Comparative Systems Biology Analysis of Microbial Pathogens. - Jonathan Monk (2015)

Systems biology of the structural proteome. - Elizabeth Brunk; Nathan Mih; Jonathan Monk; Zhen Zhang; Edward J. O'Brien; Spencer E. Bliven; Ke Chen; Roger L. Chang; Philip E. Bourne; Bernhard O. Palsson (BMC Syst. Biol., 2016)

Machine learning in computational biology to accelerate high-throughput protein expression. - Anand Sastry 002; Jonathan Monk; Hanna Tegel; Mathias Uhlen; Bernhard O. Palsson; Johan Rockberg; Elizabeth Brunk (Bioinform., 2017)

ssbio: a Python framework for structural systems biology. - Nathan Mih; Elizabeth Brunk; Ke Chen; Edward Catoiu; Anand Sastry 002; Erol S. Kavvas; Jonathan M. Monk; Zhen Zhang; Bernhard O. Palsson (Bioinform., 2018)

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)

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. - Jinyuan Yan; Henri Estanbouli; Chen Liao; Wook Kim; Jonathan M. Monk; Rayees Rahman; Mini Kamboj; Bernhard O. Palsson; Weigang Qiu; João B. Xavier (PLoS Comput. Biol., 2019)

Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. - Nathan Mih; Jonathan M. Monk; Xin Fang; Edward Catoiu; David Heckmann; Laurence Yang 001; Bernhard O. Palsson (BMC Bioinform., 2020)

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. - Jason C. Hyun; Erol S. Kavvas; Jonathan M. Monk; Bernhard O. Palsson (PLoS Comput. Biol., 2020)

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. - Colton J. Lloyd; Jonathan Monk; Laurence Yang 001; Ali Ebrahim; Bernhard O. Palsson (PLoS Comput. Biol., 2021)

High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. - Max van 't Hof; Omkar S. Mohite; Jonathan M. Monk; Tilmann Weber; Bernhard O. Palsson; Morten O. A. Sommer (BMC Bioinform., 2022)