.tcs.2006.10.012},
  month = feb,
  journal = {Theoretical Computer Science},
  volume = {371},
  number = {1-2},
  pages = {20--33}
}

P. Andras, T. Wennekers

Cortical activity pattern computation

in Biosystems, 87(2-3):179-185, February 2007

@ARTICLE{Andras2007a,
  title = {Cortical activity pattern computation},
  author = {Andras, Peter and Wennekers, Thomas},
  year = 2007,
  doi = {10.1016/j.biosystems.2006.09.012},
  month = feb,
  journal = {Biosystems},
  volume = {87},
  number = {2-3},
  pages = {179--185}
}

P. Zuliani

Quantum Programming With Mixed States

in Electronic Notes in Theoretical Computer Science, 170(C):185-199, March 2007

@ARTICLE{Zuliani2007a,
  title = {Quantum Programming With Mixed States},
  author = {Zuliani, Paolo},
  year = 2007,
  doi = {10.1016/j.entcs.2006.12.017},
  month = mar,
  journal = {Electronic Notes in Theoretical Computer Science},
  volume = {170},
  number = {C},
  pages = {185--199}
}

M. Kaiser, M. Görner, C.C. Hilgetag

Criticality of spreading dynamics in hierarchical cluster networks without inhibition

in New Journal of Physics, 9(5):110-110, May 2007

@ARTICLE{Kaiser2007a,
  title = {Criticality of spreading dynamics in hierarchical cluster networks without inhibition},
  author = {Kaiser, M and Görner, M and Hilgetag, C C},
  year = 2007,
  doi = {10.1088/1367-2630/9/5/110},
  month = may,
  journal = {New Journal of Physics},
  volume = {9},
  number = {5},
  pages = {110--110}
}

T. Wennekers, N. Ay, P. Andras

High-resolution multiple-unit EEG in cat auditory cortex reveals large spatio-temporal stochastic interactions

in Biosystems, 89(1-3):190-197, May 2007

@ARTICLE{Wennekers2007,
  title = {High-resolution multiple-unit EEG in cat auditory cortex reveals large spatio-temporal stochastic interactions},
  author = {Wennekers, Thomas and Ay, Nihat and Andras, Peter},
  year = 2007,
  doi = {10.1016/j.biosystems.2006.04.017},
  month = may,
  journal = {Biosystems},
  volume = {89},
  number = {1-3},
  pages = {190--197}
}

M. Kaiser, R. Martin, P. Andras, M.P. Young

Simulation of robustness against lesions of cortical networks

in European Journal of Neuroscience, 25(10):3185-3192, June 2007

@ARTICLE{Kaiser2007c,
  title = {Simulation of robustness against lesions of cortical networks},
  author = {Kaiser, Marcus and Martin, Robert and Andras, Peter and Young, Malcolm P.},
  year = 2007,
  doi = {10.1111/j.1460-9568.2007.05574.x},
  month = jun,
  journal = {European Journal of Neuroscience},
  volume = {25},
  number = {10},
  pages = {3185--3192}
}

M. Kaiser, C.C. Hilgetag

Development of multi-cluster cortical networks by time windows for spatial growth

in Neurocomputing, 70(10-12):1829-1832, June 2007

@ARTICLE{Kaiser2007b,
  title = {Development of multi-cluster cortical networks by time windows for spatial growth},
  author = {Kaiser, Marcus and Hilgetag, Claus C.},
  year = 2007,
  doi = {10.1016/j.neucom.2006.10.060},
  month = jun,
  journal = {Neurocomputing},
  volume = {70},
  number = {10-12},
  pages = {1829--1832}
}

Y. Sun, A. Wipat, M. Pocock, P.A. Lee, K. Flanagan, J.T. Worthington

Exploring Microbial Genome Sequences to Identify Protein Families on the Grid

in IEEE Transactions on Information Technology in Biomedicine, 11(4):435-442, July 2007

@ARTICLE{Sun2007,
  title = {Exploring Microbial Genome Sequences to Identify Protein Families on the Grid},
  author = {Sun, Yudong and Wipat, Anil and Pocock, Matthew and Lee, Peter A. and Flanagan, Keith and Worthington, James T.},
  year = 2007,
  doi = {10.1109/TITB.2007.892913},
  month = jul,
  journal = {IEEE Transactions on Information Technology in Biomedicine},
  volume = {11},
  number = {4},
  pages = {435--442}
}

F. Nisbach, M. Kaiser

Developmental time windows for spatial growth generate multiple-cluster small-world networks

in The European Physical Journal B, 58(2):185-191, July 2007

@ARTICLE{Nisbach2007,
  title = {Developmental time windows for spatial growth generate multiple-cluster small-world networks},
  author = {Nisbach, F. and Kaiser, M.},
  year = 2007,
  doi = {10.1140/epjb/e2007-00214-4},
  month = jul,
  journal = {The European Physical Journal B},
  volume = {58},
  number = {2},
  pages = {185--191}
}

P. Siepmann, C.P. Martin, I. Vancea, P.J. Moriarty, N. Krasnogor

A Genetic Algorithm Approach to Probing the Evolution of Self-Organized Nanostructured Systems

in Nano Letters, 7(7):1985-1990, July 2007

@ARTICLE{Siepmann2007,
  title = {A Genetic Algorithm Approach to Probing the Evolution of Self-Organized Nanostructured Systems},
  author = {Siepmann, Peter and Martin, Christopher P. and Vancea, Ioan and Moriarty, Philip J. and Krasnogor, Natalio},
  year = 2007,
  doi = {10.1021/nl070773m},
  month = jul,
  journal = {Nano Letters},
  volume = {7},
  number = {7},
  pages = {1985--1990}
}

P. Andras, S. Lycett

An advantage of chaotic neural dynamics

in 2007 International Joint Conference on Neural Networks, p.1417-1422, Orlando, FL, USA, August 2007

@INPROCEEDINGS{Andras2007,
  title = {An advantage of chaotic neural dynamics},
  author = {Andras, Peter and Lycett, Samantha},
  year = 2007,
  doi = {10.1109/IJCNN.2007.4371166},
  month = aug,
  booktitle = {2007 International Joint Conference on Neural Networks},
  pages = {1417--1422},
  address = {Orlando, FL, USA}
}

G. Terrazas, M. Gheorghe, G. Kendall, N. Krasnogor

Evolving tiles for automated self-assembly design

in 2007 IEEE Congress on Evolutionary Computation, p.2001-2008, Singapore, September 2007

@INPROCEEDINGS{Terrazas2007,
  title = {Evolving tiles for automated self-assembly design},
  author = {Terrazas, German and Gheorghe, Marian and Kendall, Graham and Krasnogor, Natalio},
  year = 2007,
  doi = {10.1109/CEC.2007.4424719},
  month = sep,
  booktitle = {2007 IEEE Congress on Evolutionary Computation},
  pages = {2001--2008},
  address = {Singapore}
}

S.E. Parkin, P. Andras, G. Morgan

Evolutionary optimization of parameters for distributed virtual environments

in 2007 IEEE Congress on Evolutionary Computation, p.1390-1397, Singapore, September 2007

@INPROCEEDINGS{Parkin2007,
  title = {Evolutionary optimization of parameters for distributed virtual environments},
  author = {Parkin, Simon E. and Andras, Peter and Morgan, Graham},
  year = 2007,
  doi = {10.1109/CEC.2007.4424633},
  month = sep,
  booktitle = {2007 IEEE Congress on Evolutionary Computation},
  pages = {1390--1397},
  address = {Singapore}
}

Q.H. Nguyen, Y.S. Ong, N. Krasnogor

A study on the design issues of Memetic Algorithm

in 2007 IEEE Congress on Evolutionary Computation, p.2390-2397, Singapore, September 2007

@INPROCEEDINGS{Nguyen2007,
  title = {A study on the design issues of Memetic Algorithm},
  author = {Nguyen, Q. H. and Ong, Y. S. and Krasnogor, N.},
  year = 2007,
  doi = {10.1109/CEC.2007.4424770},
  month = sep,
  booktitle = {2007 IEEE Congress on Evolutionary Computation},
  pages = {2390--2397},
  address = {Singapore}
}

H. Fellermann, S. Rasmussen, H. Ziock, R.V. Sol?

Life Cycle of a Minimal Protocell?A Dissipative Particle Dynamics Study

in Artificial Life, 13(4):319-345, October 2007

@ARTICLE{Fellermann2007,
  title = {Life Cycle of a Minimal Protocell?A Dissipative Particle Dynamics Study},
  author = {Fellermann, Harold and Rasmussen, Steen and Ziock, Hans-Joachim and Sol?, Ricard V.},
  year = 2007,
  doi = {10.1162/artl.2007.13.4.319},
  month = oct,
  journal = {Artificial Life},
  volume = {13},
  number = {4},
  pages = {319--345}
}

B.G. Charlton, P. Andras

Evaluating universities using simple scientometric research-output metrics: total citation counts per university for a retrospective seven-year rolling sample

in Science and Public Policy, 34(8):555-563, October 2007

@ARTICLE{Charlton2007a,
  title = {Evaluating universities using simple scientometric research-output metrics: total citation counts per university for a retrospective seven-year rolling sample},
  author = {Charlton, Bruce G and Andras, Peter},
  year = 2007,
  doi = {10.3152/030234207X254413},
  month = oct,
  journal = {Science and Public Policy},
  volume = {34},
  number = {8},
  pages = {555--563}
}

H. Fellermann, R.V. Sole

Minimal model of self-replicating nanocells: a physically embodied information-free scenario

in Philosophical Transactions of the Royal Society B: Biological Sciences, 362(1486):1803-1811, October 2007

@ARTICLE{Fellermann2007a,
  title = {Minimal model of self-replicating nanocells: a physically embodied information-free scenario},
  author = {Fellermann, H. and Sole, R. V},
  year = 2007,
  doi = {10.1098/rstb.2007.2072},
  month = oct,
  journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  volume = {362},
  number = {1486},
  pages = {1803--1811}
}

P. Andras, R. Gwyther, A.A. Madalinski, S.J. Lynden, A. Andras, M.P. Young

Ecological network analysis: an application to the evaluation of effects of pesticide use in an agricultural environment

in Pest Management Science, 63(10):943-953, October 2007

@ARTICLE{Andras2007b,
  title = {Ecological network analysis: an application to the evaluation of effects of pesticide use in an agricultural environment},
  author = {Andras, Peter and Gwyther, Robert and Madalinski, Agnes A and Lynden, Steven J and Andras, Alina and Young, Malcolm P},
  year = 2007,
  doi = {10.1002/ps.1347},
  month = oct,
  journal = {Pest Management Science},
  volume = {63},
  number = {10},
  pages = {943--953}
}

M. Kaiser

Brain architecture: a design for natural computation

in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 365(1861):3033-3045, December 2007

@ARTICLE{Kaiser2007,
  title = {Brain architecture: a design for natural computation},
  author = {Kaiser, M.},
  year = 2007,
  doi = {10.1098/rsta.2007.0007},
  month = dec,
  journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
  volume = {365},
  number = {1861},
  pages = {3033--3045}
}

J. Bacardit, M. Stout, J.D. Hirst, K. Sastry, X. Llorà, N. Krasnogor

Automated alphabet reduction method with evolutionary algorithms for protein structure prediction

in Proceedings of the 9th annual conference on Genetic and evolutionary computation - GECCO '07, p.346, London, England, 2007

@INPROCEEDINGS{Bacardit2007,
  title = {Automated alphabet reduction method with evolutionary algorithms for protein structure prediction},
  author = {Bacardit, Jaume and Stout, Michael and Hirst, Jonathan D. and Sastry, Kumara and Llorà, Xavier and Krasnogor, Natalio},
  year = 2007,
  doi = {10.1145/1276958.1277033},
  booktitle = {Proceedings of the 9th annual conference on Genetic and evolutionary computation  - GECCO '07},
  pages = {346},
  address = {London, England}
}

A.A. Shah, D. Barthel, N. Krasnogor

Grid and Distributed Public Computing Schemes for Structural Proteomics: A Short Overview

in Frontiers of High Performance Computing and Networking ISPA 2007 Workshops, Lecture Notes in Computer Science 4743, p.424-434, 2007

@INCOLLECTION{Shah2007,
  title = {Grid and Distributed Public Computing Schemes for Structural Proteomics: A Short Overview},
  author = {Shah, Azhar Ali and Barthel, Daniel and Krasnogor, Natalio},
  year = 2007,
  doi = {10.1007/978-3-540-74767-3_44},
  booktitle = {Frontiers of High Performance Computing and Networking ISPA 2007 Workshops},
  publisher = {Springer Berlin Heidelberg},
  volume = {4743},
  series = {Lecture Notes in Computer Science},
  pages = {424--434}
}

J. Bacardit, D.E. Goldberg, M.V. Butz

Improving the Performance of a Pittsburgh Learning Classifier System Using a Default Rule

in Learning Classifier Systems, Lecture Notes in Computer Science 4399, p.291-307, 2007

@INCOLLECTION{Bacardit2007a,
  title = {Improving the Performance of a Pittsburgh Learning Classifier System Using a Default Rule},
  author = {Bacardit, Jaume and Goldberg, David E. and Butz, Martin V.},
  year = 2007,
  doi = {10.1007/978-3-540-71231-2_20},
  booktitle = {Learning Classifier Systems},
  publisher = {Springer Berlin Heidelberg},
  volume = {4399},
  series = {Lecture Notes in Computer Science},
  pages = {291--307}
}

J. Bacardit, M.V. Butz

Data Mining in Learning Classifier Systems: Comparing XCS with GAssist

in Learning Classifier Systems, Lecture Notes in Computer Science 4399, p.282-290, 2007

@INCOLLECTION{Bacardit2007b,
  title = {Data Mining in Learning Classifier Systems: Comparing XCS with GAssist},
  author = {Bacardit, Jaume and Butz, Martin V.},
  year = 2007,
  doi = {10.1007/978-3-540-71231-2_19},
  booktitle = {Learning Classifier Systems},
  publisher = {Springer Berlin Heidelberg},
  volume = {4399},
  series = {Lecture Notes in Computer Science},
  pages = {282--290}
}

J. Bacardit, J.M. Garrell

Bloat Control and Generalization Pressure Using the Minimum Description Length Principle for a Pittsburgh Approach Learning Classifier System

in Learning Classifier Systems, Lecture Notes in Computer Science 4399, p.59-79, 2007

@INCOLLECTION{Bacardit2007c,
  title = {Bloat Control and Generalization Pressure Using the Minimum Description Length Principle for a Pittsburgh Approach Learning Classifier System},
  author = {Bacardit, Jaume and Garrell, Josep Maria},
  year = 2007,
  doi = {10.1007/978-3-540-71231-2_5},
  booktitle = {Learning Classifier Systems},
  publisher = {Springer Berlin Heidelberg},
  volume = {4399},
  series = {Lecture Notes in Computer Science},
  pages = {59--79}
}

P. Zuliani

A Formal Derivation of Grover's Quantum Search Algorithm

in First Joint IEEE/IFIP Symposium on Theoretical Aspects of Software Engineering (TASE '07), p.67-74, Shanghai, China, 2007

@INPROCEEDINGS{Zuliani2007,
  title = {A Formal Derivation of Grover's Quantum Search Algorithm},
  author = {Zuliani, Paolo},
  year = 2007,
  doi = {10.1109/TASE.2007.3},
  booktitle = {First Joint IEEE/IFIP Symposium on Theoretical Aspects of Software Engineering (TASE '07)},
  pages = {67--74},
  address = {Shanghai, China}
}

D. Barthel, J.D. Hirst, J. Błażewicz, E.K. Burke, N. Krasnogor

ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information

in BMC Bioinformatics, 8(1):416, 2007

@ARTICLE{Barthel2007,
  title = {ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information},
  author = {Barthel, Daniel and Hirst, Jonathan D and Błażewicz, Jacek and Burke, Edmund K and Krasnogor, Natalio},
  year = 2007,
  doi = {10.1186/1471-2105-8-416},
  journal = {BMC Bioinformatics},
  volume = {8},
  number = {1},
  pages = {416}
}

D. Field, G. Garrity, T. Gray, J. Selengut, P. Sterk, N. Thomson, T. Tatusova, G. Cochrane, F.O. Glöckner, R. Kottmann, A.L. Lister, Y. Tateno, R. Vaughan

eGenomics: Cataloguing Our Complete Genome Collection III

in Comparative and Functional Genomics, 2007:1-7, 2007

@ARTICLE{Field2007,
  title = {eGenomics: Cataloguing Our Complete Genome Collection III},
  author = {Field, Dawn and Garrity, George and Gray, Tanya and Selengut, Jeremy and Sterk, Peter and Thomson, Nick and Tatusova, Tatiana and Cochrane, Guy and Glöckner, Frank Oliver and Kottmann, Renzo and Lister, Allyson L. and Tateno, Yoshio and Vaughan, Robert},
  year = 2007,
  doi = {10.1155/2007/47304},
  journal = {Comparative and Functional Genomics},
  volume = {2007},
  pages = {1--7}
}

B.G. Charlton, P. Andras

Complex Biological Memory Conceptualized as an Abstract Communication System–Human Long Term Memories Grow in Complexity during Sleep and Undergo Selection while Awake

in Neurodynamics of Cognition and Consciousness, p.325-339, 2007

@INCOLLECTION{Charlton2007,
  title = {Complex Biological Memory Conceptualized as an Abstract Communication System–Human Long Term Memories Grow in Complexity during Sleep and Undergo Selection while Awake},
  author = {Charlton, Bruce G. and Andras, Peter},
  year = 2007,
  doi = {10.1007/978-3-540-73267-9_15},
  booktitle = {Neurodynamics of Cognition and Consciousness},
  publisher = {Springer Berlin Heidelberg},
  pages = {325--339}
}

V. Cutello, N. Krasnogor, G. Nicosia, M. Pavone

Immune Algorithm Versus Differential Evolution: A Comparative Case Study Using High Dimensional Function Optimization

in Adaptive and Natural Computing Algorithms, Lecture Notes in Computer Science 4431, p.93-101, 2007

@INCOLLECTION{Cutello2007,
  title = {Immune Algorithm Versus Differential Evolution: A Comparative Case Study Using High Dimensional Function Optimization},
  author = {Cutello, Vincenzo and Krasnogor, Natalio and Nicosia, Giuseppe and Pavone, Mario},
  year = 2007,
  doi = {10.1007/978-3-540-71618-1_11},
  booktitle = {Adaptive and Natural Computing Algorithms},
  publisher = {Springer Berlin Heidelberg},
  volume = {4431},
  series = {Lecture Notes in Computer Science},
  pages = {93--101}
}

K. Wolstencroft, P. Alper, D. Hull, C. Wroe, P.W. Lord, R.D. Stevens, C. Goble

The ^myGrid ontology: bioinformatics service discovery

in International Journal of Bioinformatics Research and Applications, 3(3):303, 2007

@ARTICLE{Wolstencroft2007,
  title = {The ^myGrid ontology: bioinformatics service discovery},
  author = {Wolstencroft, K. and Alper, P. and Hull, D. and Wroe, C. and Lord, P. W. and Stevens, R. D. and Goble, C.a},
  year = 2007,
  doi = {10.1504/IJBRA.2007.015005},
  journal = {International Journal of Bioinformatics Research and Applications},
  volume = {3},
  number = {3},
  pages = {303}
}

N. Miskov-Zivanov, P. Zuliani, E.M. Clarke, J.R. Faeder

Studies of biological networks with statistical model checking

in Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13, p.728-729, Wshington DC, USA, 2007

@INPROCEEDINGS{Miskov-Zivanov2007,
  title = {Studies of biological networks with statistical model checking},
  author = {Miskov-Zivanov, Natasa and Zuliani, Paolo and Clarke, Edmund M. and Faeder, James R.},
  year = 2007,
  doi = {10.1145/2506583.2512390},
  booktitle = {Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13},
  pages = {728--729},
  address = {Wshington DC, USA}
}

L.d.F. Costa, M. Kaiser, C.C. Hilgetag

Predicting the connectivity of primate cortical networks from topological and spatial node properties

in BMC Systems Biology, 1(1):16, 2007

@ARTICLE{Costa2007,
  title = {Predicting the connectivity of primate cortical networks from topological and spatial node properties},
  author = {Costa, Luciano da F and Kaiser, Marcus and Hilgetag, Claus C},
  year = 2007,
  doi = {10.1186/1752-0509-1-16},
  journal = {BMC Systems Biology},
  volume = {1},
  number = {1},
  pages = {16}
}

2006

B.G. Charlton, P. Andras

Globalization in science education: An inevitable and beneficial trend

in Medical Hypotheses, 66(5):869-873, January 2006

@ARTICLE{Charlton2006,
  title = {Globalization in science education: An inevitable and beneficial trend},
  author = {Charlton, Bruce G. and Andras, Peter},
  year = 2006,
  doi = {10.1016/j.mehy.2006.01.002},
  month = jan,
  journal = {Medical Hypotheses},
  volume = {66},
  number = {5},
  pages = {869--873}
}

S. Atkinson, C.-. Chang, R.E. Sockett, M. Camara, P. Williams

Quorum Sensing in Yersinia enterocolitica Controls Swimming and Swarming Motility

in Journal of Bacteriology, 188(4):1451-1461, February 2006

@ARTICLE{Atkinson2006,
  title = {Quorum Sensing in Yersinia enterocolitica Controls Swimming and Swarming Motility},
  author = {Atkinson, S. and Chang, C. -y. and Sockett, R. E. and Camara, M. and Williams, P.},
  year = 2006,
  doi = {10.1128/jb.188.4.1451-1461.2006},
  month = feb,
  journal = {Journal of Bacteriology},
  volume = {188},
  number = {4},
  pages = {1451--1461}
}

B.G. Charlton

How should we rate research?: Counting number of publications may be best research performance measure

in BMJ, 332(7551):1214-1215, May 2006

@ARTICLE{Charlton2006a,
  title = {How should we rate research?: Counting number of publications may be best research performance measure},
  author = {Charlton, B. G},
  year = 2006,
  doi = {10.1136/bmj.332.7551.1214-c},
  month = may,
  journal = {BMJ},
  volume = {332},
  number = {7551},
  pages = {1214--1215}
}

E. Merelli, G. Armano, N. Cannata, F. Corradini, M. d'Inverno, A. Doms, P. Lord, A. Martin, L. Milanesi, S. Moller, M. Schroeder, M. Luck

Agents in bioinformatics, computational and systems biology

in Briefings in Bioinformatics, 8(1):45-59, May 2006

@ARTICLE{Merelli2006,
  title = {Agents in bioinformatics, computational and systems biology},
  author = {Merelli, E. and Armano, G. and Cannata, N. and Corradini, F. and d'Inverno, M. and Doms, A. and Lord, P. and Martin, A. and Milanesi, L. and Moller, S. and Schroeder, M. and Luck, M.},
  year = 2006,
  doi = {10.1093/bib/bbl014},
  month = may,
  journal = {Briefings in Bioinformatics},
  volume = {8},
  number = {1},
  pages = {45--59}
}

P. Andras

Extraction of an activity pattern language from EEG data

in Neurocomputing, 69(10-12):1313-1316, June 2006

@ARTICLE{Andras2006,
  title = {Extraction of an activity pattern language from EEG data},
  author = {Andras, Peter},
  year = 2006,
  doi = {10.1016/j.neucom.2005.12.099},
  month = jun,
  journal = {Neurocomputing},
  volume = {69},
  number = {10-12},
  pages = {1313--1316}
}

O. Shaw, J. Steggles, A. Wipat

Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks

in Electronic Notes in Theoretical Computer Science, 151(3):111-129, June 2006

@ARTICLE{Shaw2006,
  title = {Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks},
  author = {Shaw, Oliver and Steggles, Jason and Wipat, Anil},
  year = 2006,
  doi = {10.1016/j.entcs.2006.03.015},
  month = jun,
  journal = {Electronic Notes in Theoretical Computer Science},
  volume = {151},
  number = {3},
  pages = {111--129}
}

K. Wolstencroft, P. Lord, L. Tabernero, A. Brass, R. Stevens

Protein classification using ontology classification

in Bioinformatics, 22(14):e530-e538, July 2006

@ARTICLE{Wolstencroft2006,
  title = {Protein classification using ontology classification},
  author = {Wolstencroft, K. and Lord, P. and Tabernero, L. and Brass, A. and Stevens, R.},
  year = 2006,
  doi = {10.1093/bioinformatics/btl208},
  month = jul,
  journal = {Bioinformatics},
  volume = {22},
  number = {14},
  pages = {e530--e538}
}

M. Stout, J. Bacardit, J.D. Hirst, J. Blazewicz, N. Krasnogor

Prediction Of Residue Exposure And Contact Number For Simplified Hp Lattice Model Proteins Using Learning Classifier Systems

in Applied Artificial Intelligence, p.601-608, Genova, Italy, July 2006

@INPROCEEDINGS{Stout2006,
  title = {Prediction Of Residue Exposure And Contact Number For Simplified Hp Lattice Model Proteins Using Learning Classifier Systems},
  author = {Stout, Michael and Bacardit, Jaume and Hirst, Jonathan D. and Blazewicz, Jacek and Krasnogor, Natalio},
  year = 2006,
  doi = {10.1142/9789812774118_0085},
  month = jul,
  booktitle = {Applied Artificial Intelligence},
  pages = {601--608},
  address = {Genova, Italy}
}

T. Oinn, M. Greenwood, M. Addis, M.N. Alpdemir, J. Ferris, K. Glover, C. Goble, A. Goderis, D. Hull, D. Marvin, P. Li, P. Lord, M.R. Pocock, M. Senger, R. Stevens, A. Wipat, C. Wroe

Taverna: lessons in creating a workflow environment for the life sciences

in Concurrency and Computation: Practice and Experience, 18(10):1067-1100, August 2006

@ARTICLE{Oinn2006,
  title = {Taverna: lessons in creating a workflow environment for the life sciences},
  author = {Oinn, Tom and Greenwood, Mark and Addis, Matthew and Alpdemir, M. Nedim and Ferris, Justin and Glover, Kevin and Goble, Carole and Goderis, Antoon and Hull, Duncan and Marvin, Darren and Li, Peter and Lord, Phillip and Pocock, Matthew R. and Senger, Martin and Stevens, Robert and Wipat, Anil and Wroe, Chris},
  year = 2006,
  doi = {10.1002/cpe.993},
  month = aug,
  journal = {Concurrency and Computation: Practice and Experience},
  volume = {18},
  number = {10},
  pages = {1067--1100}
}

S.K. Bechhofer, R.D. Stevens, P.W. Lord

GOHSE: Ontology driven linking of biology resources

in Web Semantics: Science, Services and Agents on the World Wide Web, 4(3):155-163, September 2006

@ARTICLE{Bechhofer2006,
  title = {GOHSE: Ontology driven linking of biology resources},
  author = {Bechhofer, S. K. and Stevens, R. D. and Lord, P. W.},
  year = 2006,
  doi = {10.1016/j.websem.2005.09.003},
  month = sep,
  journal = {Web Semantics: Science, Services and Agents on the World Wide Web},
  volume = {4},
  number = {3},
  pages = {155--163}
}

J. Hallinan, A. Wipat

Clustering and Cross-talk in a Yeast Functional Interaction Network

in 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, p.1-8, Toronto, ON, Canada, September 2006

@INPROCEEDINGS{Hallinan2006,
  title = {Clustering and Cross-talk in a Yeast Functional Interaction Network},
  author = {Hallinan, Jennifer and Wipat, Anil},
  year = 2006,
  doi = {10.1109/CIBCB.2006.330983},
  month = sep,
  booktitle = {2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology},
  pages = {1--8},
  address = {Toronto, ON, Canada}
}

L. Cronin, N. Krasnogor, B.G. Davis, C. Alexander, N. Robertson, J.H.G. Steinke, S.L.M. Schroeder, A.N. Khlobystov, G. Cooper, P.M. Gardner, P. Siepmann, B.J. Whitaker, D. Marsh

The imitation game—a computational chemical approach to recognizing life

in Nature Biotechnology, 24(10):1203-1206, October 2006

@ARTICLE{Cronin2006,
  title = {The imitation game—a computational chemical approach to recognizing life},
  author = {Cronin, Leroy and Krasnogor, Natalio and Davis, Benjamin G and Alexander, Cameron and Robertson, Neil and Steinke, Joachim H G and Schroeder, Sven L M and Khlobystov, Andrei N and Cooper, Geoff and Gardner, Paul M and Siepmann, Peter and Whitaker, Benjamin J and Marsh, Dan},
  year = 2006,
  doi = {10.1038/nbt1006-1203},
  month = oct,
  journal = {Nature Biotechnology},
  volume = {24},
  number = {10},
  pages = {1203--1206}
}

M. Lappe, S. Kuhlmann, B. Oerke, M. Kaiser

The fate of object features during perisaccadic mislocalization

in Journal of Vision, 6(11):11-11, November 2006

@ARTICLE{Lappe2006,
  title = {The fate of object features during perisaccadic mislocalization},
  author = {Lappe, M. and Kuhlmann, S. and Oerke, B. and Kaiser, M.},
  year = 2006,
  doi = {10.1167/6.11.11},
  month = nov,
  journal = {Journal of Vision},
  volume = {6},
  number = {11},
  pages = {11--11}
}

C. Lambert, K.A. Morehouse, C. Chang, R.E. Sockett

Bdellovibrio: growth and development during the predatory cycle

in Current Opinion in Microbiology, 9(6):639-644, December 2006

@ARTICLE{Lambert2006,
  title = {Bdellovibrio: growth and development during the predatory cycle},
  author = {Lambert, Carey and Morehouse, Karen A and Chang, Chien-Yi and Sockett, R Elizabeth},
  year = 2006,
  doi = {10.1016/j.mib.2006.10.002},
  month = dec,
  journal = {Current Opinion in Microbiology},
  volume = {9},
  number = {6},
  pages = {639--644}
}

L.J. Steggles, R. Banks, A. Wipat

Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets

in Computational Methods in Systems Biology, Lecture Notes in Computer Science 4210, p.127-141, 2006

@INCOLLECTION{Steggles2006,
  title = {Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets},
  author = {Steggles, L. J. and Banks, Richard and Wipat, Anil},
  year = 2006,
  doi = {10.1007/11885191_9},
  booktitle = {Computational Methods in Systems Biology},
  publisher = {Springer Berlin Heidelberg},
  volume = {4210},
  series = {Lecture Notes in Computer Science},
  pages = {127--141}
}

S.O. Danso

An Exploration of Classification prediction techniques in data mining: the insurance domain

in Master Degree Thesis, Bournemouth University, available online since 2006

J. Bacardit, M. Stout, N. Krasnogor, J.D. Hirst, J. Blazewicz

Coordination number prediction using learning classifier systems

in Proceedings of the 8th annual conference on Genetic and evolutionary computation - GECCO '06, p.247, Seattle, Washington, USA, 2006

@INPROCEEDINGS{Bacardit2006,
  title = {Coordination number prediction using learning classifier systems},
  author = {Bacardit, Jaume and Stout, Michael and Krasnogor, Natalio and Hirst, Jonathan D. and Blazewicz, Jacek},
  year = 2006,
  doi = {10.1145/1143997.1144041},
  booktitle = {Proceedings of the 8th annual conference on Genetic and evolutionary computation  - GECCO '06},
  pages = {247},
  address = {Seattle, Washington, USA}
}

J. Hallinan, D. Bradley, J. Wiles

Effects of Constitutive Gene Expression on the Dynamics of Random Boolean Networks

in 2006 IEEE International Conference on Evolutionary Computation, p.2355-2361, Vancouver, BC, Canada, 2006

@INPROCEEDINGS{Hallinan2006a,
  title = {Effects of Constitutive Gene Expression on the Dynamics of Random Boolean Networks},
  author = {Hallinan, J. and Bradley, D. and Wiles, J.},
  year = 2006,
  doi = {10.1109/CEC.2006.1688599},
  booktitle = {2006 IEEE International Conference on Evolutionary Computation},
  pages = {2355--2361},
  address = {Vancouver, BC, Canada}
}

P. Andras

The Language of Cortical Dynamics

in Computational Life Sciences II, Lecture Notes in Computer Science 4216, p.247-256, 2006

@INCOLLECTION{Andras2006a,
  title = {The Language of Cortical Dynamics},
  author = {Andras, Peter},
  year = 2006,
  doi = {10.1007/11875741_24},
  booktitle = {Computational Life Sciences II},
  publisher = {Springer Berlin Heidelberg},
  volume = {4216},
  series = {Lecture Notes in Computer Science},
  pages = {247--256}
}

M. Stout, J. Bacardit, J.D. Hirst, N. Krasnogor, J. Blazewicz

From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems

in Applications of Evolutionary Computing, Lecture Notes in Computer Science 3907, p.208-220, 2006

@INCOLLECTION{Stout2006a,
  title = {From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems},
  author = {Stout, Michael and Bacardit, Jaume and Hirst, Jonathan D. and Krasnogor, Natalio and Blazewicz, Jacek},
  year = 2006,
  doi = {10.1007/11732242_19},
  booktitle = {Applications of Evolutionary Computing},
  publisher = {Springer Berlin Heidelberg},
  volume = {3907},
  series = {Lecture Notes in Computer Science},
  pages = {208--220}
}

F. Bernardini, M. Gheorghe, N. Krasnogor, R.C. Muniyandi, M.J. Pérez-Jímenez, F.J. Romero-Campero

On P Systems as a Modelling Tool for Biological Systems

in Membrane Computing, Lecture Notes in Computer Science 3850, p.114-133, 2006

@INCOLLECTION{Bernardini2006,
  title = {On P Systems as a Modelling Tool for Biological Systems},
  author = {Bernardini, Francesco and Gheorghe, Marian and Krasnogor, Natalio and Muniyandi, Ravie C. and Pérez-Jímenez, Mario J. and Romero-Campero, Francisco José},
  year = 2006,
  doi = {10.1007/11603047_8},
  booktitle = {Membrane Computing},
  publisher = {Springer Berlin Heidelberg},
  volume = {3850},
  series = {Lecture Notes in Computer Science},
  pages = {114--133}
}

M. Kaiser, C.C. Hilgetag

Nonoptimal Component Placement, but Short Processing Paths, due to Long-Distance Projections in Neural Systems

in PLoS Computational Biology, 2(7):e95, 2006

@ARTICLE{Kaiser2006,
  title = {Nonoptimal Component Placement, but Short Processing Paths, due to Long-Distance Projections in Neural Systems},
  author = {Kaiser, Marcus and Hilgetag, Claus C.},
  year = 2006,
  doi = {10.1371/journal.pcbi.0020095},
  journal = {PLoS Computational Biology},
  volume = {2},
  number = {7},
  pages = {e95}
}

G. Ochoa, G. Escuela, N. Krasnogor

Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding

in Artificial Evolution, Lecture Notes in Computer Science 3871, p.247-258, 2006

@INCOLLECTION{Ochoa2006,
  title = {Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding},
  author = {Ochoa, Gabriela and Escuela, Gabi and Krasnogor, Natalio},
  year = 2006,
  doi = {10.1007/11740698_22},
  booktitle = {Artificial Evolution},
  publisher = {Springer Berlin Heidelberg},
  volume = {3871},
  series = {Lecture Notes in Computer Science},
  pages = {247--258}
}

N. Krasnogor, G. Terrazas, D.A. Pelta, G. Ochoa

A Critical View of the Evolutionary Design of Self-assembling Systems

in Artificial Evolution, Lecture Notes in Computer Science 3871, p.179-188, 2006

@INCOLLECTION{Krasnogor2006,
  title = {A Critical View of the Evolutionary Design of Self-assembling Systems},
  author = {Krasnogor, Natalio and Terrazas, Graciela and Pelta, David A. and Ochoa, Gabriela},
  year = 2006,
  doi = {10.1007/11740698_16},
  booktitle = {Artificial Evolution},
  publisher = {Springer Berlin Heidelberg},
  volume = {3871},
  series = {Lecture Notes in Computer Science},
  pages = {179--188}
}

L. Bianco, D. Pescini, P. Siepmann, N. Krasnogor, F.J. Romero-Campero, M. Gheorghe

Towards a P Systems Pseudomonas Quorum Sensing Model

in Membrane Computing, Lecture Notes in Computer Science 4361, p.197-214, 2006

@INCOLLECTION{Bianco2006,
  title = {Towards a P Systems Pseudomonas Quorum Sensing Model},
  author = {Bianco, Luca and Pescini, Dario and Siepmann, Peter and Krasnogor, Natalio and Romero-Campero, Francisco J. and Gheorghe, Marian},
  year = 2006,
  doi = {10.1007/11963516_13},
  booktitle = {Membrane Computing},
  publisher = {Springer Berlin Heidelberg},
  volume = {4361},
  series = {Lecture Notes in Computer Science},
  pages = {197--214}
}

J. Bacardit, N. Krasnogor

Smart crossover operator with multiple parents for a Pittsburgh learning classifier system

in Proceedings of the 8th annual conference on Genetic and evolutionary computation - GECCO '06, p.1441, Seattle, Washington, USA, 2006

@INPROCEEDINGS{Bacardit2006a,
  title = {Smart crossover operator with multiple parents for a Pittsburgh learning classifier system},
  author = {Bacardit, Jaume and Krasnogor, Natalio},
  year = 2006,
  doi = {10.1145/1143997.1144235},
  booktitle = {Proceedings of the 8th annual conference on Genetic and evolutionary computation  - GECCO '06},
  pages = {1441},
  address = {Seattle, Washington, USA}
}

2005

G. Succi, W. Pedrycz, S. Djokic, P. Zuliani, B. Russo

An Empirical Exploration of the Distributions of the Chidamber and Kemerer Object-Oriented Metrics Suite

in Empirical Software Engineering, 10(1):81-104, January 2005

@ARTICLE{Succi2005,
  title = {An Empirical Exploration of the Distributions of the Chidamber and Kemerer Object-Oriented Metrics Suite},
  author = {Succi, Giancarlo and Pedrycz, Witold and Djokic, Snezana and Zuliani, Paolo and Russo, Barbara},
  year = 2005,
  doi = {10.1023/B:EMSE.0000048324.12188.a2},
  month = jan,
  journal = {Empirical Software Engineering},
  volume = {10},
  number = {1},
  pages = {81--104}
}

P. Andras, C. Andras

The origins of life – the ‘protein interaction world’ hypothesis: protein interactions were the first form of self-reproducing life and nucleic acids evolved later as memory molecules

in Medical Hypotheses, 64(4):678-688, January 2005

@ARTICLE{Andras2005c,
  title = {The origins of life – the ‘protein interaction world’ hypothesis: protein interactions were the first form of self-reproducing life and nucleic acids evolved later as memory molecules},
  author = {Andras, Peter and Andras, Csaba},
  year = 2005,
  doi = {10.1016/j.mehy.2004.11.029},
  month = jan,
  journal = {Medical Hypotheses},
  volume = {64},
  number = {4},
  pages = {678--688}
}

B.G. Charlton, P. Andras

Medical research funding may have over-expanded and be due for collapse

in QJM, 98(1):53-55, January 2005

@ARTICLE{Charlton2005,
  title = {Medical research funding may have over-expanded and be due for collapse},
  author = {Charlton, B. G. and Andras, P.},
  year = 2005,
  doi = {10.1093/qjmed/hci003},
  month = jan,
  journal = {QJM},
  volume = {98},
  number = {1},
  pages = {53--55}
}

B.G. Charlton, P. Andras

Modernizing UK health services: 'short-sharp-shock' reform, the NHS subsistence economy, and the spectre of health care famine

in Journal of Evaluation in Clinical Practice, 11(2):111-119, April 2005

@ARTICLE{Charlton2005a,
  title = {Modernizing UK health services: 'short-sharp-shock' reform, the NHS subsistence economy, and the spectre of health care famine},
  author = {Charlton, Bruce G. and Andras, Peter},
  year = 2005,
  doi = {10.1111/j.1365-2753.2005.00515.x},
  month = apr,
  journal = {Journal of Evaluation in Clinical Practice},
  volume = {11},
  number = {2},
  pages = {111--119}
}

D. Pelta, N. Krasnogor, C. Bousono-Calzon, J.L. Verdegay, J. Hirst, E. Burke

A fuzzy sets based generalization of contact maps for the overlap of protein structures

in Fuzzy Sets and Systems, 152(1):103-123, May 2005

@ARTICLE{Pelta2005,
  title = {A fuzzy sets based generalization of contact maps for the overlap of protein structures},
  author = {Pelta, David and Krasnogor, Natalio and Bousono-Calzon, Carlos and Verdegay, José L. and Hirst, J. and Burke, Edmund},
  year = 2005,
  doi = {10.1016/j.fss.2004.10.017},
  month = may,
  journal = {Fuzzy Sets and Systems},
  volume = {152},
  number = {1},
  pages = {103--123}
}

P. Andras

Neural activity pattern systems

in Neurocomputing, 65-66(C):531-536, June 2005

@ARTICLE{Andras2005,
  title = {Neural activity pattern systems},
  author = {Andras, Peter},
  year = 2005,
  doi = {10.1016/j.neucom.2004.10.041},
  month = jun,
  journal = {Neurocomputing},
  volume = {65-66},
  number = {C},
  pages = {531--536}
}

P. Andras

Pattern computation in neural communication systems

in Biological Cybernetics, 92(6):452-460, June 2005

@ARTICLE{Andras2005a,
  title = {Pattern computation in neural communication systems},
  author = {Andras, Peter},
  year = 2005,
  doi = {10.1007/s00422-005-0572-0},
  month = jun,
  journal = {Biological Cybernetics},
  volume = {92},
  number = {6},
  pages = {452--460}
}

P. Zuliani

Compiling quantum programs

in Acta Informatica, 41(7-8):435-474, June 2005

@ARTICLE{Zuliani2005,
  title = {Compiling quantum programs},
  author = {Zuliani, Paolo},
  year = 2005,
  doi = {10.1007/s00236-005-0165-3},
  month = jun,
  journal = {Acta Informatica},
  volume = {41},
  number = {7-8},
  pages = {435--474}
}

B.G. Charlton, P. Andras

Universities and social progress in modernising societies: how educational expansion has replaced socialism as an instrument of political reform

in Critical Quarterly, 47(1-2):30-39, July 2005

@ARTICLE{Charlton2005c,
  title = {Universities and social progress in modernising societies: how educational expansion has replaced socialism as an instrument of political reform},
  author = {Charlton, Bruce G. and Andras, Peter},
  year = 2005,
  doi = {10.1111/j.0011-1562.2005.00612.x},
  month = jul,
  journal = {Critical Quarterly},
  volume = {47},
  number = {1-2},
  pages = {30--39}
}

B.G. Charlton, P. Andras

The Need for a New Specialist Professional Research System of “Pure” Medical Science

in PLoS Medicine, 2(8):e285, August 2005

@ARTICLE{Charlton2005b,
  title = {The Need for a New Specialist Professional Research System of “Pure” Medical Science},
  author = {Charlton, Bruce G and Andras, Peter},
  year = 2005,
  doi = {10.1371/journal.pmed.0020285},
  month = aug,
  journal = {PLoS Medicine},
  volume = {2},
  number = {8},
  pages = {e285}
}

eprint BibTeX

D. Pelta, J. Gonzales, N. Krasnogor

Protein Structure Comparison through Fuzzy Contact Maps and the Universal Similarity Metric

in Fourth Conference of the European Society for Fuzzy Logic and Technology and 11 Recontres Francophones sur la Logique Floue et ses Applications, p.1124-1129, Barcelona, Spain, September 2005

@INPROCEEDINGS{Pelta2005a,
  title = {Protein Structure Comparison through Fuzzy Contact Maps and the Universal Similarity Metric},
  author = {Pelta, D.A. and Gonzales, J.R. and Krasnogor, N.},
  year = 2005,
  month = sep,
  booktitle = {Fourth Conference of the European Society for Fuzzy Logic and Technology and 11 Recontres Francophones sur la Logique Floue et ses Applications},
  pages = {1124--1129},
  address = {Barcelona, Spain}
}

N. Krasnogor, J. Smith

A Tutorial for Competent Memetic Algorithms: Model, Taxonomy, and Design Issues

in IEEE Transactions on Evolutionary Computation, 9(5):474-488, October 2005

@ARTICLE{Krasnogor2005,
  title = {A Tutorial for Competent Memetic Algorithms: Model, Taxonomy, and Design Issues},
  author = {Krasnogor, N. and Smith, J.},
  year = 2005,
  doi = {10.1109/TEVC.2005.850260},
  month = oct,
  journal = {IEEE Transactions on Evolutionary Computation},
  volume = {9},
  number = {5},
  pages = {474--488}
}

J. Bacardit

Analysis of the initialization stage of a Pittsburgh approach learning classifier system

in Proceedings of the 2005 conference on Genetic and evolutionary computation - GECCO '05, p.1843, Washington DC, USA, 2005

@INPROCEEDINGS{Bacardit2005,
  title = {Analysis of the initialization stage of a Pittsburgh approach learning classifier system},
  author = {Bacardit, Jaume},
  year = 2005,
  doi = {10.1145/1068009.1068321},
  booktitle = {Proceedings of the 2005 conference on Genetic and evolutionary computation  - GECCO '05},
  pages = {1843},
  address = {Washington DC, USA}
}

S. Gustafson, E.K. Burke, N. Krasnogor

On Improving Genetic Programming for Symbolic Regression

in 2005 IEEE Congress on Evolutionary Computation, p.912-919, Edinburgh, Scotland, UK, 2005

@INPROCEEDINGS{Gustafson2005a,
  title = {On Improving Genetic Programming for Symbolic Regression},
  author = {Gustafson, S. and Burke, E. K. and Krasnogor, N.},
  year = 2005,
  doi = {10.1109/CEC.2005.1554780},
  booktitle = {2005 IEEE Congress on Evolutionary Computation},
  pages = {912--919},
  address = {Edinburgh, Scotland, UK}
}

F. Bernardini, M. Gheorghe, N. Krasnogor, J. Giavitto

On Self-assembly in Population P Systems

in Unconventional Computation, Lecture Notes in Computer Science 3699, p.46-57, 2005

@INCOLLECTION{Bernardini2005b,
  title = {On Self-assembly in Population P Systems},
  author = {Bernardini, Francesco and Gheorghe, Marian and Krasnogor, Natalio and Giavitto, Jean-Louis},
  year = 2005,
  doi = {10.1007/11560319_6},
  booktitle = {Unconventional Computation},
  publisher = {Springer Berlin Heidelberg},
  volume = {3699},
  series = {Lecture Notes in Computer Science},
  pages = {46--57}
}

F. Bernardini, M. Gheorghe, N. Krasnogor, G. Terrazas

Membrane Computing — Current Results and Future Problems

in New Computational Paradigms, Lecture Notes in Computer Science 3526, p.49-53, 2005

@INCOLLECTION{Bernardini2005a,
  title = {Membrane Computing — Current Results and Future Problems},
  author = {Bernardini, Francesco and Gheorghe, Marian and Krasnogor, Natalio and Terrazas, German},
  year = 2005,
  doi = {10.1007/11494645_6},
  booktitle = {New Computational Paradigms},
  publisher = {Springer Berlin Heidelberg},
  volume = {3526},
  series = {Lecture Notes in Computer Science},
  pages = {49--53}
}

P. Lord, P. Alper, C. Wroe, C. Goble

Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery

in The Semantic Web: Research and Applications, Lecture Notes in Computer Science 3532, p.17-31, 2005

@INCOLLECTION{Lord2005,
  title = {Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery},
  author = {Lord, Phillip and Alper, Pinar and Wroe, Chris and Goble, Carole},
  year = 2005,
  doi = {10.1007/11431053_2},
  booktitle = {The Semantic Web: Research and Applications},
  publisher = {Springer Berlin Heidelberg},
  volume = {3532},
  series = {Lecture Notes in Computer Science},
  pages = {17--31}
}

Y. Sun, A. Wipat, M. Pocock, P.A. Lee, P. Watson, K. Flanagan, J.T. Worthington

A grid-based system for microbial genome comparison and analysis

in CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005., p.977-984 Vol. 2, Cardiff, Wales, UK, 2005

@INPROCEEDINGS{Sun2005,
  title = {A grid-based system for microbial genome comparison and analysis},
  author = {Sun, Y. and Wipat, Anil and Pocock, M. and Lee, P. A. and Watson, P. and Flanagan, K. and Worthington, J. T.},
  year = 2005,
  doi = {10.1109/CCGRID.2005.1558667},
  booktitle = {CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.},
  pages = {977--984 Vol. 2},
  address = {Cardiff, Wales, UK}
}

K. Wolstencroft, T. Oinn, C. Goble, J. Ferris, C. Wroe, P. Lord, K. Glover, R. Stevens

Panoply of Utilities in Taverna

in First International Conference on e-Science and Grid Computing (e-Science'05), p.156-162, Pittsburg, PA, USA, 2005

@INPROCEEDINGS{Wolstencroft2005a,
  title = {Panoply of Utilities in Taverna},
  author = {Wolstencroft, K. and Oinn, T. and Goble, C. and Ferris, J. and Wroe, C. and Lord, P. and Glover, K. and Stevens, R.},
  year = 2005,
  doi = {10.1109/E-SCIENCE.2005.65},
  booktitle = {First International Conference on e-Science and Grid Computing (e-Science'05)},
  pages = {156--162},
  address = {Pittsburg, PA, USA}
}

J. Hallinan

Evolving Neural Networks for the Classification of Malignancy Associated Changes

in Intelligent Data Engineering and Automated Learning - IDEAL 2005, Lecture Notes in Computer Science 3578, p.382-389, 2005

@INCOLLECTION{Hallinan2005,
  title = {Evolving Neural Networks for the Classification of Malignancy Associated Changes},
  author = {Hallinan, Jennifer},
  year = 2005,
  doi = {10.1007/11508069_50},
  booktitle = {Intelligent Data Engineering and Automated Learning - IDEAL 2005},
  publisher = {Springer Berlin Heidelberg},
  volume = {3578},
  series = {Lecture Notes in Computer Science},
  pages = {382--389}
}

P. Andras, B.G. Charlton

Self-Aware Software – Will It Become a Reality?

in Self-star Properties in Complex Information Systems, Lecture Notes in Computer Science 3460, p.229-259, 2005

@INCOLLECTION{Andras2005b,
  title = {Self-Aware Software – Will It Become a Reality?},
  author = {Andras, Peter and Charlton, Bruce G},
  year = 2005,
  doi = {10.1007/11428589_16},
  booktitle = {Self-star Properties in Complex Information Systems},
  publisher = {Springer Berlin Heidelberg},
  volume = {3460},
  series = {Lecture Notes in Computer Science},
  pages = {229--259}
}

G. Terrazas, N. Krasnogor, G. Kendall, M. Gheorghe

Automated Tile Design for Self-Assembly Conformations

in 2005 IEEE Congress on Evolutionary Computation, p.1808-1814, Edinburgh, Scotland, UK, 2005

@INPROCEEDINGS{Terrazas2005a,
  title = {Automated Tile Design for Self-Assembly Conformations},
  author = {Terrazas, G. and Krasnogor, N. and Kendall, G. and Gheorghe, M.},
  year = 2005,
  doi = {10.1109/CEC.2005.1554907},
  booktitle = {2005 IEEE Congress on Evolutionary Computation},
  pages = {1808--1814},
  address = {Edinburgh, Scotland, UK}
}

G. Terrazas, N. Krasnogor, M. Gheorghe, F. Bernardini, S. Diggle, M. Cámara

An Environment Aware P-System Model of Quorum Sensing

in New Computational Paradigms, Lecture Notes in Computer Science 3526, p.479-485, 2005

@INCOLLECTION{Terrazas2005,
  title = {An Environment Aware P-System Model of Quorum Sensing},
  author = {Terrazas, German and Krasnogor, Natalio and Gheorghe, Marian and Bernardini, Francesco and Diggle, Steve and Cámara, Miguel},
  year = 2005,
  doi = {10.1007/11494645_59},
  booktitle = {New Computational Paradigms},
  publisher = {Springer Berlin Heidelberg},
  volume = {3526},
  series = {Lecture Notes in Computer Science},
  pages = {479--485}
}

F. Bernardini, F.J. Romero-Campero, M. Gheorghe, M.J. Perez-Jimenez, M. Margenstern, S. Verlan, N. Krasnogor

On P systems with bounded parallelism

in Seventh International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC'05), p.8 pp., Timisoara, Romania, 2005

@INPROCEEDINGS{Bernardini2005,
  title = {On P systems with bounded parallelism},
  author = {Bernardini, F. and Romero-Campero, F. J. and Gheorghe, M. and Perez-Jimenez, M. J. and Margenstern, M. and Verlan, S. and Krasnogor, N.},
  year = 2005,
  doi = {10.1109/SYNASC.2005.51},
  booktitle = {Seventh International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC'05)},
  pages = {8 pp.},
  address = {Timisoara, Romania}
}

S. Gustafson, E.K. Burke, N. Krasnogor

The Tree-String Problem: An Artificial Domain for Structure and Content Search

in Genetic Programming, Lecture Notes in Computer Science 3447, p.215-226, 2005

@INCOLLECTION{Gustafson2005,
  title = {The Tree-String Problem: An Artificial Domain for Structure and Content Search},
  author = {Gustafson, Steven and Burke, Edmund K. and Krasnogor, Natalio},
  year = 2005,
  doi = {10.1007/978-3-540-31989-4_19},
  booktitle = {Genetic Programming},
  publisher = {Springer Berlin Heidelberg},
  volume = {3447},
  series = {Lecture Notes in Computer Science},
  pages = {215--226}
}

G. Escuela, G. Ochoa, N. Krasnogor

Evolving L-Systems to Capture Protein Structure Native Conformations

in Genetic Programming, Lecture Notes in Computer Science 3447, p.74-84, 2005

@INCOLLECTION{Escuela2005,
  title = {Evolving L-Systems to Capture Protein Structure Native Conformations},
  author = {Escuela, Gabi and Ochoa, Gabriela and Krasnogor, Natalio},
  year = 2005,
  doi = {10.1007/978-3-540-31989-4_7},
  booktitle = {Genetic Programming},
  publisher = {Springer Berlin Heidelberg},
  volume = {3447},
  series = {Lecture Notes in Computer Science},
  pages = {74--84}
}

K. Garwood, P. Lord, H. Parkinson, N.W. Paton, C. Goble

Pedro Ontology Services: A Framework for Rapid Ontology Markup

in The Semantic Web: Research and Applications, Lecture Notes in Computer Science 3532, p.578-591, 2005

@INCOLLECTION{Garwood2005,
  title = {Pedro Ontology Services: A Framework for Rapid Ontology Markup},
  author = {Garwood, Kevin and Lord, Phillip and Parkinson, Helen and Paton, Norman W. and Goble, Carole},
  year = 2005,
  doi = {10.1007/11431053_39},
  booktitle = {The Semantic Web: Research and Applications},
  publisher = {Springer Berlin Heidelberg},
  volume = {3532},
  series = {Lecture Notes in Computer Science},
  pages = {578--591}
}

K. Wolstencroft, A. Brass, I. Horrocks, P. Lord, U. Sattler, D. Turi, R. Stevens

A Little Semantic Web Goes a Long Way in Biology

in The Semantic Web – ISWC 2005, Lecture Notes in Computer Science 3729, p.786-800, 2005

@INCOLLECTION{Wolstencroft2005,
  title = {A Little Semantic Web Goes a Long Way in Biology},
  author = {Wolstencroft, K. and Brass, A. and Horrocks, I. and Lord, P. and Sattler, U. and Turi, D. and Stevens, R.},
  year = 2005,
  doi = {10.1007/11574620_56},
  booktitle = {The Semantic Web – ISWC 2005},
  publisher = {Springer Berlin Heidelberg},
  volume = {3729},
  series = {Lecture Notes in Computer Science},
  pages = {786--800}
}

W.E. Hart, J.E. Smith, N. Krasnogor

Recent Advances in Memetic Algorithms

Studies in Fuzziness and Soft Computing 166, Springer-Verlag, 2005

@BOOK{Hart2005,
  title = {Recent Advances in Memetic Algorithms},
  author = {Hart, William E. and Smith, J. E. and Krasnogor, N.},
  year = 2005,
  doi = {10.1007/3-540-32363-5},
  publisher = {Springer-Verlag},
  volume = {166},
  series = {Studies in Fuzziness and Soft Computing}
}

A. Goderis, U. Sattler, P. Lord, C. Goble

Seven Bottlenecks to Workflow Reuse and Repurposing

in The Semantic Web – ISWC 2005, Lecture Notes in Computer Science 3729, p.323-337, 2005

@INCOLLECTION{Goderis2005,
  title = {Seven Bottlenecks to Workflow Reuse and Repurposing},
  author = {Goderis, Antoon and Sattler, Ulrike and Lord, Phillip and Goble, Carole},
  year = 2005,
  doi = {10.1007/11574620_25},
  booktitle = {The Semantic Web – ISWC 2005},
  publisher = {Springer Berlin Heidelberg},
  volume = {3729},
  series = {Lecture Notes in Computer Science},
  pages = {323--337}
}

2004

M. Kaiser, M. Lappe

Perisaccadic Mislocalization Orthogonal to Saccade Direction

in Neuron, 41(2):293-300, January 2004

@ARTICLE{Kaiser2004b,
  title = {Perisaccadic Mislocalization Orthogonal to Saccade Direction},
  author = {Kaiser, Marcus and Lappe, Markus},
  year = 2004,
  doi = {10.1016/S0896-6273(03)00849-3},
  month = jan,
  journal = {Neuron},
  volume = {41},
  number = {2},
  pages = {293--300}
}

C. Wroe, C. Goble, M. Greenwood, P. Lord, S. Miles, J. Papay, T. Payne, L. Moreau

Automating experiments using semantic data in a bioinformatics grid

in IEEE Intelligent Systems, 19(1):48-55, January 2004

@ARTICLE{Wroe2004,
  title = {Automating experiments using semantic data in a bioinformatics grid},
  author = {Wroe, C. and Goble, C. and Greenwood, M. and Lord, P. and Miles, S. and Papay, J. and Payne, T. and Moreau, L.},
  year = 2004,
  doi = {10.1109/MIS.2004.1265885},
  month = jan,
  journal = {IEEE Intelligent Systems},
  volume = {19},
  number = {1},
  pages = {48--55}
}

M. Kaiser, C.C. Hilgetag

Spatial growth of real-world networks

in Physical Review E, 69(3), March 2004

@ARTICLE{Kaiser2004a,
  title = {Spatial growth of real-world networks},
  author = {Kaiser, Marcus and Hilgetag, Claus C.},
  year = 2004,
  doi = {10.1103/PhysRevE.69.036103},
  month = mar,
  journal = {Physical Review E},
  volume = {69},
  number = {3}

J. Hallinan

Gene duplication and hierarchical modularity in intracellular interaction networks

in Biosystems, 74(1-3):51-62, April 2004

@ARTICLE{Hallinan2004a,
  title = {Gene duplication and hierarchical modularity in intracellular interaction networks},
  author = {Hallinan, Jennifer},
  year = 2004,
  doi = {10.1016/j.biosystems.2004.02.004},
  month = apr,
  journal = {Biosystems},
  volume = {74},
  number = {1-3},
  pages = {51--62}
}

M. Kaiser, C.C. Hilgetag

Edge vulnerability in neural and metabolic networks

in Biological Cybernetics, 90(5):311-317, May 2004

@ARTICLE{Kaiser2004,
  title = {Edge vulnerability in neural and metabolic networks},
  author = {Kaiser, Marcus and Hilgetag, Claus C.},
  year = 2004,
  doi = {10.1007/s00422-004-0479-1},
  month = may,
  journal = {Biological Cybernetics},
  volume = {90},
  number = {5},
  pages = {311--317}
}

N. Krasnogor, D.A. Pelta

Measuring the similarity of protein structures by means of the universal similarity metric

in Bioinformatics, 20(7):1015-1021, May 2004

@ARTICLE{Krasnogor2004,
  title = {Measuring the similarity of protein structures by means of the universal similarity metric},
  author = {Krasnogor, N. and Pelta, D. A.},
  year = 2004,
  doi = {10.1093/bioinformatics/bth031},
  month = may,
  journal = {Bioinformatics},
  volume = {20},
  number = {7},
  pages = {1015--1021}
}

M. Kaiser, C.C. Hilgetag

Modelling the development of cortical systems networks

in Neurocomputing, 58-60(C):297-302, June 2004

@ARTICLE{Kaiser2004c,
  title = {Modelling the development of cortical systems networks},
  author = {Kaiser, Marcus and Hilgetag, Claus C.},
  year = 2004,
  doi = {10.1016/j.neucom.2004.01.059},
  month = jun,
  journal = {Neurocomputing},
  volume = {58-60},
  number = {C},
  pages = {297--302}
}

P. Andras, B.G. Charlton

European science must embrace modernization

in Nature, 429(6993):699-699, June 2004

@ARTICLE{Andras2004,
  title = {European science must embrace modernization},
  author = {Andras, Peter and Charlton, Bruce G.},
  year = 2004,
  doi = {10.1038/429699a},
  month = jun,
  journal = {Nature},
  volume = {429},
  number = {6993},
  pages = {699--699}
}

Z. Sándor, P. András

Alternative sampling methods for estimating multivariate normal probabilities

in Journal of Econometrics, 120(2):207-234, June 2004

@ARTICLE{Sandor2004,
  title = {Alternative sampling methods for estimating multivariate normal probabilities},
  author = {Sándor, Zsolt and András, Péter},
  year = 2004,
  doi = {10.1016/S0304-4076(03)00212-4},
  month = jun,
  journal = {Journal of Econometrics},
  volume = {120},
  number = {2},
  pages = {207--234}
}

N. Krasnogor

Self Generating Metaheuristics in Bioinformatics: The Proteins Structure Comparison Case

in Genetic Programming and Evolvable Machines, 5(2):181-201, June 2004

@ARTICLE{Krasnogor2004a,
  title = {Self Generating Metaheuristics in Bioinformatics: The Proteins Structure Comparison Case},
  author = {Krasnogor, N.},
  year = 2004,
  doi = {10.1023/B:GENP.0000023687.41210.d7},
  month = jun,
  journal = {Genetic Programming and Evolvable Machines},
  volume = {5},
  number = {2},
  pages = {181--201}
}

P. Andras

Pattern languages: a new paradigm for neurocomputation

in Neurocomputing, 58-60(C):223-228, June 2004

@ARTICLE{Andras2004a,
  title = {Pattern languages: a new paradigm for neurocomputation},
  author = {Andras, Peter},
  year = 2004,
  doi = {10.1016/j.neucom.2004.01.047},
  month = jun,
  journal = {Neurocomputing},
  volume = {58-60},
  number = {C},
  pages = {223--228}
}

R. Stevens, R. McEntire, C. Goble, M. Greenwood, J. Zhao, A. Wipat, P. Li

myGrid and the drug discovery process

in Drug Discovery Today: BIOSILICO, 2(4):140-148, July 2004

@ARTICLE{Stevens2004a,
  title = {myGrid and the drug discovery process},
  author = {Stevens, Robert and McEntire, Robin and Goble, Carole and Greenwood, Mark and Zhao, Jun and Wipat, Anil and Li, Peter},
  year = 2004,
  doi = {10.1016/S1741-8364(04)02412-6},
  month = jul,
  journal = {Drug Discovery Today: BIOSILICO},
  volume = {2},
  number = {4},
  pages = {140--148}
}

B.G. Charlton

Campaign to revitalise academic medicine: Is the bubble due to burst for medical research funding?

in BMJ, 329(7460):294-294, July 2004

@ARTICLE{Charlton2004,
  title = {Campaign to revitalise academic medicine: Is the bubble due to burst for medical research funding?},
  author = {Charlton, B. G},
  year = 2004,
  doi = {10.1136/bmj.329.7460.294-a},
  month = jul,
  journal = {BMJ},
  volume = {329},
  number = {7460},
  pages = {294--294}
}

R.D. Stevens, H.J. Tipney, C.J. Wroe, T.M. Oinn, M. Senger, P.W. Lord, C.A. Goble, A. Brass, M. Tassabehji

Exploring Williams-Beuren syndrome using myGrid

in Bioinformatics, 20(Suppl 1):i303-i310, August 2004

@ARTICLE{Stevens2004,
  title = {Exploring Williams-Beuren syndrome using myGrid},
  author = {Stevens, R. D. and Tipney, H. J. and Wroe, C. J. and Oinn, T. M. and Senger, M. and Lord, P. W. and Goble, C. A. and Brass, A. and Tassabehji, M.},
  year = 2004,
  doi = {10.1093/bioinformatics/bth944},
  month = aug,
  journal = {Bioinformatics},
  volume = {20},
  number = {Suppl 1},
  pages = {i303--i310}
}

M. Lozano, F. Herrera, N. Krasnogor, D. Molina

Real-Coded Memetic Algorithms with Crossover Hill-Climbing

in Evolutionary Computation, 12(3):273-302, September 2004

@ARTICLE{Lozano2004,
  title = {Real-Coded Memetic Algorithms with Crossover Hill-Climbing},
  author = {Lozano, Manuel and Herrera, Francisco and Krasnogor, Natalio and Molina, Daniel},
  year = 2004,
  doi = {10.1162/1063656041774983},
  month = sep,
  journal = {Evolutionary Computation},
  volume = {12},
  number = {3},
  pages = {273--302}
}

W.E. Hart, N. Krasnogor, J.E. Smith

Editorial Introduction Special Issue on Memetic Algorithms

in Evolutionary Computation, 12(3):v-vi, September 2004

@ARTICLE{Hart2004,
  title = {Editorial Introduction Special Issue on Memetic Algorithms},
  author = {Hart, W. E. and Krasnogor, N. and Smith, J. E.},
  year = 2004,
  doi = {10.1162/1063656041775009},
  month = sep,
  journal = {Evolutionary Computation},
  volume = {12},
  number = {3},
  pages = {v--vi}
}

O. Sporns, D. Chialvo, M. Kaiser, C. Hilgetag

Organization, development and function of complex brain networks

in Trends in Cognitive Sciences, 8(9):418-425, September 2004

@ARTICLE{Sporns2004,
  title = {Organization, development and function of complex brain networks},
  author = {Sporns, O and Chialvo, D and Kaiser, M and Hilgetag, C},
  year = 2004,
  doi = {10.1016/j.tics.2004.07.008},
  month = sep,
  journal = {Trends in Cognitive Sciences},
  volume = {8},
  number = {9},
  pages = {418--425}
}

T. Oinn, M. Addis, J. Ferris, D. Marvin, M. Senger, M. Greenwood, T. Carver, K. Glover, M.R. Pocock, A. Wipat, P. Li

Taverna: a tool for the composition and enactment of bioinformatics workflows

in Bioinformatics, 20(17):3045-3054, November 2004

@ARTICLE{Oinn2004,
  title = {Taverna: a tool for the composition and enactment of bioinformatics workflows},
  author = {Oinn, T. and Addis, M. and Ferris, J. and Marvin, D. and Senger, M. and Greenwood, M. and Carver, T. and Glover, K. and Pocock, M. R. and Wipat, A. and Li, P.},
  year = 2004,
  doi = {10.1093/bioinformatics/bth361},
  month = nov,
  journal = {Bioinformatics},
  volume = {20},
  number = {17},
  pages = {3045--3054}
}

O.J. Shaw, C. Harwood, L.J. Steggles, A. Wipat

SARGE: a tool for creation of putative genetic networks

in Bioinformatics, 20(18):3638-3640, December 2004

@ARTICLE{Shaw2004,
  title = {SARGE: a tool for creation of putative genetic networks},
  author = {Shaw, O. J. and Harwood, C. and Steggles, L. J. and Wipat, A.},
  year = 2004,
  doi = {10.1093/bioinformatics/bth395},
  month = dec,
  journal = {Bioinformatics},
  volume = {20},
  number = {18},
  pages = {3638--3640}
}

P. Lord, S. Bechhofer, M.D. Wilkinson, G. Schiltz, D. Gessler, D. Hull, C. Goble, L. Stein

Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt

in The Semantic Web – ISWC 2004, Lecture Notes in Computer Science 3298, p.350-364, 2004

@INCOLLECTION{Lord2004,
  title = {Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt},
  author = {Lord, Phillip and Bechhofer, Sean and Wilkinson, Mark D. and Schiltz, Gary and Gessler, Damian and Hull, Duncan and Goble, Carole and Stein, Lincoln},
  year = 2004,
  doi = {10.1007/978-3-540-30475-3_25},
  booktitle = {The Semantic Web – ISWC 2004},
  publisher = {Springer Berlin Heidelberg},
  volume = {3298},
  series = {Lecture Notes in Computer Science},
  pages = {350--364}
}

J. Aguilar-Ruiz, J. Bacardit, F. Divina

Experimental Evaluation of Discretization Schemes for Rule Induction

in Genetic and Evolutionary Computation – GECCO 2004, Lecture Notes in Computer Science 3102, p.828-839, 2004

@INCOLLECTION{Aguilar-Ruiz2004,
  title = {Experimental Evaluation of Discretization Schemes for Rule Induction},
  author = {Aguilar-Ruiz, Jesus and Bacardit, Jaume and Divina, Federico},
  year = 2004,
  doi = {10.1007/978-3-540-24854-5_85},
  booktitle = {Genetic and Evolutionary Computation – GECCO 2004},
  publisher = {Springer Berlin Heidelberg},
  volume = {3102},
  series = {Lecture Notes in Computer Science},
  pages = {828--839}
}

J. Bacardit, D.E. Goldberg, M.V. Butz, X. Llorà, J.M. Garrell

Speeding-Up Pittsburgh Learning Classifier Systems: Modeling Time and Accuracy

in Parallel Problem Solving from Nature - PPSN VIII, Lecture Notes in Computer Science 3242, p.1021-1031, 2004

@INCOLLECTION{Bacardit2004a,
  title = {Speeding-Up Pittsburgh Learning Classifier Systems: Modeling Time and Accuracy},
  author = {Bacardit, Jaume and Goldberg, David E. and Butz, Martin V. and Llorà, Xavier and Garrell, Josep M.},
  year = 2004,
  doi = {10.1007/978-3-540-30217-9_103},
  booktitle = {Parallel Problem Solving from Nature - PPSN VIII},
  publisher = {Springer Berlin Heidelberg},
  volume = {3242},
  series = {Lecture Notes in Computer Science},
  pages = {1021--1031}
}

J. Bacardit, J.M. Garrell

Analysis and Improvements of the Adaptive Discretization Intervals Knowledge Representation

in Genetic and Evolutionary Computation – GECCO 2004, Lecture Notes in Computer Science 3103, p.726-738, 2004

@INCOLLECTION{Bacardit2004b,
  title = {Analysis and Improvements of the Adaptive Discretization Intervals Knowledge Representation},
  author = {Bacardit, Jaume and Garrell, Josep Maria},
  year = 2004,
  doi = {10.1007/978-3-540-24855-2_88},
  booktitle = {Genetic and Evolutionary Computation – GECCO 2004},
  publisher = {Springer Berlin Heidelberg},
  volume = {3103},
  series = {Lecture Notes in Computer Science},
  pages = {726--738}
}

J.S. Hallinan

Cluster analysis of the p53 genetic regulatory network: topology and biology

in IGARSS 2004. 2004 IEEE International Geoscience and Remote Sensing (IEEE Cat. No.04CH37612), p.1-8, La Jolla, CA, USA, 2004

@INPROCEEDINGS{Hallinan2004,
  title = {Cluster analysis of the p53 genetic regulatory network: topology and biology},
  author = {Hallinan, J. S.},
  year = 2004,
  doi = {10.1109/CIBCB.2004.1393924},
  booktitle = {IGARSS 2004. 2004 IEEE International Geoscience and Remote Sensing (IEEE Cat. No.04CH37612)},
  pages = {1--8},
  address = {La Jolla, CA, USA}
}

eprint BibTeX

J. Bacardit

Pittsburgh Genetics-Based Machine Learning in the Data Mining era: Representations, generalization, and run-time

PhD thesis, Ramon Llull University, Barcelona, Spain, 2004

@PHDTHESIS{Bacardit2004,
  title = {Pittsburgh Genetics-Based Machine Learning in the Data Mining era: Representations, generalization, and run-time},
  author = {Bacardit, Jaume},
  year = 2004,
  school = {Ramon Llull University, Barcelona, Spain}
}

N. Krasnogor, S. Gustafson

A Study on the use of ``self-generation'' in memetic algorithms

in Natural Computing, 3(1):53-76, 2004

@ARTICLE{Krasnogor2004b,
  title = {A Study on the use of ``self-generation'' in memetic algorithms},
  author = {Krasnogor, Natalio and Gustafson, Steven},
  year = 2004,
  doi = {10.1023/B:NACO.0000023419.83147.67},
  journal = {Natural Computing},
  volume = {3},
  number = {1},
  pages = {53--76}
}

O.C. Idowu, S.J. Lynden, M.P. Young, P. Andras

Bacillus subtilis protein interaction network analysis

in Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004., p.592-594, Stanford, CA, USA, 2004

@INPROCEEDINGS{Idowu2004,
  title = {Bacillus subtilis protein interaction network analysis},
  author = {Idowu, O. C. and Lynden, S. J. and Young, M. P. and Andras, P.},
  year = 2004,
  doi = {10.1109/CSB.2004.1332520},
  booktitle = {Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.},
  pages = {592--594},
  address = {Stanford, CA, USA}
}

C.C. Hilgetag, M. Kaiser

Clustered Organization of Cortical Connectivity

in Neuroinformatics, 2(3):353-360, 2004

@ARTICLE{Hilgetag2004,
  title = {Clustered Organization of Cortical Connectivity},
  author = {Hilgetag, Claus C. and Kaiser, Marcus},
  year = 2004,
  doi = {10.1385/NI:2:3:353},
  journal = {Neuroinformatics},
  volume = {2},
  number = {3},
  pages = {353--360}
}

P. Periorellis, O.C. Idowu, S.J. Lynden, M.P. Young, P. Andras

Dealing with complex networks of process interactions: a security measure

in Proceedings. Ninth IEEE International Conference on Engineering of Complex Computer Systems, p.29-36, Florence, Italy, 2004

@INPROCEEDINGS{Periorellis2004,
  title = {Dealing with complex networks of process interactions: a security measure},
  author = {Periorellis, P. and Idowu, O. C. and Lynden, S. J. and Young, M. P. and Andras, P.},
  year = 2004,
  doi = {10.1109/ICECCS.2004.1310901},
  booktitle = {Proceedings. Ninth IEEE International Conference on Engineering of Complex Computer Systems},
  pages = {29--36},
  address = {Florence, Italy}
}

2003

K. Kobayashi, S.D. Ehrlich, A. Albertini, G. Amati, K.K. Andersen, M. Arnaud, K. Asai, S. Ashikaga, S. Aymerich, P. Bessieres, F. Boland, S.C. Brignell, S. Bron, K. Bunai, J. Chapuis, L.C. Christiansen, A. Danchin, M. Debarbouille, E. Dervyn, E. Deuerling, K. Devine, S.K. Devine, O. Dreesen, J. Errington, S. Fillinger, S.J. Foster, Y. Fujita, A. Galizzi, R. Gardan, C. Eschevins, T. Fukushima, K. Haga, et al.

Essential Bacillus subtilis genes

in Proceedings of the National Academy of Sciences, 100(8):4678-4683, April 2003

@ARTICLE{Kobayashi2003,
  title = {Essential Bacillus subtilis genes},
  author = {Kobayashi, K. and Ehrlich, S. D. and Albertini, A. and Amati, G. and Andersen, K. K. and Arnaud, M. and Asai, K. and Ashikaga, S. and Aymerich, S. and Bessieres, P. and Boland, F. and Brignell, S. C. and Bron, S. and Bunai, K. and Chapuis, J. and Christiansen, L. C. and Danchin, A. and Debarbouille, M. and Dervyn, E. and Deuerling, E. and Devine, K. and Devine, S. K. and Dreesen, O. and Errington, J. and Fillinger, S. and Foster, S. J. and Fujita, Y. and Galizzi, A. and Gardan, R. and Eschevins, C. and Fukushima, T. and Haga, K. and Harwood, C. R. and Hecker, M. and Hosoya, D. and Hullo, M. F. and Kakeshita, H. and Karamata, D. and Kasahara, Y. and Kawamura, F. and Koga, K. and Koski, P. and Kuwana, R. and Imamura, D. and Ishimaru, M. and Ishikawa, S. and Ishio, I. and Le Coq, D. and Masson, A. and Mauel, C. and Meima, R. and Mellado, R. P. and Moir, A. and Moriya, S. and Nagakawa, E. and Nanamiya, H. and Nakai, S. and Nygaard, P. and Ogura, M. and Ohanan, T. and O'Reilly, M. and O'Rourke, M. and Pragai, Z. and Pooley, H. M. and Rapoport, G. and Rawlins, J. P. and Rivas, L. A. and Rivolta, C. and Sadaie, A. and Sadaie, Y. and Sarvas, M. and Sato, T. and Saxild, H. H. and Scanlan, E. and Schumann, W. and Seegers, J. F. M. L. and Sekiguchi, J. and Sekowska, A. and Seror, S. J. and Simon, M. and Stragier, P. and Studer, R. and Takamatsu, H. and Tanaka, T. and Takeuchi, M. and Thomaides, H. B. and Vagner, V. and van Dijl, J. M. and Watabe, K. and Wipat, A. and Yamamoto, H. and Yamamoto, M. and Yamamoto, Y. and Yamane, K. and Yata, K. and Yoshida, K. and Yoshikawa, H. and Zuber, U. and Ogasawara, N.},
  year = 2003,
  doi = {10.1073/pnas.0730515100},
  month = apr,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {100},
  number = {8},
  pages = {4678--4683}
}

P. Andras

Comparing neurophysiological measurements of simulated and real brains

in Neurocomputing, 52-54(C):677-682, June 2003

@ARTICLE{Andras2003,
  title = {Comparing neurophysiological measurements of simulated and real brains},
  author = {Andras, Peter},
  year = 2003,
  doi = {10.1016/S0925-2312(02)00729-4},
  month = jun,
  journal = {Neurocomputing},
  volume = {52-54},
  number = {C},
  pages = {677--682}
}

P. Andras, R. Kozma, P. Erdi

Editorial

in Journal of Integrative Neuroscience, 02(01):1-2, June 2003

@ARTICLE{Andras2003a,
  title = {Editorial},
  author = {Andras, Peter and Kozma, Robert and Erdi, Peter},
  year = 2003,
  doi = {10.1142/S0219635203000226},
  month = jun,
  journal = {Journal of Integrative Neuroscience},
  volume = {02},
  number = {01},
  pages = {1--2}
}

P.W. Lord, R.D. Stevens, A. Brass, C.A. Goble

Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation

in Bioinformatics, 19(10):1275-1283, July 2003

@ARTICLE{Lord2003,
  title = {Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation},
  author = {Lord, P. W. and Stevens, R. D. and Brass, A. and Goble, C. A.},
  year = 2003,
  doi = {10.1093/bioinformatics/btg153},
  month = jul,
  journal = {Bioinformatics},
  volume = {19},
  number = {10},
  pages = {1275--1283}
}

M. Teixidó, I. Belda, X. Roselló, S. González, M. Fabre, X. Llorá, J. Bacardit, J.M. Garrell, S. Vilaró, F. Albericio, E. Giralt

Development of a Genetic Algorithm to Design and Identify Peptides that can Cross the Blood-Brain Barrier

in QSAR & Combinatorial Science, 22(7):745-753, October 2003

@ARTICLE{Teixido2003,
  title = {Development of a Genetic Algorithm to Design and Identify Peptides that can Cross the Blood-Brain Barrier},
  author = {Teixidó, Meritxell and Belda, Ignasi and Roselló, Xavier and González, Sonia and Fabre, Myriam and Llorá, Xavier and Bacardit, Jaume and Garrell, Josep M. and Vilaró, Senen and Albericio, Fernando and Giralt, Ernest},
  year = 2003,
  doi = {10.1002/qsar.200320004},
  month = oct,
  journal = {QSAR & Combinatorial Science},
  volume = {22},
  number = {7},
  pages = {745--753}
}

S. Bechhofer, R. Volz, P. Lord

Cooking the Semantic Web with the OWL API

in The Semantic Web - ISWC 2003, Lecture Notes in Computer Science 2870, p.659-675, 2003

@INCOLLECTION{Bechhofer2003,
  title = {Cooking the Semantic Web with the OWL API},
  author = {Bechhofer, Sean and Volz, Raphael and Lord, Phillip},
  year = 2003,
  doi = {10.1007/978-3-540-39718-2_42},
  booktitle = {The Semantic Web - ISWC 2003},
  publisher = {Springer Berlin Heidelberg},
  volume = {2870},
  series = {Lecture Notes in Computer Science},
  pages = {659--675}
}

J. Hallinan

Self-Organization Leads to Hierarchical Modularity in an Internet Community

in Knowledge-Based Intelligent Information and Engineering Systems, Lecture Notes in Computer Science 2773, p.914-920, 2003

@INCOLLECTION{Hallinan2003,
  title = {Self-Organization Leads to Hierarchical Modularity in an Internet Community},
  author = {Hallinan, Jennifer},
  year = 2003,
  doi = {10.1007/978-3-540-45224-9_122},
  booktitle = {Knowledge-Based Intelligent Information and Engineering Systems},
  publisher = {Springer Berlin Heidelberg},
  volume = {2773},
  series = {Lecture Notes in Computer Science},
  pages = {914--920}
}

J. Bacardit, J.M. Garrell

Evolving Multiple Discretizations with Adaptive Intervals for a Pittsburgh Rule-Based Learning Classifier System

in Genetic and Evolutionary Computation — GECCO 2003, Lecture Notes in Computer Science 2724, p.1818-1831, 2003

@INCOLLECTION{Bacardit2003,
  title = {Evolving Multiple Discretizations with Adaptive Intervals for a Pittsburgh Rule-Based Learning Classifier System},
  author = {Bacardit, Jaume and Garrell, Josep Maria},
  year = 2003,
  doi = {10.1007/3-540-45110-2_80},
  booktitle = {Genetic and Evolutionary Computation — GECCO 2003},
  publisher = {Springer Berlin Heidelberg},
  volume = {2724},
  series = {Lecture Notes in Computer Science},
  pages = {1818--1831}
}

R. Stevens, C. Wroe, S. Bechhofer, P. Lord, A. Rector, C. Goble

Building Ontologies in DAML + OIL

in Comparative and Functional Genomics, 4(1):133-141, 2003

@ARTICLE{Stevens2003,
  title = {Building Ontologies in DAML + OIL},
  author = {Stevens, Robert and Wroe, Chris and Bechhofer, Sean and Lord, Phillip and Rector, Alan and Goble, Carole},
  year = 2003,
  doi = {10.1002/cfg.233},
  journal = {Comparative and Functional Genomics},
  volume = {4},
  number = {1},
  pages = {133--141}
}

P. Andras, G. Roberts, J. Lazarus

Environmental Risk, Cooperation, and Communication Complexity

in Adaptive Agents and Multi-Agent Systems, Lecture Notes in Computer Science 2636, p.49-65, 2003

@INCOLLECTION{Andras2003b,
  title = {Environmental Risk, Cooperation, and Communication Complexity},
  author = {Andras, Peter and Roberts, Gilbert and Lazarus, John},
  year = 2003,
  doi = {10.1007/3-540-44826-8_4},
  booktitle = {Adaptive Agents and Multi-Agent Systems},
  publisher = {Springer Berlin Heidelberg},
  volume = {2636},
  series = {Lecture Notes in Computer Science},
  pages = {49--65}
}

2002

P. Andras, S. Panzeri, M. P. Young

Toward statistically valid population decoding models

in Neurocomputing, 44-46(C):269-274, June 2002

@ARTICLE{Andras2002a,
  title = {Toward statistically valid population decoding models},
  author = {Andras, Peter and Panzeri, Stefano and P. Young, Malcolm},
  year = 2002,
  doi = {10.1016/S0925-2312(02)00349-1},
  month = jun,
  journal = {Neurocomputing},
  volume = {44-46},
  number = {C},
  pages = {269--274}
}

P. Andras, B.G. Charlton

Democratic deficit and communication hyper-inflation in health care systems

in Journal of Evaluation in Clinical Practice, 8(3):291-297, August 2002

@ARTICLE{Andras2002b,
  title = {Democratic deficit and communication hyper-inflation in health care systems},
  author = {Andras, Peter and Charlton, Bruce G.},
  year = 2002,
  doi = {10.1046/j.1365-2753.2002.00354.x},
  month = aug,
  journal = {Journal of Evaluation in Clinical Practice},
  volume = {8},
  number = {3},
  pages = {291--297}
}

P.W. Lord, J.N. Selley, T.K. Attwood

CINEMA-MX: a modular multiple alignment editor

in Bioinformatics, 18(10):1402-1403, October 2002

@ARTICLE{Lord2002a,
  title = {CINEMA-MX: a modular multiple alignment editor},
  author = {Lord, P. W. and Selley, J. N. and Attwood, T. K.},
  year = 2002,
  doi = {10.1093/bioinformatics/18.10.1402},
  month = oct,
  journal = {Bioinformatics},
  volume = {18},
  number = {10},
  pages = {1402--1403}
}

P.W. Lord, R.D. Stevens, A. Brass, C.A. Goble

Semantic Similarity Measures As Tools For Exploring The Gene Ontology

in Biocomputing 2003, p.601-612, Kauai, Hawaii, December 2002

@INPROCEEDINGS{Lord2002,
  title = {Semantic Similarity Measures As Tools For Exploring The Gene Ontology},
  author = {Lord, P. W. and Stevens, R. D. and Brass, A. and Goble, C. A.},
  year = 2002,
  doi = {10.1142/9789812776303_0056},
  month = dec,
  booktitle = {Biocomputing 2003},
  pages = {601--612},
  address = {Kauai, Hawaii}
}

N. Geard, J. Wiles, J. Hallinan, B. Tonkes, B. Skellett

A comparison of neutral landscapes - NK, NKp and NKq

in Proceedings of the 2002 Congress on Evolutionary Computation. CEC'02 (Cat. No.02TH8600), p.205-210, Honolulu, HI, USA, 2002

@INPROCEEDINGS{Geard2002,
  title = {A comparison of neutral landscapes - NK, NKp and NKq},
  author = {Geard, N. and Wiles, J. and Hallinan, J. and Tonkes, B. and Skellett, B.},
  year = 2002,
  doi = {10.1109/CEC.2002.1006234},
  booktitle = {Proceedings of the 2002 Congress on Evolutionary Computation. CEC'02 (Cat. No.02TH8600)},
  pages = {205--210},
  address = {Honolulu, HI, USA}
}

P. Andras

Spectrum-based design of sinusoidal RBF neural networks

in Proceedings of the 2002 International Joint Conference on Neural Networks. IJCNN'02 (Cat. No.02CH37290), p.1421-1426, Honolulu, HI, USA, 2002

@INPROCEEDINGS{Andras2002,
  title = {Spectrum-based design of sinusoidal RBF neural networks},
  author = {Andras, P.},
  year = 2002,
  doi = {10.1109/IJCNN.2002.1007725},
  booktitle = {Proceedings of the 2002 International Joint Conference on Neural Networks. IJCNN'02 (Cat. No.02CH37290)},
  pages = {1421--1426},
  address = {Honolulu, HI, USA}
}

E. Burke, S. Gustafson, G. Kendall, N. Krasnogor

Advanced Population Diversity Measures in Genetic Programming

in Parallel Problem Solving from Nature — PPSN VII, Lecture Notes in Computer Science 2439, p.341-350, 2002

@INCOLLECTION{Burke2002,
  title = {Advanced Population Diversity Measures in Genetic Programming},
  author = {Burke, Edmund and Gustafson, Steven and Kendall, Graham and Krasnogor, Natalio},
  year = 2002,
  doi = {10.1007/3-540-45712-7_33},
  booktitle = {Parallel Problem Solving from Nature — PPSN VII},
  publisher = {Springer Berlin Heidelberg},
  volume = {2439},
  series = {Lecture Notes in Computer Science},
  pages = {341--350}
}

J. Bacardit, J. Maria Garrell

Evolution of Multi-adaptive Discretization Intervals for a Rule-Based Genetic Learning System

in Advances in Artificial Intelligence — IBERAMIA 2002, Lecture Notes in Computer Science 2527, p.350-360, 2002

@INCOLLECTION{Bacardit2002,
  title = {Evolution of Multi-adaptive Discretization Intervals for a Rule-Based Genetic Learning System},
  author = {Bacardit, Jaume and Maria Garrell, Josep},
  year = 2002,
  doi = {10.1007/3-540-36131-6_36},
  booktitle = {Advances in Artificial Intelligence — IBERAMIA 2002},
  publisher = {Springer Berlin Heidelberg},
  volume = {2527},
  series = {Lecture Notes in Computer Science},
  pages = {350--360}
}

N. Krasnogor, B.P. Blackburne, E.K. Burke, J.D. Hirst

Multimeme Algorithms for Protein Structure Prediction

in Parallel Problem Solving from Nature — PPSN VII, Lecture Notes in Computer Science 2439, p.769-778, 2002

@INCOLLECTION{Krasnogor2002,
  title = {Multimeme Algorithms for Protein Structure Prediction},
  author = {Krasnogor, N. and Blackburne, B. P. and Burke, E. K. and Hirst, J. D.},
  year = 2002,
  doi = {10.1007/3-540-45712-7_74},
  booktitle = {Parallel Problem Solving from Nature — PPSN VII},
  publisher = {Springer Berlin Heidelberg},
  volume = {2439},
  series = {Lecture Notes in Computer Science},
  pages = {769--778}
}

2001

P. Zuliani

Logical reversibility

in IBM Journal of Research and Development, 45(6):807-818, November 2001

@ARTICLE{Zuliani2001,
  title = {Logical reversibility},
  author = {Zuliani, P.},
  year = 2001,
  doi = {10.1147/rd.456.0807},
  month = nov,
  journal = {IBM Journal of Research and Development},
  volume = {45},
  number = {6},
  pages = {807--818}
}

P.W. Lord, J.R. Reich, A. Mitchell, R.D. Stevens, C.A. Goble

PRECIS: an automated pipeline for producing concise reports about proteins

in Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001), p.57-64, Bethesda, MD, USA, 2001

@INPROCEEDINGS{Lord2001,
  title = {PRECIS: an automated pipeline for producing concise reports about proteins},
  author = {Lord, P. W. and Reich, J. R. and Mitchell, A. and Stevens, R. D. and Goble, C. A.},
  year = 2001,
  doi = {10.1109/BIBE.2001.974412},
  booktitle = {Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)},
  pages = {57--64},
  address = {Bethesda, MD, USA}
}

P. Andras

The Sierpinski brain

in IJCNN'01. International Joint Conference on Neural Networks. Proceedings (Cat. No.01CH37222), p.654-659, Washington, DC, USA, 2001

@INPROCEEDINGS{Andras2001a,
  title = {The Sierpinski brain},
  author = {Andras, P.},
  year = 2001,
  doi = {10.1109/IJCNN.2001.939101},
  booktitle = {IJCNN'01. International Joint Conference on Neural Networks. Proceedings (Cat. No.01CH37222)},
  pages = {654--659},
  address = {Washington, DC, USA}
}

P. András

The Role of Brain Chaos

in Emergent Neural Computational Architectures Based on Neuroscience, Lecture Notes in Computer Science 2036, p.296-310, 2001

@INCOLLECTION{Andras2001,
  title = {The Role of Brain Chaos},
  author = {András, Péter},
  year = 2001,
  doi = {10.1007/3-540-44597-8_22},
  booktitle = {Emergent Neural Computational Architectures Based on Neuroscience},
  publisher = {Springer Berlin Heidelberg},
  volume = {2036},
  series = {Lecture Notes in Computer Science},
  pages = {296--310}
}

C.R. Harwood, S.G. Crawshaw, A. Wipat

From Genome to Function: Systematic Analysis of the Soil Bacterium Bacillus subtilis

in Comparative and Functional Genomics, 2(1):22-24, 2001

@ARTICLE{Harwood2001,
  title = {From Genome to Function: Systematic Analysis of the Soil Bacterium Bacillus subtilis},
  author = {Harwood, Colin R. and Crawshaw, Samuel G. and Wipat, Anil},
  year = 2001,
  doi = {10.1002/cfg.69},
  journal = {Comparative and Functional Genomics},
  volume = {2},
  number = {1},
  pages = {22--24}
}

2000

J.W. Sanders, P. Zuliani

Quantum Programming

in Mathematics of Program Construction, Lecture Notes in Computer Science 1837, p.80-99, 2000

@INCOLLECTION{Sanders2000,
  title = {Quantum Programming},
  author = {Sanders, J. W. and Zuliani, P.},
  year = 2000,
  doi = {10.1007/10722010_6},
  booktitle = {Mathematics of Program Construction},
  publisher = {Springer Berlin Heidelberg},
  volume = {1837},
  series = {Lecture Notes in Computer Science},
  pages = {80--99}
}

J.S. Hallinan, J. Wiles

Modeling the spread of antibiotic resistance

in Proceedings of the 2000 Congress on Evolutionary Computation. CEC00 (Cat. No.00TH8512), p.1152-1159, La Jolla, CA, USA, 2000

@INPROCEEDINGS{Hallinan2000,
  title = {Modeling the spread of antibiotic resistance},
  author = {Hallinan, J. S. and Wiles, J.},
  year = 2000,
  doi = {10.1109/CEC.2000.870778},
  booktitle = {Proceedings of the 2000 Congress on Evolutionary Computation. CEC00 (Cat. No.00TH8512)},
  pages = {1152--1159},
  address = {La Jolla, CA, USA}
}

1999

A. Wipat

The Bacillus subtilis genome sequence: the molecular blueprint of a soil bacterium

in FEMS Microbiology Ecology, 28(1):1-9, January 1999

@ARTICLE{Wipat1999,
  title = {The Bacillus subtilis genome sequence: the molecular blueprint of a soil bacterium},
  author = {Wipat, A},
  year = 1999,
  doi = {10.1016/S0168-6496(98)00080-4},
  month = jan,
  journal = {FEMS Microbiology Ecology},
  volume = {28},
  number = {1},
  pages = {1--9}
}

1998

A. Wipat, S.C. Brignell, B.J. Guy, M. Rose, P.T. Emmerson, C.R. Harwood

The yvsA-yvqA (293 -289 ) region of the Bacillus subtilis chromosome containing genes involved in metal ion uptake and a putative sigma factor

in Microbiology, 144(6):1593-1600, June 1998

@ARTICLE{Wipat1998,
  title = {The yvsA-yvqA (293 -289 ) region of the Bacillus subtilis chromosome containing genes involved in metal ion uptake and a putative sigma factor},
  author = {Wipat, A. and Brignell, S. C. and Guy, B. J. and Rose, M. and Emmerson, P. T. and Harwood, C. R.},
  year = 1998,
  doi = {10.1099/00221287-144-6-1593},
  month = jun,
  journal = {Microbiology},
  volume = {144},
  number = {6},
  pages = {1593--1600}
}

1997

S.F. Gothel, R. Schmid, A. Wipat, N.M. Carter, P.T. Emmerson, C.R. Harwood, M.A. Marahiel

An Internal FK506-Binding Domain is the Catalytic Core of the Prolyl Isomerase Activity Associated with the Bacillus Subtilis Trigger Factor

in European Journal of Biochemistry, 244(1):59-65, February 1997

@ARTICLE{Gothel1997,
  title = {An Internal FK506-Binding Domain is the Catalytic Core of the Prolyl Isomerase Activity Associated with the Bacillus Subtilis Trigger Factor},
  author = {Gothel, Sven F. and Schmid, Roland and Wipat, Anil and Carter, Noel M. and Emmerson, Peter T. and Harwood, Colin R. and Marahiel, Mohamed A.},
  year = 1997,
  doi = {10.1111/j.1432-1033.1997.00059.x},
  month = feb,
  journal = {European Journal of Biochemistry},
  volume = {244},
  number = {1},
  pages = {59--65}
}

1996

C.R. Harwood, A. Wipat

Sequencing and functional analysis of the genome of Bacillus subtilis strain 168

in FEBS Letters, 389(1):84-87, June 1996

@ARTICLE{Harwood1996,
  title = {Sequencing and functional analysis of the genome of Bacillus subtilis strain 168},
  author = {Harwood, Colin R. and Wipat, Anil},
  year = 1996,
  doi = {10.1016/0014-5793(96)00524-8},
  month = jun,
  journal = {FEBS Letters},
  volume = {389},
  number = {1},
  pages = {84--87}
}

A. Wipat, N. Carter, S.C. Brignell, B.J. Guy, K. Piper, J. Sanders, P.T. Emmerson, C.R. Harwood

The dnaB-pheA (256 -240 ) region of the Bacillus subtilis chromosome containing genes responsible for stress responses, the utilization of plant cell walls and primary metabolism

in Microbiology, 142(11):3067-3078, November 1996

@ARTICLE{Wipat1996,
  title = {The dnaB-pheA (256 -240 ) region of the Bacillus subtilis chromosome containing genes responsible for stress responses, the utilization of plant cell walls and primary metabolism},
  author = {Wipat, A. and Carter, N. and Brignell, S. C. and Guy, B. J. and Piper, K. and Sanders, J. and Emmerson, P. T. and Harwood, C. R.},
  year = 1996,
  doi = {10.1099/13500872-142-11-3067},
  month = nov,
  journal = {Microbiology},
  volume = {142},
  number = {11},
  pages = {3067--3078}
}

U. Gerth, A. Wipat, C.R. Harwood, N. Carter, P.T. Emmerson, M. Hecker

Sequence and transcriptional analysis of clpX, a class-III heat-shock gene of Bacillus subtilis

in Gene, 181(1-2):77-83, November 1996

@ARTICLE{Gerth1996,
  title = {Sequence and transcriptional analysis of clpX, a class-III heat-shock gene of Bacillus subtilis},
  author = {Gerth, Ulf and Wipat, Anil and Harwood, Colin R. and Carter, Noel and Emmerson, Peter T. and Hecker, Michael},
  year = 1996,
  doi = {10.1016/S0378-1119(96)00467-2},
  month = nov,
  journal = {Gene},
  volume = {181},
  number = {1-2},
  pages = {77--83}
}

1994