|Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance|
ES Kavvas, E Catoiu, N Mih, JT Yurkovich, Y Seif, N Dillon, D Heckmann, ...
Nature communications 9 (1), 1-9, 2018
|Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits|
Y Seif, E Kavvas, JC Lachance, JT Yurkovich, SP Nuccio, X Fang, ...
Nature communications 9 (1), 1-12, 2018
|Engineered biomaterials to enhance stem cell‐based cardiac tissue engineering and therapy|
A Hasan, R Waters, B Roula, R Dana, S Yara, T Alexandre, A Paul
Macromolecular bioscience 16 (7), 958-977, 2016
|BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data|
JC Lachance, CJ Lloyd, JM Monk, L Yang, AV Sastry, Y Seif, BO Palsson, ...
PLoS computational biology 15 (4), e1006971, 2019
|Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions|
ES Kavvas, Y Seif, JT Yurkovich, C Norsigian, S Poudel, WW Greenwald, ...
BMC systems biology 12 (1), 1-15, 2018
|Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration|
A Anand, K Chen, L Yang, AV Sastry, CA Olson, S Poudel, Y Seif, ...
Proceedings of the National Academy of Sciences 116 (50), 25287-25292, 2019
|Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response|
S Poudel, H Tsunemoto, Y Seif, AV Sastry, R Szubin, S Xu, H Machado, ...
Proceedings of the National Academy of Sciences 117 (29), 17228-17239, 2020
|OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states|
A Anand, K Chen, E Catoiu, AV Sastry, CA Olson, TE Sandberg, Y Seif, ...
Molecular biology and evolution 37 (3), 660-667, 2020
|Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa|
X Fang, JM Monk, N Mih, B Du, AV Sastry, E Kavvas, Y Seif, L Smarr, ...
BMC systems biology 12 (1), 1-10, 2018
|A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types|
Y Seif, JM Monk, N Mih, H Tsunemoto, S Poudel, C Zuniga, J Broddrick, ...
PLoS computational biology 15 (1), e1006644, 2019
|A workflow for generating multi-strain genome-scale metabolic models of prokaryotes|
CJ Norsigian, X Fang, Y Seif, JM Monk, BO Palsson
Nature protocols 15 (1), 1-14, 2020
|Metabolic and genetic basis for auxotrophies in Gram-negative species|
Y Seif, KS Choudhary, Y Hefner, A Anand, L Yang, BO Palsson
Proceedings of the National Academy of Sciences 117 (11), 6264-6273, 2020
|iCN718, an updated and improved genome-scale metabolic network reconstruction of Acinetobacter baumannii AYE|
CJ Norsigian, E Kavvas, Y Seif, BO Palsson, JM Monk
Frontiers in genetics 9, 121, 2018
|Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media|
A Rajput, S Poudel, H Tsunemoto, M Meehan, R Szubin, CA Olson, ...
Scientific data 6 (1), 1-6, 2019
|Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media|
S Poudel, H Tsunemoto, M Meehan, R Szubin, CA Olson, A Lamsa, Y Seif, ...
Scientific data 6 (1), 1-7, 2019
|Systems Biology and Pangenome of Salmonella O-Antigens|
Y Seif, JM Monk, H Machado, E Kavvas, BO Palsson
MBio 10 (4), e01247-19, 2019
|Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus|
H Machado, LL Weng, N Dillon, Y Seif, M Holland, JE Pekar, JM Monk, ...
Applied and environmental microbiology 85 (21), e01773-19, 2019
|Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens|
A Rajput, Y Seif, KS Choudhary, C Dalldorf, S Poudel, JM Monk, ...
Msystems 6 (1), e00981-20, 2021
|Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus|
H Machado, Y Seif, G Sakoulas, CA Olson, Y Hefner, A Anand, YZ Jones, ...
Communications biology 4 (1), 1-12, 2021
|Elucidation of regulatory modes for five two-component systems in Escherichia coli reveals novel relationships|
KS Choudhary, JA Kleinmanns, K Decker, AV Sastry, Y Gao, R Szubin, ...
Msystems 5 (6), e00980-20, 2020