James C. Schaff

Biochemistry, Genetics and Molecular Biology · Life Sciences

31h-index7.0kcitations82works0.52yr avg
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Research Topics

Gene Regulatory Network Analysis(44), Microbial Metabolic Engineering and Bioproduction(20), Bioinformatics and Genomic Networks(15), Cell Image Analysis Techniques(13), Advanced Fluorescence Microscopy Techniques(7)

Publications82 total

BPS2026 - VCell 8.0: Analysis of complex spatial simulations with ImageJ and Langevin dynamics modeling of multivalent assembly with SpringSaLaD
Biophysical Journal·2026
Verification and reproducible curation of the BioModels repository
PLoS Computational Biology·2025Open Access
Visualizing mechanistic models by integrating site-specific molecular details into reaction networks
Frontiers in Molecular Biosciences·2025Open Access
From FAIR to CURE: Guidelines for Computational Models of Biological Systems.
PubMed·2025· 3 citedOpen Access
BPS2025 - Virtual Cell modeling and simulation environment
Biophysical Journal·2025
Verification and reproducible curation of the BioModels repository
2025Open Access
SBML level 3 package: spatial processes, version 1, release 1
Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics·2023· 6 citedOpen Access
Virtual cell modeling and simulation software
Biophysical Journal·2023
A systems pharmacology model for gene therapy in sickle cell disease
CPT Pharmacometrics & Systems Pharmacology·2021· 7 citedOpen Access
<scp>SBML</scp> Level 3: an extensible format for the exchange and reuse of biological models
Molecular Systems Biology·2020· 297 citedOpen Access
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2
Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics·2019· 272 citedOpen Access
Molecular Process Diagram: a precise, scalable and compact visualization of rule-based models
2018· 1 citedOpen Access
Quantitative Biology: Theory, Computational Methods, and Models
The MIT Press eBooks·2018· 31 cited
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics·2018· 43 citedOpen Access
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core
Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics·2018· 67 citedOpen Access
Modeling and analyzing an optogenetic system for photoactivatable protein dissociation
OpenCommons - UConn (University of Connecticut)·2018Open Access
Compartmental and Spatial Rule-Based Modeling with Virtual Cell
Biophysical Journal·2017· 53 citedOpen Access
Compartmental and spatial rule-based modeling with <i>Virtual Cell</i> (VCell)
2017· 1 citedOpen Access
Extending Rule-Based Modeling to the Spatial Domain with Virtual Cell (VCELL)
Biophysical Journal·2017Open Access
Multivalent Signaling Clusters have Unique Sizes Determined by Membrane Localization and Excluded Volume: the Nephrin/Nck/N-WASP System
Biophysical Journal·2017Open Access
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Frequent Co-authors

Leslie M. Loew(26), Ion I. Moraru(18), Boris M. Slepchenko(17), Michael Hucka(12), Lucian P. Smith(11), Sarah Keating(10), Frank Bergmann(10), Michael L. Blinov(10), Sven Sahle(9), Darren J. Wilkinson(9), Dagmar Waltemath(7), Andreas Dräger(7), Stefan Hoops(7), Chris J. Myers(7), Brett G. Olivier(7), Nicolas Le Novère(6), Fei Gao(5), Herbert M. Sauro(4), Dan Vasilescu(4), Oliver Ruebenacker(4)