Publications are listed in reverse chronological order.
2023
- SBcoyote: An extensible Python-based reaction editor and viewer
Jin Xu, Gary Geng, Nhan D. Nguyen, Carmen Perena-Cortes, Claire Samuels, Herbert M. Sauro
Biosystems Vol. 232, 105001, August 16, 2023 doi: 10.3389/fcell.2023.1201673
Click here to read full PDF - SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models
Jin Xu
BMC Bioinformatics Vol. 24, Article 248, June 13, 2023 doi: 10.3389/fcell.2023.1201673 - Reproducibility and FAIR principles: the case of a segment polarity network model
Pedro Mendes
Frontiers in Cell and Developmental Biology, Vol. 11, June 6, 2023 doi: 10.3389/fcell.2023.1201673 - RBAtools: a programming interface for Resource Balance Analysis models
Oliver Bodeit, Inès Ben Samir, Jonathan R Karr, Anne Goelzer, Wolfram Liebermeister
Bioinformatics Advances, Vol. 3, Issue 1, April 22, 2023. doi: 10.1093/bioadv/vbad056 - A practical guide to reproducible modeling for biochemical networks
Veronica Porubsky, Herbert Sauro
Methods in Molecular Biology (book), March 31, 2023 doi: 10.1007/978-1-0716-3008-2_5 - Standards, dissemination, and best practices in systems biology
Janis Shin, Veronica Porubsky, James Carothers, Herbert M Sauro
Current Opinions in Biotechnology, Vol. 81, March 31, 2023 doi: 10.1016/j.copbio.2023.102922 - Adapting Modeling and Simulation Credibility Standards to Computational Systems Biology
Lillian T. Tatka, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro
arXiv, January 15, 2023 doi: 10.48550/arXiv.2301.06007
2022
- libRoadRunner 2.0: a high-performance SBML simulation and analysis library
Ciaran Welsh, Jin Xu, Lucian Smith, Matthias König, Kiri Choi, Herbert M Sauro
Bioinformatics, Vol. 39, Issue 1, December 8, 2022 doi: 10.1093/bioinformatics/btac770 - SBMLDiagrams: a python package to process and visualize SBML layout and render
Jin Xu, Jessie Jiang, Herbert M Sauro
Bioinformatics, Vol. 39, Issue 1, November 12, 2022, btac730 doi: 10.1093/bioinformatics/btac730 - SBbadger: biochemical reaction networks with definable degree distributions
Michael A Kochen, H Steven Wiley, Song Feng, Herbert M Sauro
Bioinformatics, Vol. 38, Issue 22, September 16, 2022, Pages 5064–5072 doi: 10.1093/bioinformatics/btac630 - BioSimulators: a central registry of simulation engines and services for recommending specific tools
Bilal Shaikh, Lucian P Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S Andrews, Azraf Anwar, Moritz E Beber, Frank T Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G Bard Ermentrout, James R Faeder, Andrew P Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C Ison, Diego Jahn, Henry V Jakubowski, Ryann Jordan, Matúš Kalaš, Matthias König, Wolfram Liebermeister, Rahuman S Malik Sheriff, Synchon Mandal, Robert McDougal, J Kyle Medley, Pedro Mendes, Robert Müller, Chris J Myers, Aurelien Naldi, Tung V N Nguyen, David P Nickerson, Brett G Olivier, Drashti Patoliya, Loïc Paulevé, Linda R Petzold, Ankita Priya, Anand K Rampadarath, Johann M Rohwer, Ali S Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan Spangler, Jörn Starruß, Payton J Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P Goldberg, James C Schaff, Michael L Blinov, Herbert M Sauro, Ion I Moraru, Jonathan R Karr
Nucleic Acids Research, Volume 50, Issue W1, July 5, 2022, Pages W108–W114 doi: 10.1093/nar/gkac331 - NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories
Yuda Munarko, Dewan M. Sarwar, Anand Rampadarath, Koray Atalag, John H. Gennari, Maxwell L. Neal, David P. Nickerson
Frontiers in Physiology, Vol. 13, February 24, 2022 doi: 10.3389/fphys.2022.820683 - Integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualizations enable facile model reuse with biosimulations
Bilal Shaikh, Lucian P. Smith, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
Biophysical Journal, Vol. 121, Issue 3, February 11, 2022 doi: 10.1016/j.bpj.2021.11.2118
2021
- OMEX metadata specification (version 1.2)
John H. Gennari, Matthias König, Goksel Misirli , Maxwell L. Neal, David P. Nickerson, Dagmar Waltemath
Journal of Integrative Bioinformatics, Vol. 18, No. 3, 2021, pp. 20210020 October 20, 2021 doi: 10.1515/jib-2021-0020 - SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models
Woosub Shin, Joseph L. Hellerstein, Yuda Munarko, Maxwell L. Neal, David P. Nickerson, Anand K. Rampadarath, Herbert M. Sauro, John H. Gennari
bioRxiv (2021) October 9, 2021 doi: 10.1101/2021.10.09.463757 - The simulation experiment description markup language (SED-ML): language specification for level 1 version 4
Lucian P. Smith , Frank T. Bergmann , Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König
Journal of Integrative Bioinformatics, Vol. 18, No. 3, October 5, 2021 doi: 10.1515/jib-2021-0021 - SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems
Andreas Dräger, Tomáš Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar
Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3702–3706 June 24, 2021 doi: 10.1093/bioinformatics/btab229 - Centralizing data to unlock whole-cell models
Yin Hoon Chew, Jonathan R. Karr
Current Opinion in Systems Biology, Vol. 27, 100353, June 23, 2021 doi: 10.1016/j.coisb.2021.06.004 - LibOmexMeta: Enabling semantic annotation of models to support FAIR principles
Ciaran Welsh, David P Nickerson, Anand Rampadarath, Maxwell L Neal, Herbert M Sauro, John H Gennari
Bioinformatics, Volume 37, Issue 24, 15 Pages 4898–4900, June 16, 2021 doi: 10.1093/bioinformatics/btab445 - Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology.
Michael L. Blinov, John H. Gennari, Jonathan R. Karr, Ion I. Moraru, David P. Nickerson, Herbert M. Sauro
Current Opinion in Systems Biology, Vol. 21, 100350 June 10, 2021 doi: 10.1016/j.coisb.2021.06.001 - runBioSimulations: an extensible web application that simulates a wide range of mathematical modeling frameworks, algorithms, and formats
Bilal Shaikh, Gnaneswara Marupilla, Mike Wilson, Michael L Blinov, Ion I Moraru, Jonathan R Karr
Nucleic Acids Research, Volume 49, Issue W1, May 21, 2021 doi: 10.1093/nar/gkab411 - Hierarchical semantic composition of biosimulation models using bond graphs
Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran, Edmund J. Crampin, David P. Nickerson
PLOS Computational Biology (2021), May 13, 2021 doi: 10.1371/journal.pcbi.1008859 - Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling
Mazein A, Rougny A, Karr JR, Saez-Rodriguez J, Ostaszewski M & Schneider R
Briefings in Bioinformatics (2021), April 8, 2021 doi: 10.1093/bib/bbab103
2020
- Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior
Yosef D Roth, Zhouyang Lian, Saahith Pochiraju, Bilal Shaikh, Jonathan R Karr
Nucleic Acids Research, Volume 49, Issue D1, 8, Pages D516–D522 November 11, 2020 doi: 10.1093/nar/gkaa1008
Bioinformatics (2020) October 31, 2020 doi: 10.5281/zenodo.4245269 - Furthering genome design using models and algorithms
Joshua Rees-Garbutt, Jake Rightmyer, Jonathan R. Karr, Claire Grierson, Lucia Marucci
Current Opinion in Systems Biology, Dec. 2020, Vol. 24, 120–126 October 16, 2020 doi: 10.1016/j.coisb.2020.10.007 - Best Practices for Making Reproducible Biochemical Models
Veronica L. Porubsky, Arthur P. Goldberg, Anand K. Rampadarath, David P. Nickerson, Jonathan R. Karr, Herbert M. Sauro
Cell Systems Vol. 11, Issue, Pages 109-120 August 26, 2020 doi: 10.1016/j.cels.2020.06.012 - Computer-aided whole-cell design: taking a holistic approach by integrating synthetic with systems biology
Lucia Marucci, Matteo Barberis, Jonathan Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan Andreas Hoffmann, Sophie Landon, Elibio Rech, Joshua Rees-Garbutt, Richard Seabrook, William Shaw, Christopher Woods
Frontiers in Bioengineering and Biotechnology, Vol. 8, 942 (2020) August 7, 2020 doi: 10.3389/fbioe.2020.00942
- Organizing genome engineering for the gigabase scale
Bartley BA, Beal J, Karr JR & Strychalski E
Nature Communications 11, Article 689 February 4, 2020 doi: 10.1038/s41467-020-14314-z
2019
- Model annotation and discovery with the physiome model repository
Dewan M. Sarwar, Reza Kalbasi, John H. Gennari, Brian E. Carlson, Maxwell L. Neal, Bernard de Bono, Koray Atalag, Peter J. Hunter, David P. Nickerson
BMC Bioinformatics, Vol. 20 (2019) September 6, 2019 doi: 10.1186/s12859-019-2987-y