Systems Biology and Pangenome of Salmonella O-Antigens

by Yara Seif, Jonathan M. Monk, Henrique Machado, Erol Kavvas, Bernhard O. Palsson
Published 2019-08-01

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE

by Charles J. Norsigian, Erol Kavvas, Yara Seif, Bernhard O. Palsson, Jonathan M. Monk
Published 2018-04-01

Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens

by Akanksha Rajput, Yara Seif, Kumari Sonal Choudhary, Christopher Dalldorf, Saugat Poudel, Jonathan M. Monk, Bernhard O. Palsson
Published 2021-02-01

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.

by Yara Seif, Jonathan M Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuniga, Jared Broddrick, Karsten Zengler, Bernhard O Palsson
Published 2019-01-01

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

by Yara Seif, Erol Kavvas, Jean-Christophe Lachance, James T. Yurkovich, Sean-Paul Nuccio, Xin Fang, Edward Catoiu, Manuela Raffatellu, Bernhard O. Palsson, Jonathan M. Monk
Published 2018-09-01

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

by Erol S. Kavvas, Edward Catoiu, Nathan Mih, James T. Yurkovich, Yara Seif, Nicholas Dillon, David Heckmann, Amitesh Anand, Laurence Yang, Victor Nizet, Jonathan M. Monk, Bernhard O. Palsson
Published 2018-10-01

Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus

by Henrique Machado, Yara Seif, George Sakoulas, Connor A. Olson, Ying Hefner, Amitesh Anand, Ying Z. Jones, Richard Szubin, Bernhard O. Palsson, Victor Nizet, Adam M. Feist
Published 2021-06-01

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.

by Jean-Christophe Lachance, Colton J Lloyd, Jonathan M Monk, Laurence Yang, Anand V Sastry, Yara Seif, Bernhard O Palsson, Sébastien Rodrigue, Adam M Feist, Zachary A King, Pierre-Étienne Jacques
Published 2019-04-01