Publications are listed in reverse chronological order.

2024

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 the 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