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
- 2016 Toward community standards and software for whole-cell modeling IEEE Transactions on Biomedical Engineering 63 2007–2015 10.1109/TBME.2016.2560762
- 2016 MOCCASIN: converting MATLAB ODE models to SBML Bioinformatics 32 1905–1906 10.1093/bioinformatics/btw056
- 2015 JSBML 1.0: providing a smorgasbord of options to encode systems biology models Bioinformatics 31 3383–3386 10.1093/bioinformatics/btv341
- 2015 Cooperative development of logical modelling standards and tools with CoLoMoTo Bioinformatics btv013 10.1093/bioinformatics/btv013
- 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
- 2015 Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology 11 831–831 10.15252/msb.20156157
- 2015 BioModels: ten-year anniversary Nucleic Acids Research 43 D542–D548 10.1093/nar/gku1181
- 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
- 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
- 2013 A community-driven global reconstruction of human metabolism Nature Biotechnology 31 419–425 10.1038/nbt.2488
- 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
- 2013 Path2Models: large-scale generation of computational models from biochemical pathway maps BMC Systems Biology 7 116 10.1186/1752-0509-7-116
- 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
- 2011 Minimum Information About a Simulation Experiment (MIASE) PLoS Computational Biology 7 e1001122 10.1371/journal.pcbi.1001122
- 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
- 2011 JSBML: a flexible Java library for working with SBML Bioinformatics 27 2167–2178 10.1093/bioinformatics/btr361
- 2011 Controlled vocabularies and semantics in systems biology Molecular Systems Biology 7 1 10.1038/msb.2011.77
- 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
- 2010 Software that goes with the flow in systems biology BMC Biology 8 140 10.1186/1741-7007-8-140
- 2010 The BioPAX community standard for pathway data sharing Nature Biotechnology 28 935–942 10.1038/nbt.1666
- 2009 The Systems Biology Graphical Notation Nature Biotechnology 27 735–741 10.1038/nbt.1558
- 2009 SBML2LATEX: Conversion of SBML files into human-readable reports Bioinformatics 25 1455–1456 Doi 10.1093/Bioinformatics/Btp170
- 2008 A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology Nature Biotechnology 26 1155–1160 10.1038/nbt1492
- 2008 LibSBML: an API library for SBML Bioinformatics 24 880–881 10.1093/bioinformatics/btn051
- 2006 CellML2SBML: Conversion of CellML into SBML Bioinformatics 22 1018–1020 10.1093/bioinformatics/btl047
- 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
- 2006 SBMLToolbox: an SBML toolbox for MATLAB users Bioinformatics 22 1275–1277
- 2006 Rules for modeling signal-transduction systems Science's STKE: signal transduction knowledge environment 2006 re6 10.1126/stke.3442006re6
- 2005 Minimum information requested in the annotation of biochemical models (MIRIAM) Nature Biotechnology 23 1509–1015 10.1038/nbt1156
- 2005 Escalating model sizes and complexities call for standardized forms of representation Molecular Systems Biology 1 E1–E2 10.1038/msb4100015
- 2004 MathSBML: a package for manipulating SBML-based biological models Bioinformatics 20 2829–2831 Doi 10.1093/Bioinformatics/Bth271
- 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
- 2003 Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration OMICS 7 355–372 10.1089/153623103322637670
- 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
- 2003 A Software Platform for Systems Biology Nature Insight Computational Biology
- 2003 Systems biology markup language: Level 2 and beyond Biochemical Society Transactions 31 1472–1473
- 2002 NeuroML for plug and play neuronal modeling Neurocomputing 44 1077–1081 10.1016/S0925-2312(02)00420-4
- 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
- 2000 The Modeler's Workspace: Making model-based studies of the nervous system more accessible [Abstract] FASEB Journal 14 A543
- 1995 Hebb's Accomplishments Misunderstood Behavioral and Brain Sciences 18 635–636 10.1017/S0140525X00040267
- 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
- 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
- 2016 Specifications of standards in systems and synthetic biology: Status and Developments in 2016 Journal of Integrative Bioinformatics 13 289
- 2016 Software vs. data in the context of citation PeerJ Preprints 4 e2630v1
- 2016 SBML Level 3 package: Groups, Version 1 Release 1 Journal of Integrative Bioinformatics 13 290
- 2016 Software search is not a science, even among scientists Computing Resources Repository arXiv:1605.02265
- 2015 SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3 Journal of Integrative Bioinformatics 12 268 10.2390/biecoll-jib-2015-268
- 2015 Specifications of Standards in Systems and Synthetic Biology Journal of Integrative Bioinformatics 12 258 10.2390/biecoll-jib-2015-258
- 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
- 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
- 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
- 2017 A brief history of COMBINE Proceedings of the 2017 Winter Simulation Conference
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 1996 Approximate Spatial Layout Processing in Early Vision [Abstract] Proceedings of the Eighteeth Annual Meeting of the Cognitive Science Society
- 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
- 1989 Learning in tele-autonomous systems using Soar Proceedings of the NASA Conference on Space Telerobotics NASA Jet Propulsion Laboratory 415–424
Book chapters
- 2015 Systems Biology Markup Language (SBML) Dieter Jaeger, Jung Ranu Encyclopedia of Computational Neuroscience Springer Science+Business Media 2943–2944
- 2013 Systems Biology Markup Language (SBML) Werner Dubitzky, Olaf Wolkenhauer, Hiroki Yokota, Cho Kwang-Hyun Encyclopedia of Systems Biology Springer 2057–2063
- 2009 Trends and tools for modeling in modern biology Laisk Agu, Ladislav Nedbal, Govindjee Photosynthesis in silico Springer 3–15
- 2007 SBML models and MathSBML S. Choi Introduction to Systems Biology Springer 395–421
- 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
- 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
- 2003 The GENESIS Simulation System Michael A. Arbib The Handbook of Brain Theory and Neural Networks MIT Press 475–478
- 2002 The Modeler's Workspace Giorgio A. Ascoli Computational Neuroanatomy: Principles and Methods Humana Press 83–103
- 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
- 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
- 2011 SBML Level 3 Package Proposal: Annotation Nature Precedings 10.1038/npre.2011.5610.1
- 2011 SBML Level 3 Package Specification: Hierarchical Model Composition, Version 1 Draft This is the draft specification for the SBML Level 3 'comp' package
- 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
- 2009 An overview of several standardization efforts for systems biology [Abstract] Journal of Physiological Sciences 59 102 Abstract of presentation given at IUPS2009.
- 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
- 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
- 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
- 2006 Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions This is the specification for SBML Level 2 Version 2
- 2003 Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions This is the specification for SBML Level 2 Version 1
- 2003 Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions This is the specification for SBML Level 2 Version 1
- 2003 The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules
- 2003 Parameter Sets: a standard technology for use with SBML
- 2002 Systems Biology Workbench Delphi/Kylix Programmer's Manual
- 2002 Proposal for a Minimal SBML Level 2 Definition
- 2002 The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules
- 2002 Systems Biology Workbench Javatm Programmer's Manual
- 2002 The Systems Biology Workbench (SBW) Version 1.0: Framework and Modules
- 2002 Systems Biology Workbench C++ Programmer's Manual
- 2001 The Systems Biology Workbench Concept Demonstrator: Design and Implementation
- 2001 Introduction to the Systems Biology Workbench
- 2001 A Comparison of Two Alternative Message-Passing Approaches for SBW
- 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
- 2001 Systems Biology Workbench C Programmer's Manual
- 2001 Systems Biology Workbench C Programmer's Manual
- 2001 Systems Biology Workbench C Programmer's Manual
- 2000 Preliminary High-Level Design for BMF, the Biology Modeling Framework
- 2000 Society for Neuroscience Abstracts 21–69
- 2000 SCHUCS: A Notation for Describing Model Representations Intended for XML Encoding
- 1998 Approximate Spatial Layout Processing in the Visual System: Modeling Texture-Based Segmentation and Shape Estimation Doctoral Dissertation
- 1997 A model for texture-based segmentation of natural scenes [Abstract] Investigative Ophthalmology &Visual Science 38 2990 Lippincott-Raven
- 1992 A Specification of the Soar Cognitive Architecture in Z School of Computer Science, Carnegie Mellon University
- 1992 Soar-mode v5.0 User's Manual for Soar release 5.2 and 6.0 School of Computer Science, Carnegie Mellon University