Publications
all bioinformatics neuroinformatics synthetic biology systems biology complex systems machine intelligence knowledge management
2022
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Curating a longitudinal research resource using linked primary care EHR data—a UK Biobank case studyin 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
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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} }
2020
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Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineeringin 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} }
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AREA: An adaptive reference-set based evolutionary algorithm for multiobjective optimisationin 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
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SynBioHub: A Standards-Enabled Design Repository for Synthetic Biologyin 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
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Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualizationin 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} }
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Data Integration and Mining for Synthetic Biology Designin 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
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Probabilistic Latent Semantic Analysis Applied to Whole Bacterial Genomes Identifies Common Genomic Featuresin 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} }
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Composable Modular Models for Synthetic Biologyin 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
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BacillOndex: An Integrated Data Resource for Systems and Synthetic Biologyin 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
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SBML Level 3 Package Proposal: Annotationin Nature Precedings, available online since January 2011
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The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biologyin 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
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vrmlgen: An R Package for 3D Data Visualization on the Webin 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
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Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Reviewin 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} }
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Performance Evaluation of Protein Structure Comparison Algorithms Under Integrated Resource Management Environment for MPI Jobsin 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
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Grid and Distributed Public Computing Schemes for Structural Proteomics: A Short Overviewin 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} }