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2020 – today
- 2023
[j14]James C. Schaff
, Anuradha Lakshminarayana, Robert F. Murphy, Frank T. Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian P. Smith:
SBML level 3 package: spatial processes, version 1, release 1. J. Integr. Bioinform. 20(1) (2023)- 2022
- [j13]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022)
2010 – 2019
- 2019
- [j12]Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 16(2) (2019) - 2018
- [j11]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:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 15(1) (2018) - [j10]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:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J. Integr. Bioinform. 15(1) (2018) - 2016
- [j9]James C. Schaff, Dan Vasilescu, Ion I. Moraru, Leslie M. Loew, Michael L. Blinov:
Rule-based modeling with Virtual Cell. Bioinform. 32(18): 2880-2882 (2016) - [j8]James C. Schaff, Fei Gao, Li Ye, Igor L. Novak, Boris M. Slepchenko:
Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology. PLoS Comput. Biol. 12(12) (2016) - 2015
- [j7]Anthony Santella, Raúl Catena, Ismar Kovacevic, Pavak K. Shah, Zidong Yu, Javier Marquina-Solis, Abhishek Kumar, Yicong Wu, James C. Schaff, Daniel Colón-Ramos, Hari Shroff, William Mohler, Zhirong Bao:
WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. BMC Bioinform. 16: 189:1-189:9 (2015) - [j6]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:
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J. Integr. Bioinform. 12(2) (2015) - [j5]Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 12(2) (2015) - 2014
- [j4]Michael L. Blinov, James C. Schaff, Oliver Ruebenacker, Xintao Wei, Dan Vasilescu, Fei Gao, Frank Morgan, Li Ye, Anuradha Lakshminarayana, Ion I. Moraru, Leslie M. Loew:
Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling. Bioinform. 30(2): 292-294 (2014) - 2011
- [j3]Sherry-Ann Brown, Ion I. Moraru, James C. Schaff, Leslie M. Loew:
Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling. J. Comput. Neurosci. 31(2): 385-400 (2011) - 2010
- [c7]Michael L. Blinov, Oliver Ruebenacker, James C. Schaff, Ion I. Moraru:
Modeling without Borders: Creating and Annotating VCell Models Using the Web. ISBRA 2010: 3-17
2000 – 2009
- 2007
- [j2]Igor L. Novak, Fei Gao, Yung-Sze Choi, Diana Resasco, James C. Schaff, Boris M. Slepchenko:
Diffusion on a curved surface coupled to diffusion in the volume: Application to cell biology. J. Comput. Phys. 226(2): 1271-1290 (2007) - [c6]Oliver Ruebenacker, Ion I. Moraru, James C. Schaff, Michael L. Blinov:
Kinetic Modeling Using BioPAX Ontology. BIBM 2007: 339-348 - 2006
- [c5]Ion I. Moraru, James C. Schaff, Leslie M. Loew:
Think simulation - think experiment: the virtual cell paradigm. WSC 2006: 1713-1719 - 2003
- [j1]Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, Dennis Bray, Athel Cornish-Bowden, Autumn A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, Jan-Hendrik S. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, Poul M. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang:
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinform. 19(4): 524-531 (2003)
1990 – 1999
- 1999
- [c4]M. A. Sapia, Leslie M. Loew, M. D. Fox, James C. Schaff:
Ultrasound Image Deconvolution Using Adaptive Inverse Filtering. CBMS 1999: 248-253 - [c3]James C. Schaff:
A Distributed Architecture for a General Cellular Modeling and Simulation Framework. CBMS 1999: 303- - [c2]James C. Schaff, Leslie M. Loew:
The Virtual Cell. Pacific Symposium on Biocomputing 1999: 228-239 - 1998
- [c1]Dong-Guk Shin, Lei Liu, Leslie M. Loew, James C. Schaff:
Virtual Cell: A General Framework for Simulating and Visualizing Cellular Physiology. VDB 1998: 214-220
Coauthor Index
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