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 code
    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, available online since May 2017

2016

  • DOI BibTeX
    T.B. Yehezkel, A. Rival, O. Raz, R. Cohen, Z. Marx, M. Camara, J. Dubern, B. Koch, S. Heeb, N. Krasnogor, C. Delattre, E. Shapiro
    Synthesis and cell-free cloning of DNA libraries using programmable microfluidics
    in Nucleic Acids Research, 44(4):e35-e35, February 2016
    @ARTICLE{Yehezkel2015,
      title = {Synthesis and cell-free cloning of DNA libraries using programmable microfluidics},
      author = {Yehezkel, Tuval Ben and Rival, Arnaud and Raz, Ofir and Cohen, Rafael and Marx, Zipora and Camara, Miguel and Dubern, Jean-Frédéric and Koch, Birgit and Heeb, Stephan and Krasnogor, Natalio and Delattre, Cyril and Shapiro, Ehud},
      year = 2016,
      doi = {10.1093/nar/gkv1087},
      month = feb,
      journal = {Nucleic Acids Research},
      volume = {44},
      number = {4},
      pages = {e35--e35}
    }
    
  • 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
    N. Roehner, J. Beal, K. Clancy, B. Bartley, G. Misirli, R. Grünberg, E. Oberortner, M. Pocock, M. Bissell, C. Madsen, T. Nguyen, M. Zhang, Z. Zhang, Z. Zundel, D. Densmore, J.H. Gennari, A. Wipat, H.M. Sauro, C.J. Myers
    Sharing Structure and Function in Biological Design with SBOL 2.0
    in ACS Synthetic Biology, 5(6):498-506, June 2016
    @ARTICLE{Roehner2016,
      title = {Sharing Structure and Function in Biological Design with SBOL 2.0},
      author = {Roehner, Nicholas and Beal, Jacob and Clancy, Kevin and Bartley, Bryan and Misirli, Goksel and Grünberg, Raik and Oberortner, Ernst and Pocock, Matthew and Bissell, Michael and Madsen, Curtis and Nguyen, Tramy and Zhang, Michael and Zhang, Zhen and Zundel, Zach and Densmore, Douglas and Gennari, John H. and Wipat, Anil and Sauro, Herbert M. and Myers, Chris J.},
      year = 2016,
      doi = {10.1021/acssynbio.5b00215},
      month = jun,
      journal = {ACS Synthetic Biology},
      volume = {5},
      number = {6},
      pages = {498--506}
    }
    
  • DOI BibTeX
    J.A. McLaughlin, M. Pocock, G. Mısırlı, C. Madsen, A. Wipat
    VisBOL: Web-Based Tools for Synthetic Biology Design Visualization
    in ACS Synthetic Biology, 5(8):874-876, August 2016
    @ARTICLE{McLaughlin2016,
      title = {VisBOL: Web-Based Tools for Synthetic Biology Design Visualization},
      author = {McLaughlin, James Alastair and Pocock, Matthew and Mısırlı, Göksel and Madsen, Curtis and Wipat, Anil},
      year = 2016,
      doi = {10.1021/acssynbio.5b00244},
      month = aug,
      journal = {ACS Synthetic Biology},
      volume = {5},
      number = {8},
      pages = {874--876}
    }
    
  • DOI BibTeX
    G. Mısırlı, J. Hallinan, M. Pocock, P. Lord, J.A. McLaughlin, H. Sauro, A. Wipat
    Data Integration and Mining for Synthetic Biology Design
    in ACS Synthetic Biology, 5(10):1086-1097, October 2016
    @ARTICLE{Misirli2016,
      title = {Data Integration and Mining for Synthetic Biology Design},
      author = {Mısırlı, Göksel and Hallinan, Jennifer and Pocock, Matthew and Lord, Phillip and McLaughlin, James Alastair and Sauro, Herbert and Wipat, Anil},
      year = 2016,
      doi = {10.1021/acssynbio.5b00295},
      month = oct,
      journal = {ACS Synthetic Biology},
      volume = {5},
      number = {10},
      pages = {1086--1097}
    }
    

2015

  • DOI eprint code BibTeX
    D. Sanassy, P. Widera, N. Krasnogor
    Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology
    in ACS Synthetic Biology, 4(1):39-47, January 2015
    @ARTICLE{Sanassy2014,
      title = {Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology},
      author = {Sanassy, Daven and Widera, Paweł and Krasnogor, Natalio},
      year = 2015,
      doi = {10.1021/sb5001406},
      month = jan,
      journal = {ACS Synthetic Biology},
      volume = {4},
      number = {1},
      pages = {39--47}
    }
    
  • DOI BibTeX
    S. Konur, M. Gheorghe, C. Dragomir, L. Mierla, F. Ipate, N. Krasnogor
    Qualitative and Quantitative Analysis of Systems and Synthetic Biology Constructs using P Systems
    in ACS Synthetic Biology, 4(1):83-92, January 2015
    @ARTICLE{Konur2015,
      title = {Qualitative and Quantitative Analysis of Systems and Synthetic Biology Constructs using P Systems},
      author = {Konur, Savas and Gheorghe, Marian and Dragomir, Ciprian and Mierla, Laurentiu and Ipate, Florentin and Krasnogor, Natalio},
      year = 2015,
      doi = {10.1021/sb500134w},
      month = jan,
      journal = {ACS Synthetic Biology},
      volume = {4},
      number = {1},
      pages = {83--92}
    }
    
  • DOI BibTeX
    N. Roehner, E. Oberortner, M. Pocock, J. Beal, K. Clancy, C. Madsen, G. Misirli, A. Wipat, H. Sauro, C.J. Myers
    Proposed Data Model for the Next Version of the Synthetic Biology Open Language
    in ACS Synthetic Biology, 4(1):57-71, January 2015
    @ARTICLE{Roehner2014,
      title = {Proposed Data Model for the Next Version of the Synthetic Biology Open Language},
      author = {Roehner, Nicholas and Oberortner, Ernst and Pocock, Matthew and Beal, Jacob and Clancy, Kevin and Madsen, Curtis and Misirli, Goksel and Wipat, Anil and Sauro, Herbert and Myers, Chris J.},
      year = 2015,
      doi = {10.1021/sb500176h},
      month = jan,
      journal = {ACS Synthetic Biology},
      volume = {4},
      number = {1},
      pages = {57--71}
    }
    
  • DOI BibTeX
    Z. Zhang, T. Nguyen, N. Roehner, G. Misirli, M. Pocock, E. Oberortner, M. Samineni, Z. Zundel, J. Beal, K. Clancy, A. Wipat, C.J. Myers
    libSBOLj 2.0: A Java Library to Support SBOL 2.0
    in IEEE Life Sciences Letters, 1(4):34-37, December 2015
    @ARTICLE{Zhang2015,
      title = {libSBOLj 2.0: A Java Library to Support SBOL 2.0},
      author = {Zhang, Zhen and Nguyen, Tramy and Roehner, Nicholas and Misirli, Goksel and Pocock, Matthew and Oberortner, Ernst and Samineni, Meher and Zundel, Zach and Beal, Jacob and Clancy, Kevin and Wipat, Anil and Myers, Chris J.},
      year = 2015,
      doi = {10.1109/LLS.2016.2546546},
      month = dec,
      journal = {IEEE Life Sciences Letters},
      volume = {1},
      number = {4},
      pages = {34--37}
    }
    
  • BibTeX
    C. Madsen, G. Misirli, M. Pocock, J. Hallinan, A. Wipat
    SBOL Stack: The One-stop-shop for Storing and Publishing Synthetic Biology Designs
    in 7th International Workshop on Bio-Design Automation, p.26-27, Seattle, US, 2015
    @INPROCEEDINGS{Madsen2015,
      title = {SBOL Stack: The One-stop-shop for Storing and Publishing Synthetic Biology Designs},
      author = {Madsen, Curtis and Misirli, Goksel and Pocock, Matthew and Hallinan, Jennifer and Wipat, Anil},
      year = 2015,
      booktitle = {7th International Workshop on Bio-Design Automation},
      pages = {26--27},
      address = {Seattle, US}
    }
    
  • DOI BibTeX
    B. Bartley, J. Beal, K. Clancy, G. Misirli, N. Roehner, E. Oberortner, M. Pocock, M. Bissell, C. Madsen, T. Nguyen, Z. Zhang, J.H. Gennari, C. Myers, A. Wipat, H. Sauro
    Synthetic Biology Open Language (SBOL) Version 2.0.0
    in Journal of Integrative Bioinformatics, 12(2):272, 2015
    @ARTICLE{Bartley2015,
      title = {Synthetic Biology Open Language (SBOL) Version 2.0.0},
      author = {Bartley, Bryan and Beal, Jacob and Clancy, Kevin and Misirli, Goksel and Roehner, Nicholas and Oberortner, Ernst and Pocock, Matthew and Bissell, Michael and Madsen, Curtis and Nguyen, Tramy and Zhang, Zhen and Gennari, John H and Myers, Chris and Wipat, Anil and Sauro, Herbert},
      year = 2015,
      doi = {10.2390/biecoll-jib-2015-272},
      journal = {Journal of Integrative Bioinformatics},
      volume = {12},
      number = {2},
      pages = {272}
    }
    
  • DOI BibTeX
    C. Myers, K. Clancy, G. Misirli, E. Oberortner, M. Pocock, J. Quinn, N. Roehner, H.M. Sauro
    The Synthetic Biology Open Language
    in Computational Methods in Synthetic Biology, Methods in Molecular Biology 1244, p.323-336, 2015
    @INCOLLECTION{Myers2015,
      title = {The Synthetic Biology Open Language},
      author = {Myers, Chris and Clancy, Kevin and Misirli, Goksel and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline and Roehner, Nicholas and Sauro, Herbert M.},
      year = 2015,
      doi = {10.1007/978-1-4939-1878-2_16},
      booktitle = {Computational Methods in Synthetic Biology},
      publisher = {Springer New York},
      volume = {1244},
      series = {Methods in Molecular Biology},
      pages = {323--336}
    }
    
  • BibTeX
    O. Gilfellon, G. Misirli, C. Madsen, J. Hallinan, P. Zuliani, A. Wipat
    SynBad: An SVP Design Framework
    in 7th International Workshop on Bio-Design Automation, p.49-50, Seattle, US, 2015
    @INPROCEEDINGS{Gilfellon2015,
      title = {SynBad: An SVP Design Framework},
      author = {Gilfellon, Owen and Misirli, Goksel and Madsen, Curtis and Hallinan, Jennifer and Zuliani, Paolo and Wipat, Anil},
      year = 2015,
      booktitle = {7th International Workshop on Bio-Design Automation},
      pages = {49--50},
      address = {Seattle, US}
    }
    

2014

  • DOI BibTeX
    J.S. Hallinan, O. Gilfellon, G. Misirli, A. Wipat
    Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts
    in 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, p.1-8, Honolulu, HI, USA, May 2014
    @INPROCEEDINGS{Hallinan2014,
      title = {Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts},
      author = {Hallinan, J. S. and Gilfellon, O. and Misirli, G. and Wipat, A.},
      year = 2014,
      doi = {10.1109/CIBCB.2014.6845520},
      month = may,
      booktitle = {2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology},
      pages = {1--8},
      address = {Honolulu, HI, USA}
    }
    
  • DOI BibTeX
    M. Galdzicki, K.P. Clancy, E. Oberortner, M. Pocock, J.Y. Quinn, C.A. Rodriguez, N. Roehner, M.L. Wilson, L. Adam, J.C. Anderson, B.A. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grünberg, J. Hallinan, N.J. Hillson, J.D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H.A. Plahar, E. Sirin, G. Stan, A. Villalobos, A. Wipat, J.H. Gennari, C.J. Myers, H.M. Sauro
    The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
    in Nature Biotechnology, 32(6):545-550, June 2014
    @ARTICLE{Galdzicki2014,
      title = {The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology},
      author = {Galdzicki, Michal and Clancy, Kevin P and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline Y and Rodriguez, Cesar A and Roehner, Nicholas and Wilson, Mandy L and Adam, Laura and Anderson, J Christopher and Bartley, Bryan A and Beal, Jacob and Chandran, Deepak and Chen, Joanna and Densmore, Douglas and Endy, Drew and Grünberg, Raik and Hallinan, Jennifer and Hillson, Nathan J and Johnson, Jeffrey D and Kuchinsky, Allan and Lux, Matthew and Misirli, Goksel and Peccoud, Jean and Plahar, Hector A and Sirin, Evren and Stan, Guy-Bart and Villalobos, Alan and Wipat, Anil and Gennari, John H and Myers, Chris J and Sauro, Herbert M},
      year = 2014,
      doi = {10.1038/nbt.2891},
      month = jun,
      journal = {Nature Biotechnology},
      volume = {32},
      number = {6},
      pages = {545--550}
    }
    
  • 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
    S. Konur, M. Gheorge, C. Dragomir, F. Ipate, N. Krasnogor
    Conventional verification for unconventional computing: a genetic XOR gate example
    in Fundamenta Informaticae, 134(1-2):97-110, November 2014
    @ARTICLE{Konur2014,
      title = {Conventional verification for unconventional computing: a genetic XOR gate example},
      author = {Konur, Savas and Gheorge, Marian and Dragomir, Ciprian and Ipate, Florin and Krasnogor, Natalio},
      year = 2014,
      doi = {10.3233/FI-2014-1093},
      month = nov,
      journal = {Fundamenta Informaticae},
      volume = {134},
      number = {1-2},
      pages = {97--110}
    }
    
  • DOI BibTeX
    J.C. Chaplin, N. Krasnogor, N.A. Russell
    Photochromic molecular implementations of universal computation
    in Biosystems, 126(C):12-26, December 2014
    @ARTICLE{Chaplin2014,
      title = {Photochromic molecular implementations of universal computation},
      author = {Chaplin, Jack C. and Krasnogor, Natalio and Russell, Noah A.},
      year = 2014,
      doi = {10.1016/j.biosystems.2014.09.004},
      month = dec,
      journal = {Biosystems},
      volume = {126},
      number = {C},
      pages = {12--26}
    }
    
  • DOI BibTeX
    C. Madsen, Z. Zhang, N. Roehner, C. Winstead, C. Myers
    Stochastic Model Checking of Genetic Circuits
    in ACM Journal on Emerging Technologies in Computing Systems, 11(3):1-21, December 2014
    @ARTICLE{Madsen2014,
      title = {Stochastic Model Checking of Genetic Circuits},
      author = {Madsen, Curtis and Zhang, Zhen and Roehner, Nicholas and Winstead, Chris and Myers, Chris},
      year = 2014,
      doi = {10.1145/2644817},
      month = dec,
      journal = {ACM Journal on Emerging Technologies in Computing Systems},
      volume = {11},
      number = {3},
      pages = {1--21}
    }
    
  • DOI BibTeX
    H. Fellermann, M. Hadorn, R.M. Füchslin, N. Krasnogor
    Formalizing Modularization and Data Hiding in Synthetic Biology
    in ACM Journal on Emerging Technologies in Computing Systems, 11(3):1-20, December 2014
    @ARTICLE{Fellermann2014,
      title = {Formalizing Modularization and Data Hiding in Synthetic Biology},
      author = {Fellermann, Harold and Hadorn, Maik and Füchslin, Rudolf M. and Krasnogor, Natalio},
      year = 2014,
      doi = {10.1145/2667231},
      month = dec,
      journal = {ACM Journal on Emerging Technologies in Computing Systems},
      volume = {11},
      number = {3},
      pages = {1--20}
    }
    
  • DOI BibTeX
    G. Misirli, J. Hallinan, A. Wipat
    Composable Modular Models for Synthetic Biology
    in ACM Journal on Emerging Technologies in Computing Systems, 11(3):1-19, December 2014
    @ARTICLE{Misirli2014a,
      title = {Composable Modular Models for Synthetic Biology},
      author = {Misirli, Goksel and Hallinan, Jennifer and Wipat, Anil},
      year = 2014,
      doi = {10.1145/2631921},
      month = dec,
      journal = {ACM Journal on Emerging Technologies in Computing Systems},
      volume = {11},
      number = {3},
      pages = {1--19}
    }
    
  • DOI BibTeX
    H. Fellermann, N. Krasnogor
    Chemical Production and Molecular Computing in Addressable Reaction Compartments
    in Language, Life, Limits, Lecture Notes in Computer Science 8493, p.173-182, 2014
    @INCOLLECTION{Fellermann2014a,
      title = {Chemical Production and Molecular Computing in Addressable Reaction Compartments},
      author = {Fellermann, Harold and Krasnogor, Natalio},
      year = 2014,
      doi = {10.1007/978-3-319-08019-2_18},
      booktitle = {Language, Life, Limits},
      publisher = {Springer International Publishing},
      volume = {8493},
      series = {Lecture Notes in Computer Science},
      pages = {173--182}
    }
    
  • 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
    L.T. Lui, X. Xue, C. Sui, A. Brown, D.I. Pritchard, N. Halliday, K. Winzer, S.M. Howdle, F. Fernandez-Trillo, N. Krasnogor, C. Alexander
    Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes
    in Nature Chemistry, 5(12):1058-1065, November 2013
    @ARTICLE{Lui2013,
      title = {Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes},
      author = {Lui, Leong T. and Xue, Xuan and Sui, Cheng and Brown, Alan and Pritchard, David I. and Halliday, Nigel and Winzer, Klaus and Howdle, Steven M. and Fernandez-Trillo, Francisco and Krasnogor, Natalio and Alexander, Cameron},
      year = 2013,
      doi = {10.1038/nchem.1793},
      month = nov,
      journal = {Nature Chemistry},
      volume = {5},
      number = {12},
      pages = {1058--1065}
    }
    
  • DOI BibTeX
    G. Misirli, A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby, J. Hallinan
    BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology
    in Journal of Integrative Bioinformatics, 10(2):224, 2013
    @ARTICLE{Misirli2013,
      title = {BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology},
      author = {Misirli, G. and Wipat, A. and Mullen, J. and James, K. and Pocock, M. and Smith, W. and Allenby, N. and Hallinan, J.},
      year = 2013,
      doi = {10.2390/biecoll-jib-2013-224},
      journal = {Journal of Integrative Bioinformatics},
      volume = {10},
      number = {2},
      pages = {224}
    }
    

2012

  • DOI BibTeX
    J.C. Chaplin, N.A. Russell, N. Krasnogor
    Implementing conventional logic unconventionally: Photochromic molecular populations as registers and logic gates
    in Biosystems, 109(1):35-51, July 2012
    @ARTICLE{Chaplin2012,
      title = {Implementing conventional logic unconventionally: Photochromic molecular populations as registers and logic gates},
      author = {Chaplin, J. C. and Russell, N. A. and Krasnogor, N.},
      year = 2012,
      doi = {10.1016/j.biosystems.2011.12.005},
      month = jul,
      journal = {Biosystems},
      volume = {109},
      number = {1},
      pages = {35--51}
    }
    
  • DOI BibTeX
    M. Galdzicki, M.L. Wilson, C.A. Rodriguez, M.R. Pocock, E. Oberortner, L. Adam, A. Adler, J.C. Anderson, J. Beal, Y. Cai, D. Chandran, D. Densmore, O.A. Drory, D. Endy, J.H. Gennari, R. Grünberg, T.S. Ham, N.J. Hillson, J.D. Johnson, A. Kuchinsky, M.W. Lux, C. Madsen, G. Misirli, C.J. Myers, C. Olguin, J. Peccoud, H. Plahar, D. Platt, N. Roehner, E. Sirin, T.F. Smith, G. Stan, et al.
    Synthetic Biology Open Language (SBOL) Version 1.1.0
    The BioBricks Foundation technical report, BBF RFC #87, 2012
    @TECHREPORT{Galdzicki2012,
      title = {Synthetic Biology Open Language (SBOL) Version 1.1.0},
      author = {Galdzicki, Michal and Wilson, Mandy L. and Rodriguez, Cesar A. and Pocock, Matthew R. and Oberortner, Ernst and Adam, Laura and Adler, Aaron and Anderson, J. Christopher and Beal, Jacob and Cai, Yizhi and Chandran, Deepak and Densmore, Douglas and Drory, Omri A. and Endy, Drew and Gennari, John H. and Grünberg, Raik and Ham, Timothy S. and Hillson, Nathan J. and Johnson, Jeffrey D. and Kuchinsky, Allan and Lux, Matthew W. and Madsen, Curtis and Misirli, Goksel and Myers, Chris J. and Olguin, Carlos and Peccoud, Jean and Plahar, Hector and Platt, Darren and Roehner, Nicholas and Sirin, Evren and Smith, Trevor F. and Stan, Guy-Bart and Villalobos, Alan and Wipat, Anil and Sauro, Herbert M.},
      year = 2012,
      doi = {1721.1/73909},
      number = {BBF RFC #87},
      institution = {The BioBricks Foundation}
    }
    

2011

  • DOI BibTeX
    G. Misirli, J.S. Hallinan, T. Yu, J.R. Lawson, S.M. Wimalaratne, M.T. Cooling, A. Wipat
    Model annotation for synthetic biology: automating model to nucleotide sequence conversion
    in Bioinformatics, 27(7):973-979, April 2011
    @ARTICLE{Misirli2011,
      title = {Model annotation for synthetic biology: automating model to nucleotide sequence conversion},
      author = {Misirli, G. and Hallinan, J. S. and Yu, T. and Lawson, J. R. and Wimalaratne, S. M. and Cooling, M. T. and Wipat, A.},
      year = 2011,
      doi = {10.1093/bioinformatics/btr048},
      month = apr,
      journal = {Bioinformatics},
      volume = {27},
      number = {7},
      pages = {973--979}
    }
    
  • DOI BibTeX
    M. Porcar, A. Danchin, V. de Lorenzo, V.A. dos Santos, N. Krasnogor, S. Rasmussen, A. Moya
    The ten grand challenges of synthetic life
    in Systems and Synthetic Biology, 5(1-2):1-9, June 2011
    @ARTICLE{Porcar2011,
      title = {The ten grand challenges of synthetic life},
      author = {Porcar, Manuel and Danchin, Antoine and de Lorenzo, Victor and dos Santos, Vitor A. and Krasnogor, Natalio and Rasmussen, Steen and Moya, Andrés},
      year = 2011,
      doi = {10.1007/s11693-011-9084-5},
      month = jun,
      journal = {Systems and Synthetic Biology},
      volume = {5},
      number = {1-2},
      pages = {1--9}
    }
    
  • DOI BibTeX
    J. Blakes, J. Twycross, F.J. Romero-Campero, N. Krasnogor
    The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
    in Bioinformatics, 27(23):3323-3324, December 2011
    @ARTICLE{Blakes2011,
      title = {The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology},
      author = {Blakes, J. and Twycross, J. and Romero-Campero, F. J. and Krasnogor, N.},
      year = 2011,
      doi = {10.1093/bioinformatics/btr571},
      month = dec,
      journal = {Bioinformatics},
      volume = {27},
      number = {23},
      pages = {3323--3324}
    }
    

2010

  • DOI BibTeX
    H. Cao, F.J. Romero-Campero, S. Heeb, M. Cámara, N. Krasnogor
    Evolving cell models for systems and synthetic biology
    in Systems and Synthetic Biology, 4(1):55-84, March 2010
    @ARTICLE{Cao2010,
      title = {Evolving cell models for systems and synthetic biology},
      author = {Cao, Hongqing and Romero-Campero, Francisco J. and Heeb, Stephan and Cámara, Miguel and Krasnogor, Natalio},
      year = 2010,
      doi = {10.1007/s11693-009-9050-7},
      month = mar,
      journal = {Systems and Synthetic Biology},
      volume = {4},
      number = {1},
      pages = {55--84}
    }
    
  • DOI BibTeX
    M.T. Cooling, V. Rouilly, G. Misirli, J. Lawson, T. Yu, J. Hallinan, A. Wipat
    Standard virtual biological parts: a repository of modular modeling components for synthetic biology
    in Bioinformatics, 26(7):925-931, April 2010
    @ARTICLE{Cooling2010,
      title = {Standard virtual biological parts: a repository of modular modeling components for synthetic biology},
      author = {Cooling, M. T. and Rouilly, V. and Misirli, G. and Lawson, J. and Yu, T. and Hallinan, J. and Wipat, A.},
      year = 2010,
      doi = {10.1093/bioinformatics/btq063},
      month = apr,
      journal = {Bioinformatics},
      volume = {26},
      number = {7},
      pages = {925--931}
    }
    
  • DOI BibTeX
    J.S. Hallinan, G. Misirli, A. Wipat
    Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits
    in 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology, p.768-774, Buenos Aires, August 2010
    @INPROCEEDINGS{Hallinan2010,
      title = {Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits},
      author = {Hallinan, J S and Misirli, G and Wipat, A},
      year = 2010,
      doi = {10.1109/IEMBS.2010.5626353},
      month = aug,
      booktitle = {2010 Annual International Conference of the IEEE Engineering in Medicine and Biology},
      pages = {768--774},
      address = {Buenos Aires}
    }
    
  • DOI eprint BibTeX
    D. Gilbert, A. Jaramillo, N. Krasnogor, V. de Lorenzo
    Synthetic biology gains momentum in Europe
    in Systems and Synthetic Biology, 4(3):145-147, September 2010
    @ARTICLE{Gilbert2010,
      title = {Synthetic biology gains momentum in Europe},
      author = {Gilbert, David and Jaramillo, Alfonso and Krasnogor, Natalio and de Lorenzo, Victor},
      year = 2010,
      doi = {10.1007/s11693-010-9065-0},
      month = sep,
      journal = {Systems and Synthetic Biology},
      volume = {4},
      number = {3},
      pages = {145--147}
    }
    
  • DOI eprint BibTeX
    J. Smaldon, F.J. Romero-Campero, F. Fernández Trillo, M. Gheorghe, C. Alexander, N. Krasnogor
    A computational study of liposome logic: towards cellular computing from the bottom up
    in Systems and Synthetic Biology, 4(3):157-179, September 2010
    @ARTICLE{Smaldon2010,
      title = {A computational study of liposome logic: towards cellular computing from the bottom up},
      author = {Smaldon, James and Romero-Campero, Francisco J. and Fernández Trillo, Francisco and Gheorghe, Marian and Alexander, Cameron and Krasnogor, Natalio},
      year = 2010,
      doi = {10.1007/s11693-010-9060-5},
      month = sep,
      journal = {Systems and Synthetic Biology},
      volume = {4},
      number = {3},
      pages = {157--179}
    }
    
  • DOI BibTeX
    G. Pasparakis, N. Krasnogor, L. Cronin, B.G. Davis, C. Alexander
    Controlled polymer synthesis—from biomimicry towards synthetic biology
    in Chem. Soc. Rev., 39(1):286-300, 2010
    @ARTICLE{Pasparakis2010,
      title = {Controlled polymer synthesis—from biomimicry towards synthetic biology},
      author = {Pasparakis, George and Krasnogor, Natalio and Cronin, Leroy and Davis, Benjamin G. and Alexander, Cameron},
      year = 2010,
      doi = {10.1039/B809333B},
      journal = {Chem. Soc. Rev.},
      volume = {39},
      number = {1},
      pages = {286--300}
    }
    
  • DOI BibTeX
    C. García-Martínez, C. Lima, J. Twycross, N. Krasnogor, M. Lozano
    P system model optimisation by means of evolutionary based search algorithms
    in Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10, p.187, Portland, Oregon, USA, 2010
    @INPROCEEDINGS{Garcia-Martinez2010,
      title = {P system model optimisation by means of evolutionary based search algorithms},
      author = {García-Martínez, Carlos and Lima, Claudio and Twycross, Jamie and Krasnogor, Natalio and Lozano, Manuel},
      year = 2010,
      doi = {10.1145/1830483.1830517},
      booktitle = {Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10},
      pages = {187},
      address = {Portland, Oregon, USA}
    }
    

2009

  • DOI BibTeX
    F.J. Romero-Campero, J. Twycross, M. Cámara, M. Bennett, M. Gheorghe, N. Krasnogor
    Modular Assembly Of Cell Systems Biology Models Using P Systems
    in International Journal of Foundations of Computer Science, 20(03):427-442, June 2009
    @ARTICLE{Romero-Campero2009,
      title = {Modular Assembly Of Cell Systems Biology Models Using P Systems},
      author = {Romero-Campero, Francisco J. and Twycross, Jamie and Cámara, Miguel and Bennett, Malcolm and Gheorghe, Marian and Krasnogor, Natalio},
      year = 2009,
      doi = {10.1142/S0129054109006668},
      month = jun,
      journal = {International Journal of Foundations of Computer Science},
      volume = {20},
      number = {03},
      pages = {427--442}
    }
    
  • DOI BibTeX
    A. Moya, N. Krasnogor, J. Peretó, A. Latorre
    Goethe's dream. Challenges and opportunities for synthetic biology
    in EMBO reports, 10(S1):S28-S32, August 2009
    @ARTICLE{Moya2009,
      title = {Goethe's dream. Challenges and opportunities for synthetic biology},
      author = {Moya, Andrés and Krasnogor, Natalio and Peretó, Juli and Latorre, Amparo},
      year = 2009,
      doi = {10.1038/embor.2009.120},
      month = aug,
      journal = {EMBO reports},
      volume = {10},
      number = {S1},
      pages = {S28--S32}
    }
    
  • DOI BibTeX
    F.J. Romero-Campero, N. Krasnogor
    An Approach to the Engineering of Cellular Models Based on P Systems
    in Mathematical Theory and Computational Practice, Lecture Notes in Computer Science 5635, p.430-436, 2009
    @INCOLLECTION{Romero-Campero2009b,
      title = {An Approach to the Engineering of Cellular Models Based on P Systems},
      author = {Romero-Campero, Francisco J. and Krasnogor, Natalio},
      year = 2009,
      doi = {10.1007/978-3-642-03073-4_44},
      booktitle = {Mathematical Theory and Computational Practice},
      publisher = {Springer Berlin Heidelberg},
      volume = {5635},
      series = {Lecture Notes in Computer Science},
      pages = {430--436}
    }
    
  • DOI BibTeX
    F.J. Romero-Campero, J. Twycross, H. Cao, J. Blakes, N. Krasnogor
    A Multiscale Modeling Framework Based on P Systems
    in Membrane Computing, Lecture Notes in Computer Science 5391, p.63-77, 2009
    @INCOLLECTION{Romero-Campero2009a,
      title = {A Multiscale Modeling Framework Based on P Systems},
      author = {Romero-Campero, Francisco José and Twycross, Jamie and Cao, Hongqing and Blakes, Jonathan and Krasnogor, Natalio},
      year = 2009,
      doi = {10.1007/978-3-540-95885-7_5},
      booktitle = {Membrane Computing},
      publisher = {Springer Berlin Heidelberg},
      volume = {5391},
      series = {Lecture Notes in Computer Science},
      pages = {63--77}
    }
    
  • DOI BibTeX
    G. Pasparakis, M. Vamvakaki, N. Krasnogor, C. Alexander
    Diol–boronic acid complexes integrated by responsive polymers—a route to chemical sensing and logic operations
    in Soft Matter, 5(20):3839, 2009
    @ARTICLE{Pasparakis2009,
      title = {Diol–boronic acid complexes integrated by responsive polymers—a route to chemical sensing and logic operations},
      author = {Pasparakis, George and Vamvakaki, Maria and Krasnogor, Natalio and Alexander, Cameron},
      year = 2009,
      doi = {10.1039/b911341j},
      journal = {Soft Matter},
      volume = {5},
      number = {20},
      pages = {3839}
    }
    
  • DOI BibTeX
    J. Smaldon, N. Krasnogor, C. Alexander, M. Gheorghe
    Liposome logic
    in Proceedings of the 11th Annual conference on Genetic and evolutionary computation - GECCO '09, p.161, Montreal, Québec, Canada, 2009
    @INPROCEEDINGS{Smaldon2009,
      title = {Liposome logic},
      author = {Smaldon, James and Krasnogor, Natalio and Alexander, Cameron and Gheorghe, Marian},
      year = 2009,
      doi = {10.1145/1569901.1569924},
      booktitle = {Proceedings of the 11th Annual conference on Genetic and evolutionary computation - GECCO '09},
      pages = {161},
      address = {Montreal, Québec, Canada}
    }
    

2008

  • DOI eprint BibTeX
    F.J. Romero-Campero, H. Cao, M. Camara, N. Krasnogor
    Structure and parameter estimation for cell systems biology models
    in Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, p.331, Atlanta, GA, USA, 2008
    @INPROCEEDINGS{Romero-Campero2008,
      title = {Structure and parameter estimation for cell systems biology models},
      author = {Romero-Campero, Francisco J. and Cao, Hongqing and Camara, Miguel and Krasnogor, Natalio},
      year = 2008,
      doi = {10.1145/1389095.1389153},
      booktitle = {Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08},
      pages = {331},
      address = {Atlanta, GA, USA}
    }
    
  • DOI BibTeX
    J. Smaldon, J. Blakes, N. Krasnogor, D. Lancet
    A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics
    in Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, p.249, Atlanta, GA, USA, 2008
    @INPROCEEDINGS{Smaldon2008,
      title = {A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics},
      author = {Smaldon, James and Blakes, Jonathan and Krasnogor, Natalio and Lancet, Doron},
      year = 2008,
      doi = {10.1145/1389095.1389134},
      booktitle = {Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08},
      pages = {249},
      address = {Atlanta, GA, USA}
    }
    

2006

  • DOI BibTeX
    L. Cronin, N. Krasnogor, B.G. Davis, C. Alexander, N. Robertson, J.H.G. Steinke, S.L.M. Schroeder, A.N. Khlobystov, G. Cooper, P.M. Gardner, P. Siepmann, B.J. Whitaker, D. Marsh
    The imitation game—a computational chemical approach to recognizing life
    in Nature Biotechnology, 24(10):1203-1206, October 2006
    @ARTICLE{Cronin2006,
      title = {The imitation game—a computational chemical approach to recognizing life},
      author = {Cronin, Leroy and Krasnogor, Natalio and Davis, Benjamin G and Alexander, Cameron and Robertson, Neil and Steinke, Joachim H G and Schroeder, Sven L M and Khlobystov, Andrei N and Cooper, Geoff and Gardner, Paul M and Siepmann, Peter and Whitaker, Benjamin J and Marsh, Dan},
      year = 2006,
      doi = {10.1038/nbt1006-1203},
      month = oct,
      journal = {Nature Biotechnology},
      volume = {24},
      number = {10},
      pages = {1203--1206}
    }
    
  • DOI BibTeX
    F. Bernardini, M. Gheorghe, N. Krasnogor, R.C. Muniyandi, M.J. Pérez-Jímenez, F.J. Romero-Campero
    On P Systems as a Modelling Tool for Biological Systems
    in Membrane Computing, Lecture Notes in Computer Science 3850, p.114-133, 2006
    @INCOLLECTION{Bernardini2006,
      title = {On P Systems as a Modelling Tool for Biological Systems},
      author = {Bernardini, Francesco and Gheorghe, Marian and Krasnogor, Natalio and Muniyandi, Ravie C. and Pérez-Jímenez, Mario J. and Romero-Campero, Francisco José},
      year = 2006,
      doi = {10.1007/11603047_8},
      booktitle = {Membrane Computing},
      publisher = {Springer Berlin Heidelberg},
      volume = {3850},
      series = {Lecture Notes in Computer Science},
      pages = {114--133}
    }
    

2005

  • DOI eprint BibTeX
    G. Terrazas, N. Krasnogor, M. Gheorghe, F. Bernardini, S. Diggle, M. Cámara
    An Environment Aware P-System Model of Quorum Sensing
    in New Computational Paradigms, Lecture Notes in Computer Science 3526, p.479-485, 2005
    @INCOLLECTION{Terrazas2005,
      title = {An Environment Aware P-System Model of Quorum Sensing},
      author = {Terrazas, German and Krasnogor, Natalio and Gheorghe, Marian and Bernardini, Francesco and Diggle, Steve and Cámara, Miguel},
      year = 2005,
      doi = {10.1007/11494645_59},
      booktitle = {New Computational Paradigms},
      publisher = {Springer Berlin Heidelberg},
      volume = {3526},
      series = {Lecture Notes in Computer Science},
      pages = {479--485}
    }