Michael Hucka: Publications

This is a manually-curated list of my notable publications. An automatically-generated list of nearly all my publications is available on my Google Scholar page, where you can also find some bibliometric statistics such as citation counts.

Peer-reviewed journal publications

  1. Dagmar Waltemath, Jonathan Karr, Frank Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris Myers, Pinar Pir, Begum Alaybeyoglu, Naveen Aranganathan, Kambiz Baghalian, Arne Bittig, Paulo Burke, Matteo Cantarelli, Yin Chew, Rafael Costa, Joseph Cursons, Tobias Czauderna, Arthur Goldberg, Harold Gómez, Jens Hahn, Tuure Hameri, Daniel Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek Varusai, Leandro Watanabe, Florian Wendland, Markus Wolfien, James Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber 2016 Toward community standards and software for whole-cell modeling IEEE Transactions on Biomedical Engineering 63 2007–2015 10.1109/TBME.2016.2560762
  2. Harold F. Gómez, Michael Hucka, Sarah M. Keating, German Nudelman, Dagmar Iber, Stuart C. Sealfon 2016 MOCCASIN: converting MATLAB ODE models to SBML Bioinformatics 32 1905–1906 10.1093/bioinformatics/btw056
  3. Nicolas Rodriguez, Alex Thomas, Leandro Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, Andreas Dräger 2015 JSBML 1.0: providing a smorgasbord of options to encode systems biology models Bioinformatics 31 3383–3386 10.1093/bioinformatics/btv341
  4. Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomas Helikar, Claudine Chaouiya 2015 Cooperative development of logical modelling standards and tools with CoLoMoTo Bioinformatics btv013 10.1093/bioinformatics/btv013
  5. Michael Hucka, David P. Nickerson, Gary D. Bader, Frank T. Bergmann, Jonathan Cooper, Emek Demir, Alan Garny, Martin Golebiewski, Chris J. Myers, Falk Schreiber, Dagmar Waltemath, Nicolas Le Novère 2015 Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative Frontiers in Bioengineering and Biotechnology 3 19 10.3389/fbioe.2015.00019
  6. A. Ebrahim, E. Almaas, E. Bauer, A. Bordbar, A. P. Burgard, R. L. Chang, A. Drager, I. Famili, A. M. Feist, R. M. Fleming, S. S. Fong, V. Hatzimanikatis, M. J. Herrgard, A. Holder, M. Hucka, D. Hyduke, N. Jamshidi, S. Y. Lee, N. Le Novere, J. A. Lerman, N. E. Lewis, D. Ma, R. Mahadevan, C. Maranas, H. Nagarajan, A. Navid, J. Nielsen, L. K. Nielsen, J. Nogales, A. Noronha, C. Pal, B. O. Palsson, J. A. Papin, K. R. Patil, N. D. Price, J. L. Reed, M. Saunders, R. S. Senger, N. Sonnenschein, Y. Sun, I. Thiele 2015 Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology 11 831–831 10.15252/msb.20156157
  7. Vijayalakshmi Chelliah, Nick Juty, Ishan Ajmera, Raza Ali, Marine Dumousseau, Mihai Glont, Michael Hucka, Gaël Jalowicki, Sarah Keating, Vincent Knight-Schrijver 2015 BioModels: ten-year anniversary Nucleic Acids Research 43 D542–D548 10.1093/nar/gku1181
  8. Dagmar Waltemath, Frank T. Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet 2014 Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) Standards in Genomic Sciences 9 1285–1301 10.4056/sigs.5279417
  9. Frank T. Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère 2014 COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project BMC Bioinformatics 15 369 10.1186/s12859-014-0369-z
  10. Ines Thiele, Neil Swainston, Ronan M. T. Fleming, Andreas Hoppe, Swagatika Sahoo, Maike K. Aurich, Hulda Haraldsdottir, Monica L. Mo, Ottar Rolfsson, Miranda D. Stobbe, Stefan G. Thorleifsson, Rasmus Agren, Christian Bölling, Sergio Bordel, Arvind K. Chavali, Paul Dobson, Warwick B. Dunn, Lukas Endler, David Hala, Michael Hucka, Duncan Hull, Daniel Jameson, Neema Jamshidi, Jon J. Jonsson, Nick Juty, Sarah Keating, Intawat Nookaew, Nicolas Le Novère, Naglis Malys, Alexander Mazein, Jason A. Papin, Nathan D. Price, Evgeni Selkov Sr, Martin I. Sigurdsson, Evangelos Simeonidis, Nikolaus Sonnenschein, Kieran Smallbone, Anatoly Sorokin, Johannes H. G. M. van Beek, Dieter Weichart, Igor Goryanin, Jens Nielsen, Hans V. Westerhoff, Douglas B. Kell, Pedro Mendes, Bernhard Ø. Palsson 2013 A community-driven global reconstruction of human metabolism Nature Biotechnology 31 419–425 10.1038/nbt.2488
  11. Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomá\u s. Helikar 2013 SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools BMC Systems Biology 7 135 10.1186/1752-0509-7-135
  12. Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère 2013 Path2Models: large-scale generation of computational models from biochemical pathway maps BMC Systems Biology 7 116 10.1186/1752-0509-7-116
  13. Dagmar Waltemath, Richard Adams, Frank T. Bergmann, Michael Hucka, Fedor Kolpakov, Andrew K. Miller, Ion I. Moraru, David Nickerson, Sven Sahle, Jacky L. Snoep, Nicolas Le Novère 2011 Reproducible computational biology experiments with SED-ML–the Simulation Experiment Description Markup Language BMC Systems Biology 5 198 10.1186/1752-0509-5-198
  14. Dagmar Waltemath, Richard Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Michael T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion Moraru, David Nickerson, Poul Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic Tolle, Olaf Wolkenhauer, Nicolas Le Novère 2011 Minimum Information About a Simulation Experiment (MIASE) PLoS Computational Biology 7 e1001122 10.1371/journal.pcbi.1001122
  15. Nicolas Le Novère, Michael Hucka, Nadia Anwar, Gary D. Bader, Emek Demir, Stuart Moodie, Anatoly Sorokin 2011 Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE) Standards in Genomic Sciences 5 230–242 10.4056/sigs.2034671
  16. Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau, Alexander Dörr, Clemens Wrzodek, Nicolas Le Novère, Andreas Zell, Michael Hucka 2011 JSBML: a flexible Java library for working with SBML Bioinformatics 27 2167–2178 10.1093/bioinformatics/btr361
  17. Mélanie Courtot, Nick J. Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B. Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice J. Villeger, Darren J. Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novère 2011 Controlled vocabularies and semantics in systems biology Molecular Systems Biology 7 1 10.1038/msb.2011.77
  18. Chen Li, Marco Donizelli, Nicolas Rodriguez, Harish Dharuri, Lukas Endler, Vijayalakshmi Chelliah, Lu Li, Enuo U. He, Arnaud Henry, Melanie I. Stefan, Jacky L. Snoep, Michael Hucka, Nicolas Le Novère, Camille Laibe 2010 BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models BMC Systems Biology 4 92 10.1186/1752-0509-4-92
  19. Michael Hucka, Nicolas Le Novère 2010 Software that goes with the flow in systems biology BMC Biology 8 140 10.1186/1741-7007-8-140
  20. Emek Demir, Michael P. Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming N. Wu, Peter D'Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenzjun J. Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran Kandasamy, Alejandra C. Lopez-Fuentes, Huaiyu Y. Mi, Elgar Pichler, Igor Rodchenkov, Andrea Splendiani, Sasha Tkachev, Jeremy Zucker, Gopal Gopinath, Harsha Rajasimha, Ranjani Ramakrishnan, Imran Shah, Mustafa Syed, Nadia Anwar, Özgün O. Babur, Michael Blinov, Erik Brauner, Dan Corwin, Sylva Donaldson, Frank Gibbons, Robert Goldberg, Peter Hornbeck, Augustin Luna, Peter Murray-Rust, Eric Neumann, Oliver Reubenacker, Matthias Samwald, Martijn van Iersel, Sarala Wimalaratne, Keith Allen, Burk Braun, Michelle Whirl-Carrillo, Kei-Hoi H. Cheung, Kam Dahlquist, Andrew Finney, Marc Gillespie, Elizabeth Glass, Li Gong, Robin Haw, Michael Honig, Olivier Hubaut, David Kane, Shiva Krupa, Martina Kutmon, Julie Leonard, Debbie Marks, David Merberg, Victoria Petri, Alex Pico, Dean Ravenscroft, Liya Y. Ren, Nigam Shah, Margot Sunshine, Rebecca Tang, Ryan Whaley, Stan Letovksy, Kenneth H. Buetow, Andrey Rzhetsky, Vincent Schachter, Bruno S. Sobral, Ugur Dogrusoz, Shannon McWeeney, Mirit Aladjem, Ewan Birney, Julio Collado-Vides, Susumu Goto, Michael Hucka, Nicolas Le Novère, Natalia Maltsev, Akhilesh Pandey, Paul Thomas, Edgar Wingender, Peter D. Karp, Chris Sander, Gary D. Bader 2010 The BioPAX community standard for pathway data sharing Nature Biotechnology 28 935–942 10.1038/nbt.1666
  21. Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, 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 E. Boyd, Laurence Calzone, Melanie Courtot, Ugur Dogrusoz, Tom C. Freeman, Akira Funahashi, Samik Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin, Douglas B. Kell, Chris Sander, Herbert Sauro, Jacky L. Snoep, Kurt Kohn, Hiroaki Kitano 2009 The Systems Biology Graphical Notation Nature Biotechnology 27 735–741 10.1038/nbt.1558
  22. Andreas Dräger, Hannes Planatscher, Dieudonné M. Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, Andreas Zell 2009 SBML2LATEX: Conversion of SBML files into human-readable reports Bioinformatics 25 1455–1456 Doi 10.1093/Bioinformatics/Btp170
  23. Markus J. Herrg$\aa$rd, Neil Swainston, Paul Dobson, Warwick B. Dunn, K. Yalçin Arga, Mikko Arvas, Nils Blüthgen, Simon Border, Roeland Costenoble, Matthias Heinemann, Michael Hucka, Nicolas Le Novère, Peter Li, Wolfram Liebermeister, Monica L. Mo, Ana Paula Oliveria, Dina Petranovic, Stephen Pettifer, Evangelos Simeonidis, Kieran Smallbone, Irena Spasić, Dieter Weichart, Roger Brent, David S. Broomhead, Hans V. Westerhoff, Betül Kirdar, Merja Penttilä, Edda Klipp, Bernhard Ø. Palsson, Uwe Sauer, Stephen G. Oliver, Pedro Mendes, Jens Nielsen, Douglas B. Kell 2008 A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology Nature Biotechnology 26 1155–1160 10.1038/nbt1492
  24. Benjamin J. Bornstein, Sarah M. Keating, Akiya Jouraku, Michael Hucka 2008 LibSBML: an API library for SBML Bioinformatics 24 880–881 10.1093/bioinformatics/btn051
  25. Maria J. Schilstra, Lu Li, JoAnne Matthews, Andrew Finney, Michael Hucka, Nicolas Le Novère 2006 CellML2SBML: Conversion of CellML into SBML Bioinformatics 22 1018–1020 10.1093/bioinformatics/btl047
  26. Nicolas Le Novère, Benjamin Bornstein, Alexander Broicher, Mélanie Courtot, Marco Donizelli, Harish Dharuri, Lu Li, Herbert Sauro, Maria Schilstra, Bruce Shapiro, Jacky L. Snoep, Michael Hucka 2006 BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems Nucleic Acids Research 34 D689–D691 10.1093/nar/gkj092
  27. Sarah M. Keating, Benjamin J. Bornstein, Andrew Finney, Michael Hucka 2006 SBMLToolbox: an SBML toolbox for MATLAB users Bioinformatics 22 1275–1277
  28. William S. S. Hlavacek, James R. R. Faeder, Michael L. L. Blinov, Richard G. G. Posner, Michael Hucka, Walter Fontana 2006 Rules for modeling signal-transduction systems Science's STKE: signal transduction knowledge environment 2006 re6 10.1126/stke.3442006re6
  29. Nicolas Le Novère, Andrew Finney, Michael Hucka, Upinder S. Bhalla, Fabien Campagne, Julio Collado-Vides, Edmund J. Crampin, Matt Halstead, Edda Klipp, Pedro Mendes, Poul Nielsen, Herbert Sauro, Bruce E. Shapiro, Jacky L. Snoep, Hugh D. Spence, Barry L. Wanner 2005 Minimum information requested in the annotation of biochemical models (MIRIAM) Nature Biotechnology 23 1509–1015 10.1038/nbt1156
  30. Michael Hucka, Andrew Finney 2005 Escalating model sizes and complexities call for standardized forms of representation Molecular Systems Biology 1 E1–E2 10.1038/msb4100015
  31. Bruce E. Shapiro, Michael Hucka, Andrew Finney, John Doyle 2004 MathSBML: a package for manipulating SBML-based biological models Bioinformatics 20 2829–2831 Doi 10.1093/Bioinformatics/Bth271
  32. Michael Hucka, Andrew Finney, Benjamin J. Bornstein, Sarah M. Keating, Bruce E. Shapiro, JoAnne Matthews, Benjamin L. Kovitz, Maria J. Schilstra, Akira Funahashi, John C. Doyle, Hiroaki Kitano 2004 Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project Systems Biology 1 41–53 10.1049/sb:20045008
  33. Herbert M. Sauro, Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, Hiroaki Kitano 2003 Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration OMICS 7 355–372 10.1089/153623103322637670
  34. Michael Hucka, Andrew Finney, Herbert M. Sauro, Hamid Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, Dennis Bray, Athel Cornish-Bowden, Autumn A. Cuellar, Sergey Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor I. Goryanin, Warren J. Hedley, T. Charles Hodgman, Jan-Hendrik -. H. S. Hofmeyr, Peter J. Hunter, Nick S. Juty, Jay L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, Daniel Lucio, Pedro Mendes, Eric Minch, Eric D. Mjolsness, Yoichi Nakayama, Melanie R. Nelson, Poul F. Nielsen, Takeshi Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas S. Shimizu, Hugh D. Spence, Jörg Stelling, Kouichi Takahashi, Masaru Tomita, John M. Wagner, J. Wang 2003 The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics 19 524–531 10.1093/bioinformatics/btg015
  35. Akira Funahashi, Mineo Morohashi, Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri, John Doyle, Hiroaki Kitano 2003 A Software Platform for Systems Biology Nature Insight Computational Biology
  36. Andrew M. Finney, Michael Hucka 2003 Systems biology markup language: Level 2 and beyond Biochemical Society Transactions 31 1472–1473
  37. Nigel H. Goddard, David Beeman, Robert Cannon, Hugo Cornelis, Marc-Oliver O. Gewaltig, Greg Hood, Fred Howell, Paul Rogister, Erik D. De Schutter, Kavita Shankar, Michael Hucka 2002 NeuroML for plug and play neuronal modeling Neurocomputing 44 1077–1081 10.1016/S0925-2312(02)00420-4
  38. Nigel H. Goddard, Michael Hucka, Fred Howell, Hugo Cornelis, Kavita Shankar, David Beeman 2001 Towards NeuroML: Model Description Methods for Collaborative Modelling in Neuroscience Philosophical Transactions of the Royal Society B 356 1209–1228 10.1098/rstb.2001.0910
  39. Michael Hucka, Jenny Forss, Sara M. Emardson, Kavita Shankar, David Beeman, James M. Bower 2000 The Modeler's Workspace: Making model-based studies of the nervous system more accessible [Abstract] FASEB Journal 14 A543
  40. Michael Hucka, Mark Weaver, Stephen S. Kaplan 1995 Hebb's Accomplishments Misunderstood Behavioral and Brain Sciences 18 635–636 10.1017/S0140525X00040267
  41. John E. Laird, Eric S. Yager, Michael Hucka, Christopher m. Tuck 1991 Robo-Soar: An integration of external interaction, planning, and learning using Soar Robotics and Autonomous Systems 8 113–129 10.1016/0921-8890(91)90017-F
  42. John Laird, Mike Hucka, Scott Huffman, Paul Rosenbloom 1991 An analysis of Soar as an integrated architecture SIGART Bulletin 2 98–103 10.1145/122344.122364

Preprints and non-peer reviewed journal publications

  1. Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Summer, Dagmar Waltemath 2016 Specifications of standards in systems and synthetic biology: Status and Developments in 2016 Journal of Integrative Bioinformatics 13 289
  2. Daniel S. Katz, Kyle E. Niemeyer, Arfon M. Smith, William L. Anderson, Carl Boettiger, Konrad Hinsen, Rob Hooft, Michael Hucka, Allen Lee, Frank Löffler 2016 Software vs. data in the context of citation PeerJ Preprints 4 e2630v1
  3. Michael Hucka, Lucian P. J. P. Smith 2016 SBML Level 3 package: Groups, Version 1 Release 1 Journal of Integrative Bioinformatics 13 290
  4. Michael Hucka, Matthew J. Graham 2016 Software search is not a science, even among scientists Computing Resources Repository arXiv:1605.02265
  5. Lucian Paul Smith, Michael Hucka, Stefan Hoops, Andrew Finney, Martin Ginkel, Chris J. Myers, Ion Moraru, Wolfram Liebermeister 2015 SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3 Journal of Integrative Bioinformatics 12 268 10.2390/biecoll-jib-2015-268
  6. Falk Schreiber, Gary D. Bader, Martin Golebiewski, Michael Hucka, Benjamin Kormeier, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath, Stephan Weise 2015 Specifications of Standards in Systems and Synthetic Biology Journal of Integrative Bioinformatics 12 258 10.2390/biecoll-jib-2015-258
  7. Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson 2015 The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core Journal of Integrative Bioinformatics 12 266 10.2390/biecoll-jib-2015-266
  8. Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson 2015 Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions Journal of Integrative Bioinformatics 12 271 10.2390/biecoll-jib-2015-271
  9. Frank T. Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère 2014 One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project Computer Resources Repository arXiv:1407.4992

Peer-reviewed conference publications

  1. Chris J. Myers, Gary Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, David P. Nickerson, Falk Schreiber, Dagmar Waltemath 2017 A brief history of COMBINE Proceedings of the 2017 Winter Simulation Conference
  2. Michael Hucka 2015 Organizing Community-Based Data Standards: Lessons from Developing a Successful Open Standard in Systems Biology A.R. Taylor, E. Rosolowsky Astronomical Data Analysis Software an Systems XXIV (ADASS XXIV) Astronomical Society of the Pacific 575–578
  3. Michael Hucka, Frank T. Bergmann, Sarah M. Keating, Lucian Smith 2011 A profile of today's SBML-compatible software eScience 2011: 7th IEEE International Conference on e-Science IEEE Press 143–150 10.1109/eScienceW.2011.28
  4. Herbert M. Sauro, Adelinde M. Uhrmacher, David Harel, Michael Hucka, Martha Kwiatkowska, Pedro Mendes, Cliff A. Shaffer, Lena Strömback, John J. Tyson 2006 Challenges for modeling and simulation methods in systems biology L.F. Perrone, F.P. Wieland, J. Liu, B.G. Lawson, D.M. Nicol, R.M. Fujimoto Proceedings of the 2006 Winter Simulation Conference IEEE Press 1720–1730
  5. Michael Hucka, Andrew Finney, Herbert M. Sauro, Hamid Bolouri, John C. Doyle, Hiroaki Kitano 2002 The ERATO Systems Biology Workbench: Enabling interaction and exchange between software tools for computational biology Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Kevin Lauderdale, Teri E. Klein Pacific Symposium on Biocomputing World Scientific Press 450–461
  6. Michael Hucka, Andrew Finney, Herbert M. Sauro, Hamid Bolouri, John C. Doyle, Hiroaki Kitano 2001 The ERATO Systems Biology Workbench: Architectural Evolution Tau-Mu Yi, Michael Hucka, Mineo Morohashi, Hiroaki Kitano Proceedings of the Second International Conference on Systems Biology (ICSB2001) Omnipress 352–361
  7. Andrew Finney, Michael Hucka, Herbert M. Sauro, John C. Doyle, Hiroaki Kitano 2001 An Overview of the ERATO Systems Biology Workbench Project [Abstract] Ursula Kummer, Ralph Gauges, C. van Gend 2nd Workshop on Computation and Biochemical Pathways Logos-Verlag 115–122
  8. Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri, John Doyle, Hiroaki Kitano 2001 The Systems Biology Markup Language (SBML): A Standard for the Exchange of Biochemical Network Models Proceedings of the International Conference on Systems Biology (ICSB) 130
  9. Michael Hucka, Stephen Kaplan 1996 Texture-Based Processing in Early Vision and a Proposed Role for Coarse-Scale Segmentation M. Gasser Online Proceedings of the 1996 Midwest Artificial Intelligence and Cognitive Science Conference (MAICS '96) 1–6
  10. Michael Hucka, Stephen Kaplan 1996 Approximate Spatial Layout Processing in Early Vision [Abstract] Proceedings of the Eighteeth Annual Meeting of the Cognitive Science Society
  11. John E. Laird, Michael Hucka, Eric S. Yager, Christopher M. Tuck 1990 Correcting and extending domain knowledge using outside guidance Proceedings of the Seventh International Conference (1990) on Machine Learning Morgan Kaufmann Publishers Inc. 235–243
  12. John Laird, Eric Yager, Christopher Tuck, Michael Hucka 1989 Learning in tele-autonomous systems using Soar Proceedings of the NASA Conference on Space Telerobotics NASA Jet Propulsion Laboratory 415–424

Book chapters

  1. Michael Hucka 2015 Systems Biology Markup Language (SBML) Dieter Jaeger, Jung Ranu Encyclopedia of Computational Neuroscience Springer Science+Business Media 2943–2944
  2. Michael Hucka 2013 Systems Biology Markup Language (SBML) Werner Dubitzky, Olaf Wolkenhauer, Hiroki Yokota, Cho Kwang-Hyun Encyclopedia of Systems Biology Springer 2057–2063
  3. Michael Hucka, James Schaff 2009 Trends and tools for modeling in modern biology Laisk Agu, Ladislav Nedbal, Govindjee Photosynthesis in silico Springer 3–15
  4. Bruce E. Shapiro, Andrew Finney, Michael Hucka, Benjamin Bornstein, Akira Funahashi, Akiya Jouraku, Sarah M. Keating, Nicolas Le Novère, Joanne Matthews, Maria J. Schilstra 2007 SBML models and MathSBML S. Choi Introduction to Systems Biology Springer 395–421
  5. Andrew Finney, Michael Hucka, Benjamin J. Bornstein, Sarah M. Keating, Bruce E. Shapiro, Joanne Matthews, Ben L. Kovitz, Maria J. Schilstra, Akira Funahashi, John C. Doyle, Hiroaki Kitano 2006 Software Infrastructure for Effective Communication and Reuse of Computational Models Zoltan Szallasi, Jörg Stelling, Vipul Periwal System Modeling in Cell Biology: From Concepts to Nuts and Bolts MIT Press 357–378
  6. Barry Wanner, Andrew Finney, Michael Hucka 2005 Modeling the E. coli cell: The need for computing, cooperation, and consortia Lila Alberghina, H. V. Westerhoff Systems Biology: Definitions and Perspectives Springer Berlin / Heidelberg 1353–1355 10.1007/b138743
  7. James M. Bower, David Beeman, Michael Hucka 2003 The GENESIS Simulation System Michael A. Arbib The Handbook of Brain Theory and Neural Networks MIT Press 475–478
  8. M. Hucka, K. Shankar, D. Beeman, J. M. Bower 2002 The Modeler's Workspace Giorgio A. Ascoli Computational Neuroanatomy: Principles and Methods Humana Press 83–103
  9. Michael Hucka, Herbert M. Sauro, Andrew Finney, Hamid Bolouri, John Doyle, Hiroaki Kitano 2001 The ERATO Systems Biology Workbench: An integrated environment for multiscale and multitheoretic simulations in systems biology H. Kitano Foundations of Systems Biology MIT Press 125–143
  10. John E. W. Laird, Eric S. Yager, Michael Hucka, Christopher M. Tuck 1993 Robo-Soar: an integration of external interaction, planning, and learning using Soar Walter de Van Velde Towards Learning Robots MIT Press 113–130

Editorials, reports, and other non-peer-reviewed publications

  1. Dagmar Waltemath, Neil Swainston, Allyson L. Lister, Frank Bergmann, Ron Henkel, Stefan Hoops, Michael Hucka, Nick Juty, Sarah Keating, Christian Knüpfer, Falko Krause, Camille Laibe, Wolfram Liebermeister, Catherine Lloyd, Goksel Misirli, Marvin Schulz, Morgan Taschuk, Nicolas Le Novère 2011 SBML Level 3 Package Proposal: Annotation Nature Precedings 10.1038/npre.2011.5610.1
  2. Lucian P. Smith, Michael Hucka 2011 SBML Level 3 Package Specification: Hierarchical Model Composition, Version 1 Draft This is the draft specification for the SBML Level 3 'comp' package
  3. Michael Hucka, Frank T. Bergmann, Stephan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith 2010 The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core Nature Precedings 10.1038/npre.2010.4959.1 This is the specification for SBML Level 3 Version 1
  4. Michael Hucka 2009 An overview of several standardization efforts for systems biology [Abstract] Journal of Physiological Sciences 59 102 Abstract of presentation given at IUPS2009.
  5. Nicolas Le Novère, Stuart Moodie, Anatoloy Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Yukiko Matsuoka, Katja Wegner, Hiroaki Kitano 2008 Systems Biology Graphical Notation: Process Diagram Level 1 Nature Precedings 10101/npre.2008.2320.1 This is the specification for SBGN PD Level 1 Release 1.0
  6. Michael Hucka, Stephan Hoops, Sarah M. Keating, Nicolas Le Novère, Sven Sahle, Darren J. Wilkinson 2008 Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions Nature Precedings doi:10.1038/npre.2008.2715.1 This is the specification for SBML Level 2 Version 4
  7. Michael Hucka, Andrew Finney, Stephan Hoops, Sarah M. Keating, Nicolas Le Novère 2007 Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions Nature Precedings doi:10101/npre.2007.58.1 This is the specification for SBML Level 2 Version 3
  8. Michael Hucka, Andrew Finney, Nicolas Le Novère 2006 Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions This is the specification for SBML Level 2 Version 2
  9. Michael Hucka, Andrew Finney 2003 Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions This is the specification for SBML Level 2 Version 1
  10. Michael Hucka, Andrew Finney 2003 Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions This is the specification for SBML Level 2 Version 1
  11. Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri, Akira Funahashi, Ben Bornstein, Ben Kovitz, Joanne Matthews, Bruce E. Shapiro, Sarah Keating, John Doyle, Hiroaki Kitano 2003 The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules
  12. Andrew Finney, Michael Hucka, Ben Bornstein 2003 Parameter Sets: a standard technology for use with SBML
  13. Herbert M. Sauro, Michael Hucka, Andrew Finney, Hamid Bolouri 2002 Systems Biology Workbench Delphi/Kylix Programmer's Manual
  14. Michael Hucka, Herbert Sauro 2002 Proposal for a Minimal SBML Level 2 Definition
  15. Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri, John Doyle, Hiroaki Kitano 2002 The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules
  16. Michael Hucka, Andrew Finney, Herbert M. Sauro, Hamid Bolouri 2002 Systems Biology Workbench Javatm Programmer's Manual
  17. Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri, Akira Funahashi, Ben Bornstein, Ben Kovitz, Joanne Matthews, Bruce E. Shapiro, Sarah Keating, John Doyle, Hiroaki Kitano 2002 The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules
  18. Andrew Finney, Michael Hucka, Herbert M. Sauro, Hamid Bolouri 2002 Systems Biology Workbench C++ Programmer's Manual
  19. H. M. Sauro, M. Hucka, A. Finney, H. Bolouri 2001 The Systems Biology Workbench Concept Demonstrator: Design and Implementation
  20. M. Hucka, A. Finney, H. M. Sauro, H. Bolouri 2001 Introduction to the Systems Biology Workbench
  21. M. Hucka, A. Finney, H. M. Sauro, H. Bolouri 2001 A Comparison of Two Alternative Message-Passing Approaches for SBW
  22. Michael Hucka, Andrew Finney, Herbert M. Sauro 2001 Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions This is the specification for SBML Level 1 Version 1
  23. Andrew Finney, Michael Hucka, Herbert M. Sauro, Hamid Bolouri 2001 Systems Biology Workbench C Programmer's Manual
  24. Andrew Finney, Michael Hucka, Herbert M. Sauro, Hamid Bolouri 2001 Systems Biology Workbench C Programmer's Manual
  25. Andrew Finney, Michael Hucka, Herbert M. Sauro, Hamid Bolouri 2001 Systems Biology Workbench C Programmer's Manual
  26. M. Hucka, A. Finney, H. Sauro, H. Bolouri 2000 Preliminary High-Level Design for BMF, the Biology Modeling Framework
  27. M. Hucka, D. Beeman, K. Shankar, S. Emardson, J. M. Bower 2000 Society for Neuroscience Abstracts 21–69
  28. M. Hucka 2000 SCHUCS: A Notation for Describing Model Representations Intended for XML Encoding
  29. Michael Hucka 1998 Approximate Spatial Layout Processing in the Visual System: Modeling Texture-Based Segmentation and Shape Estimation Doctoral Dissertation
  30. M. Hucka, S. Kaplan 1997 A model for texture-based segmentation of natural scenes [Abstract] Investigative Ophthalmology &Visual Science 38 2990 Lippincott-Raven
  31. John Laird, Robert Doorenbos, Garrett Pelton, Michael Hucka, Paul Rosenbloom 1992 A Specification of the Soar Cognitive Architecture in Z School of Computer Science, Carnegie Mellon University
  32. Michael Hucka, Frank Ritter, Tom McGinnis 1992 Soar-mode v5.0 User's Manual for Soar release 5.2 and 6.0 School of Computer Science, Carnegie Mellon University