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
  N. Partridge
  Research Briefing - Governing synthetic biology: A food policy approach
  Newcastle University technical report, 1, March 2023

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

• 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
  H. Fellermann, R.M. Füchslin
  Editorial: The 2019 Conference on Artificial Life Special Issue
  in Artificial Life, 28(2):171-172, June 2022

  @ARTICLE{Fellermann2022,
    title = {Editorial: The 2019 Conference on Artificial Life Special Issue},
    author = {Fellermann, Harold and Füchslin, Rudolf M.},
    year = 2022,
    doi = {10.1162/artl_e_00380},
    month = jun,
    journal = {Artificial Life},
    volume = {28},
    number = {2},
    pages = {171--172}
  }
  

• DOI BibTeX
  E. Torelli, B. Shirt-Ediss, S.A. Navarro, M. Manzano, P. Vizzini, N. Krasnogor
  Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing
  in bioRxiv, 2022.07.20.500791v1, July 2022

  @ARTICLE{Torelli2022,
    title = {Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing},
    author = {Torelli, Emanuela and Shirt-Ediss, Benjamin and Navarro, Silvia A. and Manzano, Marisa and Vizzini, Priya and Krasnogor, Natalio},
    year = 2022,
    doi = {10.1101/2022.07.20.500791},
    month = jul,
    journal = {bioRxiv},
    volume = {2022.07.20.500791v1}
  

• DOI BibTeX
  C. Atallah, K. James, Z. Ou, J. Skelton, D. Markham, J. Finnigan, S. Charnock, A. Wipat
  Automatic Diverse Subset Selection From Enzyme Families by Solving the Maximum Diversity Problem
  in 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), p.1-9, Ottawa, ON, Canada, August 2022

  @INPROCEEDINGS{Atallah2022,
    title = {Automatic Diverse Subset Selection From Enzyme Families by Solving the Maximum Diversity Problem},
    author = {Atallah, Christian and James, Katherine and Ou, Zhen and Skelton, James and Markham, David and Finnigan, James and Charnock, Simon and Wipat, Anil},
    year = 2022,
    doi = {10.1109/CIBCB55180.2022.9863021},
    month = aug,
    booktitle = {2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)},
    pages = {1--9},
    address = {Ottawa, ON, Canada}
  }
  

• DOI BibTeX
  J. Tellechea-Luzardo, L. Hobbs
  Versioning biological cells for trustworthy cell engineering
  in Nature Communications, 13(765):12, 2022

  @ARTICLE{Tellechea-Luzardo2022,
    title = {Versioning biological cells for trustworthy cell engineering},
    author = {Tellechea-Luzardo, J and Hobbs, L},
    year = 2022,
    doi = {10.1038/s41467-022-28350-4},
    journal = {Nature Communications},
    volume = {13},
    number = {765},
    pages = {12}
  }
  

• URL BibTeX
  B. Li, N. Mackenzie, B. Shirt-Ediss, N. Krasnogor, P. Zuliani
  Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking
  in 28th International Conference on DNA Computing and Molecular Programming (DNA 28), p.1-22, Dagstuhl, Germany, 2022

  @INPROCEEDINGS{Li2022,
    title = {Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking},
    author = {Li, Bowen and Mackenzie, Neil and Shirt-Ediss, Ben and Krasnogor, Natalio and Zuliani, Paolo},
    year = 2022,
    url = {https://doi.org/10.4230/LIPIcs.DNA.28.5},
    booktitle = {28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
    pages = {1--22},
    address = {Dagstuhl, Germany}
  }
  

2021

• DOI BibTeX
  V. de Lorenzo, N. Krasnogor, M. Schmidt
  For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!
  in New Biotechnology, 60(C):44-51, January 2021

  @ARTICLE{Lorenzo2021,
    title = {For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!},
    author = {de Lorenzo, Víctor and Krasnogor, Natalio and Schmidt, Markus},
    year = 2021,
    doi = {10.1016/j.nbt.2020.08.004},
    month = jan,
    journal = {New Biotechnology},
    volume = {60},
    number = {C},
    pages = {44--51}
  }
  

• 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
  A. Lopiccolo, B. Shirt-Ediss, E. Torelli, A.F.A. Olulana, M. Castronovo, H. Fellermann, N. Krasnogor
  A last-in first-out stack data structure implemented in DNA
  in Nature Communications, 12(1), August 2021

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

• DOI BibTeX
  N. Partridge
  Towards greater transparency: Digital opportunities to promote traceability in genetic engineering.
  Newcastle University technical report, 1, August 2021
  This Policy Brief is an output from the N8 AgriFood Food Systems Policy Hub. It is one of a collection produced by participants on the Rapid Evidence Synthesis Training (REST) programme. REST was delivered through a collaboration between the University of Leeds, Newcastle University and the N8 AgriFood Programme, supported by Research England QR-SPF funds from the University of Leeds and the University of York.

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

• DOI BibTeX
  E. Velázquez, Y. Al-Ramahi, J. Tellechea-Luzardo, N. Krasnogor, V. de Lorenzo
  Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection
  in ACS Synthetic Biology, 10(10):2552-2565, October 2021

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

• DOI BibTeX
  G. Mısırlı, B. Yang, K. James, A. Wipat
  Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits
  in ACS Synthetic Biology, 10(12):3304-3315, December 2021
  Portabolomics paper

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

• 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
  J. Tellechea-Luzardo, C. Winterhalter, P. Widera, J. Kozyra, V. de Lorenzo, N. Krasnogor
  Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering
  in ACS Synthetic Biology, 9(3):536-545, March 2020

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

• DOI BibTeX
  G. Mısırlı, J. Beal, T.E. Gorochowski, G. Stan, A. Wipat, C.J. Myers
  SBOL Visual 2 Ontology
  in ACS Synthetic Biology, 9(4):972-977, April 2020

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

• DOI BibTeX
  M. Crowther, L. Grozinger, M. Pocock, C.P.D. Taylor, J.A. McLaughlin, G. Mısırlı, B.A. Bartley, J. Beal, A. Goñi-Moreno, A. Wipat
  ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL)
  in ACS Synthetic Biology, 9(4):962-966, April 2020

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

• 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
  T.E. Gorochowski, S. Hauert, J. Kreft, L. Marucci, N.R. Stillman, T.-.D. Tang, L. Bandiera, V. Bartoli, D.O.R. Dixon, A.J.H. Fedorec, H. Fellermann, A.G. Fletcher, T. Foster, L. Giuggioli, A. Matyjaszkiewicz, S. McCormick, S. Montes Olivas, J. Naylor, A. Rubio Denniss, D. Ward
  Toward Engineering Biosystems With Emergent Collective Functions
  in Frontiers in Bioengineering and Biotechnology, 8, June 2020

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

• DOI BibTeX
  E. Torelli, J. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor
  Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami
  in ACS Synthetic Biology, 9(7):1682-1692, July 2020

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

• DOI BibTeX
  B. Brown, B. Bartley, J. Beal, J.E. Bird, Á. Goñi-Moreno, J.A. McLaughlin, G. Mısırlı, N. Roehner, D.J. Skelton, C.L. Poh, I.D. Ofiteru, K. James, A. Wipat
  Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)
  in ACS Synthetic Biology, 9(9):2410-2417, September 2020

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

• DOI BibTeX
  J.A. McLaughlin, J. Beal, G. Mısırlı, R. Grünberg, B.A. Bartley, J. Scott-Brown, P. Vaidyanathan, P. Fontanarrosa, E. Oberortner, A. Wipat, T.E. Gorochowski, C.J. Myers
  The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering
  in Frontiers in Bioengineering and Biotechnology, 8, September 2020

  @ARTICLE{McLaughlin2020,
    title = {The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering},
    author = {McLaughlin, James Alastair and Beal, Jacob and Mısırlı, Göksel and Grünberg, Raik and Bartley, Bryan A. and Scott-Brown, James and Vaidyanathan, Prashant and Fontanarrosa, Pedro and Oberortner, Ernst and Wipat, Anil and Gorochowski, Thomas E. and Myers, Chris J.},
    year = 2020,
    doi = {10.3389/fbioe.2020.01009},
    month = sep,
    journal = {Frontiers in Bioengineering and Biotechnology},
    volume = {8}
  

• 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}
  }
  

• DOI BibTeX
  D. Flumini, M.S. Weyland, J.J. Schneider, H. Fellermann, R.M. Füchslin
  Towards Programmable Chemistries
  in Artificial Life and Evolutionary Computation, Communications in Computer and Information Science 1200, p.145-157, 2020

  @INCOLLECTION{Flumini2020,
    title = {Towards Programmable Chemistries},
    author = {Flumini, Dandolo and Weyland, Mathias S. and Schneider, Johannes J. and Fellermann, Harold and Füchslin, Rudolf M.},
    year = 2020,
    doi = {10.1007/978-3-030-45016-8_15},
    booktitle = {Artificial Life and Evolutionary Computation},
    publisher = {Springer International Publishing},
    volume = {1200},
    series = {Communications in Computer and Information Science},
    pages = {145--157}
  }
  

2019

• DOI BibTeX
  B. Corominas-Murtra, H. Fellermann, R. Solé
  Protocell Cycles as Thermodynamic Cycles
  in The Energetics of Computing in Life and Machines, p.149-167, June 2019

  @INCOLLECTION{Corominas-Murtra2019,
    title = {Protocell Cycles as Thermodynamic Cycles},
    author = {Corominas-Murtra, Bernat and Fellermann, Harold and Solé, Ricard},
    year = 2019,
    doi = {10.37911/9781947864078.06},
    month = jun,
    booktitle = {The Energetics of Computing in Life and Machines},
    publisher = {SFI Press},
    pages = {149--167}
  }
  

• DOI BibTeX
  J. Beal, T. Nguyen, T.E. Gorochowski, A. Goñi-Moreno, J. Scott-Brown, J.A. McLaughlin, C. Madsen, B. Aleritsch, B. Bartley, S. Bhakta, M. Bissell, S. Castillo Hair, K. Clancy, A. Luna, N. Le Novère, Z. Palchick, M. Pocock, H. Sauro, J.T. Sexton, J.J. Tabor, C.A. Voigt, Z. Zundel, C. Myers, A. Wipat
  Communicating Structure and Function in Synthetic Biology Diagrams
  in ACS Synthetic Biology, 8(8):1818-1825, August 2019

  @ARTICLE{Beal2019,
    title = {Communicating Structure and Function in Synthetic Biology Diagrams},
    author = {Beal, Jacob and Nguyen, Tramy and Gorochowski, Thomas E. and Goñi-Moreno, Angel and Scott-Brown, James and McLaughlin, James Alastair and Madsen, Curtis and Aleritsch, Benjamin and Bartley, Bryan and Bhakta, Shyam and Bissell, Mike and Castillo Hair, Sebastian and Clancy, Kevin and Luna, Augustin and Le Novère, Nicolas and Palchick, Zach and Pocock, Matthew and Sauro, Herbert and Sexton, John T. and Tabor, Jeffrey J. and Voigt, Christopher A. and Zundel, Zach and Myers, Chris and Wipat, Anil},
    year = 2019,
    doi = {10.1021/acssynbio.9b00139},
    month = aug,
    journal = {ACS Synthetic Biology},
    volume = {8},
    number = {8},
    pages = {1818--1825}
  }
  

• DOI BibTeX
  J. Naylor, H. Fellermann, N. Krasnogor
  Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations
  in Bioinformatics, 35(19):3859-3860, October 2019

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

• DOI BibTeX
  L. Grozinger, M. Amos, T.E. Gorochowski, P. Carbonell, D.A. Oyarzún, R. Stoof, H. Fellermann, P. Zuliani, H. Tas, A. Goñi-Moreno
  Pathways to cellular supremacy in biocomputing
  in Nature Communications, 10(1), November 2019

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

2018

• DOI BibTeX
  J.A. McLaughlin, C.J. Myers, Z. Zundel, G. Mısırlı, M. Zhang, I.D. Ofiteru, A. Goñi-Moreno, A. Wipat
  SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology
  in ACS Synthetic Biology, 7(2):682-688, February 2018

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

• BibTeX
  S. Jiang, M. Torres, D. Pelta, P. Krabben, R. Daniel, J.T. Luzardo, M. Kaiser, N. Krasnogor
  Improving microbial strain design via multiobjective optimisation and decision making
  in FAIM Workshop on AI for Sythetic Biology 2, p.1-6, Stockholm, Sweden, July 2018

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

• DOI BibTeX
  M. Torres, S. Jiang, D. Pelta, M. Kaiser, N. Krasnogor
  Strain Design as Multiobjective Network Interdiction Problem: A Preliminary Approach
  in Advances in Artificial Intelligence, Lecture Notes in Computer Science 11160, p.273-282, 2018

  @INCOLLECTION{Torres2018,
    title = {Strain Design as Multiobjective Network Interdiction Problem: A Preliminary Approach},
    author = {Torres, Marina and Jiang, Shouyong and Pelta, David and Kaiser, Marcus and Krasnogor, Natalio},
    year = 2018,
    doi = {10.1007/978-3-030-00374-6_26},
    booktitle = {Advances in Artificial Intelligence},
    publisher = {Springer International Publishing},
    volume = {11160},
    series = {Lecture Notes in Computer Science},
    pages = {273--282}
  }
  

2017

• DOI BibTeX
  F.E. Hutchings, C.B. Thornton, M. Kaiser
  Implementation and comparison of non-invasive stimulation modalities in the VERTEX simulation tool
  in Brain Stimulation, 10(2):477, March 2017

  @ARTICLE{Hutchings2017,
    title = {Implementation and comparison of non-invasive stimulation modalities in the VERTEX simulation tool},
    author = {Hutchings, F. E. and Thornton, C. B. and Kaiser, M.},
    year = 2017,
    doi = {10.1016/j.brs.2017.01.398},
    month = mar,
    journal = {Brain Stimulation},
    volume = {10},
    number = {2},
    pages = {477}
  }
  

• DOI BibTeX
  A. Goñi-Moreno, A. Wipat, N. Krasnogor
  CSBB: synthetic biology research at Newcastle University
  in Biochemical Society Transactions, 45(3):781-783, June 2017

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

• DOI eprint BibTeX
  B. Shirt-Ediss, S. Murillo-Sánchez, K. Ruiz-Mirazo
  Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research
  in Beilstein Journal of Organic Chemistry, 13:1388-1395, July 2017

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

• 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
  J. Kozyra, A. Ceccarelli, E. Torelli, A. Lopiccolo, J. Gu, H. Fellermann, U. Stimming, N. Krasnogor
  Designing Uniquely Addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami
  in ACS Synthetic Biology, 6(7):1140-1149, July 2017

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

• DOI eprint BibTeX
  J. Kozyra, H. Fellermann, B. Shirt-Ediss, A. Lopiccolo, N. Krasnogor
  Optimizing nucleic acid sequences for a molecular data recorder
  in Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '17, p.1145-1152, Berlin, Germany, 2017

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

• DOI BibTeX
  R. Bauer, M. Kaiser
  Organisational Principles of Connectomes: Changes During Evolution and Development
  in Brain Evolution by Design, p.387-401, 2017

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

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
  H. Fellermann, O. Markovitch, O. Gilfellon, C. Madsen, A. Phillips
  Toward Programmable Biology
  in ACS Synthetic Biology, 5(8):793-794, August 2016

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

• 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}
  }
  

• DOI BibTeX
  H. Fellermann, A. Lopiccolo, J. Kozyra, N. Krasnogor
  In Vitro Implementation of a Stack Data Structure Based on DNA Strand Displacement
  in Unconventional Computation and Natural Computation, Lecture Notes in Computer Science 9726, p.87-98, 2016

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

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
  H. Fellermann, L. Cardelli
  Programming chemistry in DNA-addressable bioreactors
  in Journal of The Royal Society Interface, 11(99):20130987-20130987, August 2014

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

• DOI BibTeX
  D. Sanassy, H. Fellermann, N. Krasnogor, S. Konur, L.M. Mierla, M. Gheorghe, C. Ladroue, S. Kalvala
  Modelling and Stochastic Simulation of Synthetic Biological Boolean Gates
  in 2014 IEEE Intl Conf on High Performance Computing and Communications, 2014 IEEE 6th Intl Symp on Cyberspace Safety and Security, 2014 IEEE 11th Intl Conf on Embedded Software and Syst (HPCC,CSS,ICESS), p.404-408, Paris, France, August 2014

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

• 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}
  }
  

• DOI BibTeX
  M.S. Weyland, H. Fellermann, M. Hadorn, D. Sorek, D. Lancet, S. Rasmussen, R.M. F?chslin
  The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers
  in Computational and Mathematical Methods in Medicine, 2013:1-8, 2013

  @ARTICLE{Weyland2013,
    title = {The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers},
    author = {Weyland, Mathias S. and Fellermann, Harold and Hadorn, Maik and Sorek, Daniel and Lancet, Doron and Rasmussen, Steen and F?chslin, Rudolf M.},
    year = 2013,
    doi = {10.1155/2013/467428},
    journal = {Computational and Mathematical Methods in Medicine},
    volume = {2013},
    pages = {1--8}
  }
  

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. Hadorn, E. Boenzli, K.T. Sorensen, H. Fellermann, P. Eggenberger Hotz, M.M. Hanczyc
  Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets
  in Proceedings of the National Academy of Sciences, 109(50):20320-20325, December 2012

  @ARTICLE{Hadorn2012,
    title = {Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets},
    author = {Hadorn, M. and Boenzli, E. and Sorensen, K. T. and Fellermann, H. and Eggenberger Hotz, P. and Hanczyc, M. M.},
    year = 2012,
    doi = {10.1073/pnas.1214386109},
    month = dec,
    journal = {Proceedings of the National Academy of Sciences},
    volume = {109},
    number = {50},
    pages = {20320--20325}
  }
  

• 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
  H. Fellermann, S. Rasmussen
  On the Growth Rate of Non-Enzymatic Molecular Replicators
  in Entropy, 13(12):1882-1903, October 2011

  @ARTICLE{Fellermann2011,
    title = {On the Growth Rate of Non-Enzymatic Molecular Replicators},
    author = {Fellermann, Harold and Rasmussen, Steen},
    year = 2011,
    doi = {10.3390/e13101882},
    month = oct,
    journal = {Entropy},
    volume = {13},
    number = {12},
    pages = {1882--1903}
  }
  

• 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, 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
  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
  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}
  }
  

2007

• DOI BibTeX
  H. Fellermann, S. Rasmussen, H. Ziock, R.V. Sol?
  Life Cycle of a Minimal Protocell?A Dissipative Particle Dynamics Study
  in Artificial Life, 13(4):319-345, October 2007

  @ARTICLE{Fellermann2007,
    title = {Life Cycle of a Minimal Protocell?A Dissipative Particle Dynamics Study},
    author = {Fellermann, Harold and Rasmussen, Steen and Ziock, Hans-Joachim and Sol?, Ricard V.},
    year = 2007,
    doi = {10.1162/artl.2007.13.4.319},
    month = oct,
    journal = {Artificial Life},
    volume = {13},
    number = {4},
    pages = {319--345}
  }
  

• DOI BibTeX
  H. Fellermann, R.V. Sole
  Minimal model of self-replicating nanocells: a physically embodied information-free scenario
  in Philosophical Transactions of the Royal Society B: Biological Sciences, 362(1486):1803-1811, October 2007

  @ARTICLE{Fellermann2007a,
    title = {Minimal model of self-replicating nanocells: a physically embodied information-free scenario},
    author = {Fellermann, H. and Sole, R. V},
    year = 2007,
    doi = {10.1098/rstb.2007.2072},
    month = oct,
    journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
    volume = {362},
    number = {1486},
    pages = {1803--1811}
  }
  

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}
  }