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)

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)

Optimal dimensionality selection for independent component analysis of transcriptomic data. - John Luke McConn; Cameron R. Lamoureux; Saugat Poudel; Bernhard O. Palsson; Anand V. Sastry (BMC Bioinform., 2021)

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. - Kevin Rychel; Katherine Decker; Anand V. Sastry; Patrick V. Phaneuf; Saugat Poudel; Bernhard O. Palsson (Nucleic Acids Res., 2021)

Independent component analysis recovers consistent regulatory signals from disparate datasets. - Anand V. Sastry; Alyssa Hu; David Heckmann; Saugat Poudel; Erol S. Kavvas; Bernhard O. Palsson (PLoS Comput. Biol., 2021)

Spatio-temporal approach for classification of COVID-19 pandemic fake news. - Isha Y. Agarwal; Dipti P. Rana; M. Shaikh; Saugat Poudel (Soc. Netw. Anal. Min., 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)