Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway. - Edmund M. Clarke; James R. Faeder; Christopher James Langmead; Leonard A. Harris; Sumit Kumar Jha 001; Axel Legay (CMSB, 2008)

Compartmental Rule-based Modeling of Biochemical Systems. - Leonard A. Harris; Justin S. Hogg; James R. Faeder (WSC, 2009)

MOSBIE: a tool for comparison and analysis of rule-based biochemical models. - John E. Wenskovitch; Leonard A. Harris; José Juan Tapia; James R. Faeder; G. Elisabeta Marai (BMC Bioinform., 2014)

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems. - Justin S. Hogg; Leonard A. Harris; Lori J. Stover; Niketh S. Nair; James R. Faeder (PLoS Comput. Biol., 2014)

BioNetGen 2.2: advances in rule-based modeling. - Leonard A. Harris; Justin S. Hogg; José Juan Tapia; John A. P. Sekar; Sanjana Gupta; Ilya Korsunsky; Arshi Arora; Dipak Barua; Robert P. Sheehan; James R. Faeder (Bioinform., 2016)

GPU-powered model analysis with PySB/cupSODA. - Leonard A. Harris; Marco S. Nobile; James C. Pino; Alexander L. R. Lubbock; Daniela Besozzi; Giancarlo Mauri; Paolo Cazzaniga; Carlos F. Lopez (Bioinform., 2017)

Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective. - Julia Chifman; Seda Arat; Zhiyong Deng; Erica Lemler; James C. Pino; Leonard A. Harris; Michael A. Kochen; Carlos F. Lopez; Steven A. Akman; Frank M. Torti; Suzy V. Torti; Reinhard C. Laubenbacher (PLoS Comput. Biol., 2017)

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. - Fengkai Zhang; Lucian P. Smith; Michael L. Blinov; James R. Faeder; William S. Hlavacek; José Juan Tapia; Sarah M. Keating; Nicolas Rodriguez 001; Andreas Dräger; Leonard A. Harris; Andrew Finney; Bin Hu 025; et al. (J. Integr. Bioinform., 2020)

Thunor: visualization and analysis of high-throughput dose-response datasets. - Alexander L. R. Lubbock; Leonard A. Harris; Vito Quaranta; Darren R. Tyson; Carlos F. Lopez (Nucleic Acids Res., 2021)

Unsupervised logic-based mechanism inference for network-driven biological processes. - Martina Prugger; Lukas Einkemmer; Samantha P. Beik; Perry T. Wasdin; Leonard A. Harris; Carlos F. Lopez (PLoS Comput. Biol., 2021)

Unified tumor growth mechanisms from multimodel inference and dataset integration. - Samantha P. Beik; Leonard A. Harris; Michael A. Kochen; Julien Sage; Vito Quaranta; Carlos F. Lopez (PLoS Comput. Biol., 2023)