Publications

2024

  • DOI BibTeX
    L. Schmidt, S. Mohamed, N. Meader, J. Bacardit, D. Craig
    Automated data analysis of unstructured grey literature in health research: A mapping review
    in Research Synthesis Methods, 15(2):178-197, March 2024
    @ARTICLE{Schmidt2024,
  title = {Automated data analysis of unstructured grey literature in health research: A mapping review},
  author = {Schmidt, Lena and Mohamed, Saleh and Meader, Nick and Bacardit, Jaume and Craig, Dawn},
  year = 2024,
  doi = {10.1002/jrsm.1692},
  month = mar,
  journal = {Research Synthesis Methods},
  volume = {15},
  number = {2},
  pages = {178--197}
}

2022

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

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
    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}
}

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

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}
}

2016

  • DOI BibTeX
    G. Misirli, M. Cavaliere, W. Waites, M. Pocock, C. Madsen, O. Gilfellon, R. Honorato-Zimmer, P. Zuliani, V. Danos, A. Wipat
    Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization
    in Bioinformatics, 32(6):908-917, March 2016
    @ARTICLE{Misirli2015,
  title = {Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization},
  author = {Misirli, Goksel and Cavaliere, Matteo and Waites, William and Pocock, Matthew and Madsen, Curtis and Gilfellon, Owen and Honorato-Zimmer, Ricardo and Zuliani, Paolo and Danos, Vincent and Wipat, Anil},
  year = 2016,
  doi = {10.1093/bioinformatics/btv660},
  month = mar,
  journal = {Bioinformatics},
  volume = {32},
  number = {6},
  pages = {908--917}
}
  • DOI BibTeX
    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}
}

2014

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

2013

  • 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}
}

2011

  • DOI
    M. Hucka, C. Laibe, N. Juty, W. Liebermeister, S. Keating, C. Lloyd, C. Knuepfer, G. Misirli, M. Schulz, D. Waltemath, M. Taschuk, N. Swainston, N. Le Novère, A. Lister, F. Bergmann, R. Henkel, F. Krause, S. Hoops
    SBML Level 3 Package Proposal: Annotation
    in Nature Precedings, available online since January 2011
  • 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

  • URL code BibTeX
    E. Glaab, J.M. Garibaldi, N. Krasnogor
    vrmlgen: An R Package for 3D Data Visualization on the Web
    in Journal of Statistical Software, 36(8):1-18, 2010
    @ARTICLE{Glaab2010b,
  title = {vrmlgen: An R Package for 3D Data Visualization on the Web},
  author = {Glaab, Enrico and Garibaldi, Jonathan Mark and Krasnogor, Natalio},
  year = 2010,
  url = {http://www.jstatsoft.org/v36/i08/},
  journal = {Journal of Statistical Software},
  volume = {36},
  number = {8},
  pages = {1--18}
}

2008

  • DOI eprint BibTeX
    N. Krasnogor, A. Shah, D. Barthel, P. Lukasiak, J. Blazewicz
    Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review
    in Current Bioinformatics, 3(1):10-31, January 2008
    @ARTICLE{Krasnogor2008b,
  title = {Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review},
  author = {Krasnogor, Natalio and Shah, Azhar and Barthel, Daniel and Lukasiak, Piotr and Blazewicz, Jacek},
  year = 2008,
  doi = {10.2174/157489308783329850},
  month = jan,
  journal = {Current Bioinformatics},
  volume = {3},
  number = {1},
  pages = {10--31}
}
  • DOI BibTeX
    A.A. Shah, D. Barthel, G. Folino, N. Krasnogor
    Performance Evaluation of Protein Structure Comparison Algorithms Under Integrated Resource Management Environment for MPI Jobs
    in 2008 IEEE International Symposium on Parallel and Distributed Processing with Applications, p.817-822, Sydney, Australia, December 2008
    @INPROCEEDINGS{Shah2008,
  title = {Performance Evaluation of Protein Structure Comparison Algorithms Under Integrated Resource Management Environment for MPI Jobs},
  author = {Shah, Azhar A. and Barthel, Daniel and Folino, Gianluigi and Krasnogor, Natalio},
  year = 2008,
  doi = {10.1109/ISPA.2008.41},
  month = dec,
  booktitle = {2008 IEEE International Symposium on Parallel and Distributed Processing with Applications},
  pages = {817--822},
  address = {Sydney, Australia}
}

2007

  • DOI BibTeX
    A.A. Shah, D. Barthel, N. Krasnogor
    Grid and Distributed Public Computing Schemes for Structural Proteomics: A Short Overview
    in Frontiers of High Performance Computing and Networking ISPA 2007 Workshops, Lecture Notes in Computer Science 4743, p.424-434, 2007
    @INCOLLECTION{Shah2007,
  title = {Grid and Distributed Public Computing Schemes for Structural Proteomics: A Short Overview},
  author = {Shah, Azhar Ali and Barthel, Daniel and Krasnogor, Natalio},
  year = 2007,
  doi = {10.1007/978-3-540-74767-3_44},
  booktitle = {Frontiers of High Performance Computing and Networking ISPA 2007 Workshops},
  publisher = {Springer Berlin Heidelberg},
  volume = {4743},
  series = {Lecture Notes in Computer Science},
  pages = {424--434}
}