Publications

2017

  • DOI
    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, available online since April 2017
  • 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 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}
    }
    
  • 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 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}
    }
    
  • 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}
    }