Publications

2024

• DOI BibTeX
  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}
  }
  

2023

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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},
    month = apr,
    journal = {mSystems},
    volume = {7},
    number = {2}
  

• DOI BibTeX
  K. James, A. Wipat, S.J. Cockell
  Expanding interactome analyses beyond model eukaryotes
  in Briefings in Functional Genomics, 21(4):243-269, July 2022

  @ARTICLE{James2022b,
    title = {Expanding interactome analyses beyond model eukaryotes},
    author = {James, Katherine and Wipat, Anil and Cockell, Simon J},
    year = 2022,
    doi = {10.1093/bfgp/elac007},
    month = jul,
    journal = {Briefings in Functional Genomics},
    volume = {21},
    number = {4},
    pages = {243--269}
  }
  

• DOI BibTeX
  Z. Wang, J. Li, I. Daly, J. Li
  Machine Learning for Multi-Action Classification of Lower Limbs for BCI
  in 2022 International Conference on Computing, Electronics & Communications Engineering (iCCECE), p.84-89, Southend, United Kingdom, August 2022

  @INPROCEEDINGS{Wang2022,
    title = {Machine Learning for Multi-Action Classification of Lower Limbs for BCI},
    author = {Wang, Zilu and Li, Jichun and Daly, Ian and Li, Junhua},
    year = 2022,
    doi = {10.1109/iCCECE55162.2022.9875092},
    month = aug,
    booktitle = {2022 International Conference on Computing, Electronics & Communications Engineering (iCCECE)},
    pages = {84--89},
    address = {Southend, United Kingdom}
  }
  

• DOI BibTeX
  K. James, A. Alsobhe, S.J. Cockell, A. Wipat, M. Pocock
  Integration of probabilistic functional networks without an external Gold Standard
  in BMC Bioinformatics, 23(1), December 2022

  @ARTICLE{James2022a,
    title = {Integration of probabilistic functional networks without an external Gold Standard},
    author = {James, Katherine and Alsobhe, Aoesha and Cockell, Simon J and Wipat, Anil and Pocock, Matthew},
    year = 2022,
    doi = {10.1186/s12859-022-04834-4},
    month = dec,
    journal = {BMC Bioinformatics},
    volume = {23},
    number = {1}
  

2021

• DOI BibTeX
  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
  in Sensors, 21(7):2436, April 2021

  @ARTICLE{Huang2021,
    title = {Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis},
    author = {Huang, Yiming and Smith, Wendy and Harwood, Colin and Wipat, Anil and Bacardit, Jaume},
    year = 2021,
    doi = {10.3390/s21072436},
    month = apr,
    journal = {Sensors},
    volume = {21},
    number = {7},
    pages = {2436}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  

• DOI BibTeX
  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}
  

2020

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  

• DOI BibTeX
  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 BibTeX
  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}
  }
  

• DOI BibTeX
  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

  @ARTICLE{Koch2020,
    title = {Protein interactions within and between two F‐type type IV secretion systems},
    author = {Koch, Birgit and Callaghan, Melanie M. and Tellechea‐Luzardo, Jonathan and Seeger, Ami Y. and Dillard, Joseph P. and Krasnogor, Natalio},
    year = 2020,
    doi = {10.1111/mmi.14582},
    month = nov,
    journal = {Molecular Microbiology},
    volume = {114},
    number = {5},
    pages = {823--838}
  }
  

2019

• DOI BibTeX
  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},
    year = 2019,
    doi = {10.1016/j.biomaterials.2019.01.028},
    month = apr,
    journal = {Biomaterials},
    volume = {199},
    number = {C},
    pages = {63--75}
  }
  

• DOI BibTeX
  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

  @ARTICLE{Mutha2019,
    title = {Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq},
    author = {Mutha, Naresh V. R. and Mohammed, Waleed K. and Krasnogor, Natalio and Tan, Geok Y. A. and Wee, Wei Yee and Li, Yongming and Choo, Siew Woh and Jakubovics, Nicholas S.},
    year = 2019,
    doi = {10.1038/s41598-019-43979-w},
    month = may,
    journal = {Scientific Reports},
    volume = {9},
    number = {1}
  

• DOI BibTeX
  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

  @ARTICLE{Swan2019,
    title = {Immunodeficiency, autoimmune thrombocytopenia and enterocolitis caused by autosomal recessive deficiency of PIK3CD -encoded phosphoinositide 3-kinase δ},
    author = {Swan, David J. and Aschenbrenner, Dominik and Lamb, Christopher A. and Chakraborty, Krishnendu and Clark, Jonathan and Pandey, Sumeet and Engelhardt, Karin R. and Chen, Rui and Cavounidis, Athena and Ding, Yuchun and Krasnogor, Natalio and Carey, Christopher D. and Acres, Meghan and Needham, Stephanie and Cant, Andrew J. and Arkwright, Peter D. and Chandra, Anita and Okkenhaug, Klaus and Uhlig, Holm H. and Hambleton, Sophie},
    year = 2019,
    doi = {10.3324/haematol.2018.208397},
    month = oct,
    journal = {Haematologica},
    volume = {104},
    number = {10},
    pages = {e483--e486}
  }
  

2018

• DOI BibTeX
  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}
  }
  

2017

• 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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  

• DOI BibTeX
  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}
  }
  

2016

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• 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}
  

2015

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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},
    author = {Eduati, Federica and Mangravite, Lara M and Wang, Tao and Tang, Hao and Bare, J Christopher and Huang, Ruili and Norman, Thea and Kellen, Mike and Menden, Michael P and Yang, Jichen and Zhan, Xiaowei and Zhong, Rui and Xiao, Guanghua and Xia, Menghang and Abdo, Nour and Kosyk, Oksana and Eduati, Federica and Mangravite, Lara M and Bare, J Christopher and Norman, Thea and Kellen, Mike and Menden, Michael P and Friend, Stephen and Stolovitzky, Gustavo and Dearry, Allen and Tice, Raymond R and Huang, Ruili and Xia, Menghang and Simeonov, Anton and Abdo, Nour and Kosyk, Oksana and Rusyn, Ivan and Wright, Fred A and Wang, Tao and Tang, Hao and Zhan, Xiaowei and Yang, Jichen and Zhong, Rui and Xiao, Guanghua and Xie, Yang and Tang, Hao and Yang, Jichen and Wang, Tao and Xiao, Guanghua and Xie, Yang and Alaimo, Salvatore and Amadoz, Alicia and Ammad-Ud-din, Muhammad and Azencott, Chloé-Agathe and Bacardit, Jaume and Barron, Pelham and Bernard, Elsa and Beyer, Andreas and Bin, Shao and van Bömmel, Alena and Borgwardt, Karsten and Brys, April M and Caffrey, Brian and Chang, Jeffrey and Chang, Jungsoo and Christodoulou, Eleni G and Clément-Ziza, Mathieu and Cohen, Trevor and Cowherd, Marianne and Demeyer, Sofie and Dopazo, Joaquin and Elhard, Joel D and Falcao, Andre O and Ferro, Alfredo and Friedenberg, David A and Giugno, Rosalba and Gong, Yunguo and Gorospe, Jenni W and Granville, Courtney A and Grimm, Dominik and Heinig, Matthias and Hernansaiz, Rosa D and Hochreiter, Sepp and Huang, Liang-Chin and Huska, Matthew and Jiao, Yunlong and Klambauer, Günter and Kuhn, Michael and Kursa, Miron Bartosz and Kutum, Rintu and Lazzarini, Nicola and Lee, Inhan and Leung, Michael K K and Lim, Weng Khong and Liu, Charlie and López, Felipe Llinares and Mammana, Alessandro and Mayr, Andreas and Michoel, Tom and Mongiovì, Misael and Moore, Jonathan D and Narasimhan, Ravi and Opiyo, Stephen O and Pandey, Gaurav and Peabody, Andrea L and Perner, Juliane and Pulvirenti, Alfredo and Rawlik, Konrad and Reinhardt, Susanne and Riffle, Carol G and Ruderfer, Douglas and Sander, Aaron J and Savage, Richard S and Scornet, Erwan and Sebastian-Leon, Patricia and Sharan, Roded and Simon-Gabriel, Carl Johann and Stoven, Veronique and Sun, Jingchun and Tang, Hao and Teixeira, Ana L and Tenesa, Albert and Vert, Jean-Philippe and Vingron, Martin and Wang, Tao and Walter, Thomas and Whalen, Sean and Wiśniewska, Zofia and Wu, Yonghui and Xiao, Guanghua and Xie, Yang and Xu, Hua and Yang, Jichen and Zhan, Xiaowei and Zhang, Shihua and Zhao, Junfei and Zheng, W Jim and Zhong, Rui and Ziwei, Dai and Friend, Stephen and Dearry, Allen and Simeonov, Anton and Tice, Raymond R and Rusyn, Ivan and Wright, Fred A and Stolovitzky, Gustavo and Xie, Yang and Saez-Rodriguez, Julio},
    year = 2015,
    doi = {10.1038/nbt.3299},
    month = aug,
    journal = {Nature Biotechnology},
    volume = {33},
    number = {9},
    pages = {933--940}
  }
  

2014

• 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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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
  in PeerJ, 2:e674, December 2014

  @ARTICLE{Alkurashi2014,
    title = {Susceptibility to experimental infection of the invertebrate locusts ( Schistocerca gregaria ) with the apicomplexan parasite Neospora caninum },
    author = {Alkurashi, Mamdowh M. and May, Sean T. and Kong, Kenny and Bacardit, Jaume and Haig, David and Elsheikha, Hany M.},
    year = 2014,
    doi = {10.7717/peerj.674},
    month = dec,
    journal = {PeerJ},
    volume = {2},
    pages = {e674}
  }
  

• URL BibTeX
  G. Misirli, J. Hallinan, R. Röttger, J. Baumbach, A. Wipat
  BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species
  in Journal of Integrative Bioinformatics, 11(2):244, 2014

  @ARTICLE{Misirli2014,
    title = {BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species},
    author = {Misirli, G. and Hallinan, J. and Röttger, R. and Baumbach, J. and Wipat, A.},
    year = 2014,
    url = {http://journal.imbio.de/article.php?aid=244},
    journal = {Journal of Integrative Bioinformatics},
    volume = {11},
    number = {2},
    pages = {244}
  }
  

• DOI BibTeX
  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
  in Applications of Membrane Computing in Systems and Synthetic Biology, Emergence, Complexity and Computation 7, p.1-41, 2014

  @INCOLLECTION{Blakes2014a,
    title = {Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology},
    author = {Blakes, Jonathan and Twycross, Jamie and Konur, Savas and Romero-Campero, Francisco Jose and Krasnogor, Natalio and Gheorghe, Marian},
    year = 2014,
    doi = {10.1007/978-3-319-03191-0_1},
    booktitle = {Applications of Membrane Computing in Systems and Synthetic Biology},
    publisher = {Springer International Publishing},
    volume = {7},
    series = {Emergence, Complexity and Computation},
    pages = {1--41}
  }
  

2013

• DOI BibTeX
  H. Gong, P. Zuliani, E. M. Clarke
  Model Checking a Synchronous Diabetes-Cancer Logical Network
  in Current Bioinformatics, 8(1):9-15, February 2013

  @ARTICLE{Gong2013,
    title = {Model Checking a Synchronous Diabetes-Cancer Logical Network},
    author = {Gong, Haijun and Zuliani, Paolo and M. Clarke, Edmund},
    year = 2013,
    doi = {10.2174/157489313804871542},
    month = feb,
    journal = {Current Bioinformatics},
    volume = {8},
    number = {1},
    pages = {9--15}
  }
  

• DOI BibTeX
  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

  @ARTICLE{Dekkers2013,
    title = {Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed Germination},
    author = {Dekkers, B. J. W. and Pearce, S. and van Bolderen-Veldkamp, R. P. and Marshall, A. and Widera, P. and Gilbert, J. and Drost, H. -g. and Bassel, G. W. and Muller, K. and King, J. R. and Wood, A. T. A. and Grosse, I. and Quint, M. and Krasnogor, N. and Leubner-Metzger, G. and Holdsworth, M. J. and Bentsink, L.},
    year = 2013,
    doi = {10.1104/pp.113.223511},
    month = sep,
    journal = {PLANT PHYSIOLOGY},
    volume = {163},
    number = {1},
    pages = {205--215}
  }
  

• DOI BibTeX
  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

  @ARTICLE{Swan2013,
    title = {Application of Machine Learning to Proteomics Data: Classification and Biomarker Identification in Postgenomics Biology},
    author = {Swan, Anna Louise and Mobasheri, Ali and Allaway, David and Liddell, Susan and Bacardit, Jaume},
    year = 2013,
    doi = {10.1089/omi.2013.0017},
    month = dec,
    journal = {OMICS: A Journal of Integrative Biology},
    volume = {17},
    number = {12},
    pages = {595--610}
  }
  

• DOI BibTeX
  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}
  }
  

2012

• 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}
  }
  

• DOI BibTeX
  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}
  }
  

• 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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

2011

• 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 BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

2010

• 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}
  }
  

• DOI eprint BibTeX
  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}
  }
  

• DOI eprint BibTeX
  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}
  }
  

• DOI eprint BibTeX
  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}
  }
  

• 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}
  }
  

• DOI BibTeX
  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 BibTeX
  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}
  }
  

2009

• DOI BibTeX
  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}
  }
  

• DOI eprint BibTeX
  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}
  }
  

• DOI eprint BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI eprint BibTeX
  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

• DOI eprint BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI eprint BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

2007

• DOI eprint BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI eprint BibTeX
  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}
  }
  

2006

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

• DOI BibTeX
  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}
  }
  

2005

• DOI BibTeX
  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}
  }
  

• 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}
  }
  

• DOI eprint BibTeX
  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}
  }
  

2004

• DOI BibTeX
  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}
  }
  

• DOI eprint BibTeX
  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}
  }
  

2002

• DOI eprint BibTeX
  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}
  }