Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. - James T. Yurkovich; Miguel A. Alcantar; Zachary B. Haiman; Bernhard O. Palsson (PLoS Comput. Biol., 2018)

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. - Zachary B. Haiman; Daniel C. Zielinski; Yuko Koike; James T. Yurkovich; Bernhard O. Palsson (PLoS Comput. Biol., 2021)

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. (CoRR, 2022)

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)

iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. - Anand V. Sastry; Yuan Yuan; Saugat Poudel; Kevin Rychel; Reo Yoo; Cameron R. Lamoureux; Gaoyuan Li; Joshua T. Burrows; Siddharth Chauhan; Zachary B. Haiman; Tahani Al Bulushi; Yara Seif; et al. (PLoS Comput. Biol., 2024)

RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell. - Zachary B. Haiman; Alicia Key; Angelo D'alessandro; Bernhard O. Palsson (PLoS Comput. Biol., 2025)