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)

PyDREAM: high-dimensional parameter inference for biological models in python. - Erin M. Shockley; Jasper A. Vrugt; Carlos F. Lopez (Bioinform., 2018)

Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers. - David J. Wooten; Sarah M. Groves; Darren R. Tyson; Qi Liu 024; Jing S. Lim; Réka Albert; Carlos F. Lopez; Julien Sage; Vito Quaranta (PLoS Comput. Biol., 2019)

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)

Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python. - Alexander L. R. Lubbock; Carlos F. Lopez (Bioinform., 2022)

A dynamical low-rank approach to solve the chemical master equation for biological reaction networks. - Martina Prugger; Lukas Einkemmer; Carlos F. Lopez (J. Comput. Phys., 2023)

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)

Model certainty in cellular network-driven processes with missing data. - Michael W. Irvin; Arvind Ramanathan; Carlos F. Lopez (PLoS Comput. Biol., 2023)