Virtual Cell: A General Framework for Simulating and Visualizing Cellular Physiology. - Dong-Guk Shin; Lei Liu; Leslie M. Loew; James C. Schaff (VDB, 1998)

Ultrasound Image Deconvolution Using Adaptive Inverse Filtering. - M. A. Sapia; Leslie M. Loew; M. D. Fox; James C. Schaff (CBMS, 1999)

A Distributed Architecture for a General Cellular Modeling and Simulation Framework. - James C. Schaff (CBMS, 1999)

The Virtual Cell. - James C. Schaff; Leslie M. Loew (Pacific Symposium on Biocomputing, 1999)

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. - Michael Hucka; Andrew Finney; Herbert M. Sauro; H. Bolouri; John C. Doyle 001; Hiroaki Kitano; Adam P. Arkin; Benjamin J. Bornstein; Dennis Bray; Athel Cornish-Bowden; Autumn A. Cuellar; Serge Dronov; et al. (Bioinform., 2003)

Think simulation - think experiment: the virtual cell paradigm. - Ion I. Moraru; James C. Schaff; Leslie M. Loew (WSC, 2006)

Kinetic Modeling Using BioPAX Ontology. - Oliver Ruebenacker; Ion I. Moraru; James C. Schaff; Michael L. Blinov (BIBM, 2007)

Diffusion on a curved surface coupled to diffusion in the volume: Application to cell biology. - Igor L. Novak; Fei Gao; Yung-Sze Choi; Diana Resasco; James C. Schaff; Boris M. Slepchenko (J. Comput. Phys., 2007)

Modeling without Borders: Creating and Annotating VCell Models Using the Web. - Michael L. Blinov; Oliver Ruebenacker; James C. Schaff; Ion I. Moraru (ISBRA, 2010)

Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling. - Sherry-Ann Brown; Ion I. Moraru; James C. Schaff; Leslie M. Loew (J. Comput. Neurosci., 2011)

Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling. - 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 (Bioinform., 2014)

WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. - 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; et al. (BMC Bioinform., 2015)

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. - 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; et al. (J. Integr. Bioinform., 2015)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. - Michael Hucka; Frank T. Bergmann; Stefan Hoops; Sarah M. Keating; Sven Sahle; James C. Schaff; Lucian P. Smith; Darren J. Wilkinson (J. Integr. Bioinform., 2015)

Rule-based modeling with Virtual Cell. - James C. Schaff; Dan Vasilescu; Ion I. Moraru; Leslie M. Loew; Michael L. Blinov (Bioinform., 2016)

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology. - James C. Schaff; Fei Gao; Li Ye; Igor L. Novak; Boris M. Slepchenko (PLoS Comput. Biol., 2016)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. - 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; et al. (J. Integr. Bioinform., 2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. - 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; et al. (J. Integr. Bioinform., 2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. - Michael Hucka; Frank T. Bergmann; Claudine Chaouiya; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Matthias König 003; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; et al. (J. Integr. Bioinform., 2019)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - 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 006; et al. (Nucleic Acids Res., 2022)

SBML level 3 package: spatial processes, version 1, release 1. - James C. Schaff; Anuradha Lakshminarayana; Robert F. Murphy; Frank T. Bergmann; Akira Funahashi; Devin P. Sullivan; Lucian P. Smith (J. Integr. Bioinform., 2023)