Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. - Xin Fang; Jonathan M. Monk; Nathan Mih; Bin Du; Anand Sastry 002; Erol S. Kavvas; Yara Seif; Larry Smarr; Bernhard O. Palsson (BMC Syst. Biol., 2018)

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. - Erol S. Kavvas; Yara Seif; James T. Yurkovich; Charles J. Norsigian; Saugat Poudel; William W. Greenwald; Sankha Ghatak; Bernhard O. Palsson; Jonathan M. Monk (BMC Syst. Biol., 2018)

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. - Jean-Christophe Lachance; Colton J. Lloyd; Jonathan M. Monk; Laurence Yang 001; Anand Sastry 002; Yara Seif; Bernhard O. Palsson; Sébastien Rodrigue; Adam M. Feist; Zachary A. King; Pierre-Étienne Jacques (PLoS Comput. Biol., 2019)

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. - Yara Seif; Jonathan M. Monk; Nathan Mih; Hannah Tsunemoto; Saugat Poudel; Cristal Zuñiga; Jared Broddrick; Karsten Zengler; Bernhard O. Palsson (PLoS Comput. Biol., 2019)

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)