M
Michael Hucka
Researcher at California Institute of Technology
Publications - 126
Citations - 15161
Michael Hucka is an academic researcher from California Institute of Technology. The author has contributed to research in topics: SBML & Systems Biology Ontology. The author has an hindex of 42, co-authored 124 publications receiving 13785 citations. Previous affiliations of Michael Hucka include University of Michigan.
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Journal ArticleDOI
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Michael Hucka,Andrew Finney,Herbert M. Sauro,Hamid Bolouri,Hamid Bolouri,John Doyle,Hiroaki Kitano,Adam P. Arkin,Benjamin Bornstein,Dennis Bray,Athel Cornish-Bowden,Autumn A. Cuellar,S. Dronov,E. D. Gilles,Martin Ginkel,V. Gor,Igor Goryanin,W. J. Hedley,T. C. Hodgman,J.-H.S. Hofmeyr,Peter Hunter,Nick Juty,J. L. Kasberger,Andreas Kremling,Ursula Kummer,N Le Novère,Leslie M. Loew,D. Lucio,Pedro Mendes,E. Minch,Eric Mjolsness,Yoichi Nakayama,Melanie R. Nelson,Poul M. F. Nielsen,T. Sakurada,James C. Schaff,Bruce E. Shapiro,Thomas S. Shimizu,H. D. Spence,Jörg Stelling,Koichi Takahashi,Masaru Tomita,John Wagner,J. Wang +43 more
TL;DR: This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
Journal ArticleDOI
A community-driven global reconstruction of human metabolism
Ines Thiele,Neil Swainston,Ronan M. T. Fleming,Andreas Hoppe,Swagatika Sahoo,Maike K. Aurich,Hulda S. Haraldsdóttir,Monica L. Mo,Ottar Rolfsson,Miranda D. Stobbe,Miranda D. Stobbe,Stefan Gretar Thorleifsson,Rasmus Agren,Christian Bölling,Sergio Bordel,Arvind K. Chavali,Paul D. Dobson,Warwick B. Dunn,Warwick B. Dunn,Lukas Endler,David Hala,Michael Hucka,Duncan Hull,Daniel Jameson,Neema Jamshidi,Jon J. Jonsson,Nick Juty,Sarah M. Keating,Intawat Nookaew,Nicolas Le Novère,Nicolas Le Novère,Naglis Malys,Naglis Malys,Alexander Mazein,Jason A. Papin,Nathan D. Price,Evgeni Selkov,Martin I. Sigurdsson,Evangelos Simeonidis,Evangelos Simeonidis,Nikolaus Sonnenschein,Kieran Smallbone,Anatoly Sorokin,Anatoly Sorokin,Johannes H. G. M. van Beek,Dieter Weichart,Igor Goryanin,Jens Nielsen,Hans V. Westerhoff,Douglas B. Kell,Pedro Mendes,Pedro Mendes,Bernhard O. Palsson,Bernhard O. Palsson +53 more
TL;DR: Recon 2, a community-driven, consensus 'metabolic reconstruction', is described, which is the most comprehensive representation of human metabolism that is applicable to computational modeling and has improved topological and functional features.
Journal ArticleDOI
The Systems Biology Graphical Notation
Nicolas Le Novère,Michael Hucka,Huaiyu Mi,Stuart L. Moodie,Falk Schreiber,Falk Schreiber,Anatoly Sorokin,Emek Demir,Katja Wegner,Mirit I. Aladjem,Sarala M. Wimalaratne,Frank T Bergman,Ralph Gauges,Peter Ghazal,Hideya Kawaji,Lu Li,Yukiko Matsuoka,Alice Villéger,Sarah Elizabeth Boyd,Laurence Calzone,Mélanie Courtot,Ugur Dogrusoz,Tom C. Freeman,Akira Funahashi,Samik Ghosh,Akiya Jouraku,Sohoung Kim,Fedor A. Kolpakov,Augustin Luna,Sven Sahle,Esther Schmidt,Steven Watterson,Steven Watterson,Guanming Wu,Igor Goryanin,Douglas B. Kell,Chris Sander,Herbert M. Sauro,Jacky L. Snoep,Kurt W. Kohn,Hiroaki Kitano +40 more
TL;DR: The Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists, believes that it will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge.
Journal ArticleDOI
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
Nicolas Le Novère,Benjamin Bornstein,Alexander Broicher,Mélanie Courtot,Marco Donizelli,Harish Dharuri,Lu Li,Herbert M. Sauro,Maria J. Schilstra,Bruce E. Shapiro,Jacky L. Snoep,Michael Hucka +11 more
TL;DR: TheBioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems.
Journal ArticleDOI
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Laurent Heirendt,Sylvain Arreckx,Thomas Pfau,Sebastián N. Mendoza,Anne Richelle,Almut Heinken,Hulda S. Haraldsdóttir,Jacek Wachowiak,Sarah M. Keating,Vanja Vlasov,Stefania Magnusdottir,Chiam Yu Ng,German Preciat,Alise Žagare,Siu Hung Joshua Chan,Maike K. Aurich,Catherine M. Clancy,Jennifer Modamio,John T. Sauls,Alberto Noronha,Aarash Bordbar,Benjamin Cousins,Diana C. El Assal,Luis Vitores Valcárcel,Iñigo Apaolaza,Susan Ghaderi,Masoud Ahookhosh,Marouen Ben Guebila,Andrejs Kostromins,Nicolas Sompairac,Hoai M. Le,Ding Ma,Yuekai Sun,Lin Wang,James T. Yurkovich,Miguel A.P. Oliveira,Phan Tu Vuong,Lemmer P. El Assal,Inna Kuperstein,Andrei Zinovyev,H. Scott Hinton,William A. Bryant,Francisco J. Aragón Artacho,Francisco J. Planes,Egils Stalidzans,Alejandro Maass,Santosh Vempala,Michael Hucka,Michael A. Saunders,Costas D. Maranas,Nathan E. Lewis,Thomas Sauter,Bernhard O. Palsson,Bernhard O. Palsson,Ines Thiele,Ronan M. T. Fleming,Ronan M. T. Fleming +56 more
TL;DR: This protocol provides an overview of all new features of the COBRA Toolbox and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios.