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A community-driven global reconstruction of human metabolism I Thiele, N Swainston, RMT Fleming, A Hoppe, S Sahoo, MK Aurich, ... Nature biotechnology 31 (5), 419-425, 2013 | 1171 | 2013 |
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Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0 L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ... Nature protocols 14 (3), 639-702, 2019 | 977 | 2019 |
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The BioPAX community standard for pathway data sharing E Demir, MP Cary, S Paley, K Fukuda, C Lemer, I Vastrik, G Wu, ... Nature biotechnology 28 (9), 935-942, 2010 | 782 | 2010 |
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Minimum information requested in the annotation of biochemical models (MIRIAM) N Le Novère, A Finney, M Hucka, US Bhalla, F Campagne, ... Nature biotechnology 23 (12), 1509-1515, 2005 | 690 | 2005 |
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LibSBML: an API library for SBML BJ Bornstein, SM Keating, A Jouraku, M Hucka Bioinformatics 24 (6), 880, 2008 | 485 | 2008 |
Rules for modeling signal-transduction systems WS Hlavacek, JR Faeder, ML Blinov, RG Posner, M Hucka, W Fontana Sci STKE 344, 2006, 2006 | 450 | 2006 |
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration HM Sauro, M Hucka, A Finney, C Wellock, H Bolouri, J Doyle, H Kitano Omics A Journal of Integrative Biology 7 (4), 355-372, 2003 | 347 | 2003 |
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Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project M Hucka, A Finney, BJ Bornstein, SM Keating, BE Shapiro, J Matthews, ... Systems Biology 1 (1), 41-53, 2004 | 327 | 2004 |
BioModels: ten-year anniversary V Chelliah, N Juty, I Ajmera, R Ali, M Dumousseau, M Glont, M Hucka, ... Nucleic acids research 43 (D1), D542-D548, 2015 | 320 | 2015 |
BioModels—15 years of sharing computational models in life science RS Malik-Sheriff, M Glont, TVN Nguyen, K Tiwari, MG Roberts, A Xavier, ... Nucleic acids research 48 (D1), D407-D415, 2020 | 294 | 2020 |
Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language D Waltemath, R Adams, FT Bergmann, M Hucka, F Kolpakov, AK Miller, ... BMC systems biology 5, 1-10, 2011 | 290 | 2011 |
FAIRsharing as a community approach to standards, repositories and policies Nature Biotechnology 37 (4), 358, 2019 | 284 | 2019 |
Systems biology markup language: Level 2 and beyond A Finney, M Hucka Biochemical Society Transactions 31 (6), 1472-1473, 2003 | 272 | 2003 |
SBML Level 3: an extensible format for the exchange and reuse of biological models SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ... Molecular systems biology 16 (8), e9110, 2020 | 196 | 2020 |
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools C Chaouiya, D Bérenguier, SM Keating, A Naldi, MP Van Iersel, ... BMC systems biology 7, 1-15, 2013 | 189 | 2013 |
SBMLToolbox: an SBML toolbox for MATLAB users SM Keating, BJ Bornstein, A Finney, M Hucka Bioinformatics 22 (10), 1275-1277, 2006 | 183 | 2006 |
Towards NeuroML: model description methods for collaborative modelling in neuroscience NH Goddard, M Hucka, F Howell, H Cornelis, K Shankar, D Beeman Philosophical Transactions of the Royal Society of London. Series B …, 2001 | 180 | 2001 |
Path2Models: large-scale generation of computational models from biochemical pathway maps F Büchel, N Rodriguez, N Swainston, C Wrzodek, T Czauderna, R Keller, ... BMC systems biology 7, 1-19, 2013 | 175 | 2013 |
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COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project FT Bergmann, R Adams, S Moodie, J Cooper, M Glont, M Golebiewski, ... BMC bioinformatics 15, 1-9, 2014 | 146 | 2014 |
The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology M Hucka, A Finney, HM Sauro, H Bolouri, J Doyle, H Kitano Pac Symp Biocomput 1, 450-461, 2002 | 118 | 2002 |
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Systems Biology Markup Language (SBML) Level 1: Structures and facilities for basic model definitions M Hucka, A Finney, H Sauro, H Bolouri August, 2003 | 91 | 2003 |
Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative M Hucka, DP Nickerson, GD Bader, FT Bergmann, J Cooper, E Demir, ... Frontiers in bioengineering and biotechnology 3, 19, 2015 | 85 | 2015 |
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The genesis simulation system JM Bower, D Beeman, M Hucka The Handbook of Brain Theory and Neural Networks 2, 2002 | 75 | 2002 |
MathSBML: a package for manipulating SBML-based biological models BE Shapiro, M Hucka, A Finney, J Doyle Bioinformatics 20 (16), 2829, 2004 | 74 | 2004 |
Systems biology markup language (SBML) Level 2: structures and facilities for model definitions M Hucka, S Hoops, SM Keating, N Le Novère, S Sahle, D Wilkinson Nature Publishing Group, 2008 | 66 | 2008 |
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Do genome‐scale models need exact solvers or clearer standards? A Ebrahim, E Almaas, E Bauer, A Bordbar, AP Burgard, RL Chang, ... Molecular systems biology 11 (10), 831, 2015 | 64 | 2015 |
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Systems biology markup language (sbml) level 2: Structures and facilities for model definitions A Finney, M Hucka, H Bolouri June, 2003 | 53 | 2003 |
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SBML level 3 package: hierarchical model composition, version 1 release 3 LP Smith, M Hucka, S Hoops, A Finney, M Ginkel, CJ Myers, I Moraru, ... Journal of integrative bioinformatics 12 (2), 603-659, 2015 | 51 | 2015 |
CellML2SBML: conversion of CellML into SBML MJ Schilstra, L Li, J Matthews, A Finney, M Hucka, N Le Novère Bioinformatics 22 (8), 1018-1020, 2006 | 49 | 2006 |
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Challenges for modeling and simulation methods in systems biology HM Sauro, D Harel, M Kwiatkowska, CA Shaffer, AM Uhrmacher, M Hucka, ... Proceedings of the 2006 Winter Simulation Conference, 1720-1730, 2006 | 46 | 2006 |
Specifications of standards in systems and synthetic biology: status and developments in 2020 F Schreiber, B Sommer, T Czauderna, M Golebiewski, TE Gorochowski, ... Journal of integrative bioinformatics 17 (2-3), 20200022, 2020 | 37 | 2020 |
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Software Infrastructure for Effective Communication and Reuse of Computational Models A Finney, M Hucka, BJ Bornstein, SM Keating, BE Shapiro, J Matthews, ... | 27 | 2006 |
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Meeting report from the fourth meeting of the computational modeling in biology network (COMBINE) D Waltemath, FT Bergmann, C Chaouiya, T Czauderna, P Gleeson, ... Standards in Genomic Sciences 9, 1285-1301, 2014 | 21 | 2014 |
Systems biology graphical notation: process diagram level 1 N Le Novere, S Moodie, A Sorokin, M Hucka, F Schreiber, E Demir, H Mi, ... Nature Precedings, 1-1, 2008 | 20 | 2008 |
Introduction to the Systems Biology Workbench M Hucka, A Finney, HM Sauro, H Bolouri Available via the World Wide Web at http://www. cds. caltech. edu/erato/sbw …, 2001 | 18 | 2001 |
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A brief history of COMBINE CJ Myers, G Bader, P Gleeson, M Golebiewski, M Hucka, N Le Novere, ... 2017 Winter Simulation Conference (WSC), 884-895, 2017 | 8 | 2017 |
Modeling the E. coli cell: The need for computing, cooperation, and consortia B Wanner, A Finney, M Hucka Systems Biology, 1353-1355, 2005 | 8 | 2005 |
Nine best practices for research software registries and repositories D Garijo, H Ménager, L Hwang, A Trisovic, M Hucka, T Morrell, A Allen PeerJ Computer Science 8, e1023, 2022 | 7 | 2022 |
Data management in computational systems biology: exploring standards, tools, databases, and packaging best practices NJ Stanford, M Scharm, PD Dobson, M Golebiewski, M Hucka, ... Yeast Systems Biology: Methods and Protocols, 285-314, 2019 | 7 | 2019 |
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Software that goes with the flow in systems biology M Hucka, N Le Novère BMC biology 8, 1-3, 2010 | 6 | 2010 |
The Modeler's Workspace: making model-based studies of the nervous system more accessible M Hucka, K Shankar, D Beeman, JM Bower Computational neuroanatomy: principles and methods (ed. G. Ascoli). Humana Press, 2001 | 6 | 2001 |
Foundations of Systems Biology M Hucka, A Finney, H Sauro, H Bolouri, J Doyle, K Kitano First International Symposium on Computational Cell Biology, Lenox …, 2001 | 6 | 2001 |
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Trends and tools for modeling in modern biology M Hucka, J Schaff Photosynthesis in silico: Understanding Complexity from Molecules to …, 2009 | 3 | 2009 |
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Systems Biology Workbench Java programmer’s manual M Hucka, A Finney, HM Sauro, H Bolouri, F Bergmann Available via the World Wide Web at http://www. cds. caltech. edu/erato/sbw/docs, 2002 | 3 | 2002 |