M. Hucka

Most-cited papers

A community-driven global reconstruction of human metabolism
I. Thiele, Neil Swainston, R. Fleming, A. Hoppe +42 more
2013Nature Biotechnology1,081 citations Open access
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Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0
Laurent Heirendt, Sylvain Arreckx, T. Pfau, Sebastián N. Mendoza +51 more
2019Nature Protocols1,072 citations Open access
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The Systems Biology Graphical Notation
N. Le Novère, M. Hucka, H. Mi, S. Moodie +35 more
2009Nature Biotechnology977 citations
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Erratum: GM alfalfa—who wins?
E. Demir, Michael P. Cary, Suzanne M. Paley, Ken Fukuda +86 more
2010Nature Biotechnology736 citations Open access
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BioPAX – A community standard for pathway data sharing
E. Demir, Michael P. Cary, Suzanne M. Paley, Ken Fukuda +86 more
2010Nature Biotechnology725 citations Open access
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A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
Markus J. Herrgård, Neil Swainston, P. Dobson, W. Dunn +30 more
2008Nature Biotechnology623 citations Open access
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BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
Chen Li, M. Donizelli, Nicolas Rodriguez, Harish Dharuri +10 more
2010BMC Systems Biology596 citations Open access
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LibSBML: an API Library for SBML
B. Bornstein, Sarah M. Keating, A. Jouraku, M. Hucka
2008Bioinform.422 citations Open access
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BioModels—15 years of sharing computational models in life science
Rahuman S. Malik-Sheriff, M. Glont, Tung V. N. Nguyen, Krishna Tiwari +20 more
2019Nucleic Acids Res.383 citations Open access
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Controlled vocabularies and semantics in systems biology
Mélanie Courtot, N. Juty, C. Knüpfer, Dagmar Waltemath +23 more
2011Molecular Systems Biology326 citations Open access
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BioModels: ten-year anniversary
V. Chelliah, N. Juty, I. Ajmera, Raza Ali +16 more
2014Nucleic Acids Res.289 citations Open access
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SBML Level 3: an extensible format for the exchange and reuse of biological models
Sarah M. Keating, D. Waltemath, Matthias König, Feng-Kai Zhang +137 more
2020Molecular Systems Biology269 citations Open access
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Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language
Dagmar Waltemath, R. Adams, Frank T. Bergmann, M. Hucka +7 more
2011BMC Systems Biology268 citations Open access
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Path2Models: large-scale generation of computational models from biochemical pathway maps
F. Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek +22 more
2013BMC Systems Biology174 citations Open access
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Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0.
Laurent Heirendt, Sylvain Arreckx, T. Pfau, Sebastián N. Mendoza +47 more
2017168 citations
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SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
C. Chaouiya, D. Bérenguier, Sarah M. Keating, A. Naldi +20 more
2013BMC Systems Biology162 citations Open access
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COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
Frank T. Bergmann, R. Adams, S. Moodie, Jonathan Cooper +14 more
2014BMC Bioinformatics159 citations Open access
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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2
M. Hucka, Frank T. Bergmann, C. Chaouiya, Andreas Dräger +13 more
2018Journal of Integrative Bioinformatics145 citations Open access
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Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
M. Hucka, Stefan Hoops, Sarah M. Keating, N. Le Novère +2 more
2007The Web Conference137 citations Open access
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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
M. Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops +9 more
2010Journal of Integrative Bioinformatics130 citations Open access
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JSBML: a flexible Java library for working with SBML
Andreas Dräger, Nicolas Rodriguez, M. Dumousseau, Alexander Dörr +4 more
2011Bioinform.82 citations Open access
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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core
M. Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops +9 more
2018Journal of Integrative Bioinformatics77 citations Open access
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Do genome-scale models need exact solvers or clearer standards?
A. Ebrahim, E. Almaas, Eugen Bauer, A. Bordbar +37 more
2015Molecular Systems Biology66 citations Open access
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Harmonizing semantic annotations for computational models in biology
M. Neal, Matthias König, D. Nickerson, Goksel Misirli +25 more
2018bioRxiv64 citations Open access
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Toward community standards and software for whole-cell modeling
Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, V. Chelliah +53 more
2016IEEE Transactions on Biomedical Engineering54 citations Open access
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Magic state cultivation on a superconducting quantum processor.
E. Rosenfeld, C. Gidney, G. Roberts, A. Morvan +292 more
2025Science53 citations Open access
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Profiling PARP inhibitors
E. Demir, Michael P. Cary, Suzanne M. Paley, Ken Fukuda +86 more
2012Nature Biotechnology50 citations Open access
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Explorer Minimum Information About a Simulation Experiment ( MIASE )
Dagmar Waltemath, R. Adams, D. Beard, Frank T. Bergmann +24 more
201748 citations
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Systems Biology Markup Language (SBML)
M. Hucka
2014Encyclopedia of Computational Neuroscience44 citations
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SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3
Lucian P. Smith, M. Hucka, Stefan Hoops, A. Finney +4 more
2015Journal of Integrative Bioinformatics43 citations
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JSBML 1.0: providing a smorgasbord of options to encode systems biology models
Nicolas Rodriguez, Alex Thomas, Leandro H. Watanabe, Ibrahim Y. Vazirabad +18 more
2015Bioinform.42 citations Open access
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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate)
M. Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating +2 more
201041 citations Open access
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Software vs. data in the context of citation
D. Katz, Kyle E. Niemeyer, Arfon M. Smith, William L. Anderson +8 more
2016PeerJ Preprints40 citations Open access
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Spiral: splitters for identifiers in source code files
M. Hucka
2018Journal of Open Source Software36 citations Open access
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Software search is not a science, even among scientists
M. Hucka, M. Graham
2016Journal of Systems and Software32 citations Open access
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Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)
Dagmar Waltemath, Frank T. Bergmann, C. Chaouiya, Tobias Czauderna +17 more
2011Standards in Genomic Sciences31 citations Open access
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SBML Level 3 package: Groups, Version 1 Release 1
M. Hucka, Lucian P. Smith
2016Journal of Integrative Bioinformatics29 citations Open access
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Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions
M. Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops +9 more
2015Journal of Integrative Bioinformatics27 citations Open access
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SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3
Lucian P. Smith, M. Hucka, Stefan Hoops, A. Finney +4 more
2015Journal of Integrative Bioinformatics23 citations Open access
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Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016
Falk Schreiber, Gary D Bader, Padraig Gleeson, Martin Golebiewski +6 more
2016Journal of Integrative Bioinformatics20 citations Open access
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Specifications of Standards in Systems and Synthetic Biology
Falk Schreiber, Gary D Bader, Martin Golebiewski, M. Hucka +7 more
2015Journal of Integrative Bioinformatics20 citations Open access
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Erratum: The Systems Biology Graphical Notation
N. Le Novère, M. Hucka, H. Mi, S. Moodie +35 more
2009Nature Biotechnology20 citations Open access
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Minimum Information About a Simulation Experiment (MIASE)
Dagmar Waltemath, R. Adams, Daniel Beard, Frank T. Bergmann +24 more
2011PLoS Comput. Biol.19 citations Open access
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Nine best practices for research software registries and repositories
D. Garijo, Herv'e M'enager, L. Hwang, Ana Trišović +3 more
2022PeerJ Computer Science17 citations Open access
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Quantum computation of molecular geometry via many-body nuclear spin echoes
C. Zhang, R. Cortiñas, A. Karamlou, N. Noll +319 more
202516 citations
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Specifications of standards in systems and synthetic biology: status and developments in 2020
Falk Schreiber, B. Sommer, Tobias Czauderna, Martin Golebiewski +7 more
2020Journal of Integrative Bioinformatics16 citations Open access
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MOCCASIN: converting MATLAB ODE models to SBML
H. Gómez, M. Hucka, Sarah M. Keating, German Nudelman +2 more
2016Bioinform.16 citations Open access
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Systems Biology Graphical Notation: Process Diagram Level 1
N. Le Novère, S. Moodie, A. Sorokin, M. Hucka +6 more
200816 citations Open access
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Nine Best Practices for Research Software Registries and Repositories: A Concise Guide
Alain Monteil, A. González-Beltrán, Alexandros Ioannidis, Alice Allen +27 more
2020arXiv.org14 citations
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Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
Falk Schreiber, B. Sommer, Gary D Bader, Padraig Gleeson +7 more
2019Journal of Integrative Bioinformatics14 citations Open access
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