Academic lineage
Video highlight
Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes
- Erol S Kavvas, Christopher P Long, Anand Sastry, …, Jonathan M Monk, Adam M Feist, Bernhard O Palsson
- mSystems, 10.1128/msystems.00165-22
Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli
- Morgan M Matson, Mateo M Cepeda, Angela Zhang, …, Austin L Carroll, Ilias Tagkopoulos, Shota Atsumi
- Metab Eng, 10.1016/j.ymben.2021.11.002
Independent component analysis recovers consistent regulatory signals from disparate datasets
- Anand V Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol Kavvas, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1008647
A biochemically-interpretable machine learning classifier for microbial GWAS
- Erol S Kavvas, Laurence Yang, Jonathan M Monk, David Heckmann, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-020-16310-9
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, 10.1371/journal.pcbi.1007608
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
- Erol S Kavvas, Edward Catoiu, Nathan Mih, …, Victor Nizet, Jonathan M Monk, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-018-06634-y
Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
- Yara Seif, Erol Kavvas, Jean-Christophe Lachance, …, Manuela Raffatellu, Bernhard O Palsson, Jonathan M Monk
- Nat Commun, 10.1038/s41467-018-06112-5
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, …, Yara Seif, Larry Smarr, Bernhard O Palsson
- None, 10.1186/s12918-018-0587-5
The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures
- Kumari S Choudhary, Nathan Mih, Jonathan Monk, …, James T Yurkovich, George Sakoulas, Bernhard O Palsson
- None, 10.3389/fmicb.2018.01082
iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE
- Charles J Norsigian, Erol Kavvas, Yara Seif, Bernhard O Palsson, Jonathan M Monk
- None, 10.3389/fgene.2018.00121
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, …, Sankha Ghatak, Bernhard O Palsson, Jonathan M Monk
- None, 10.1186/s12918-018-0557-y
ssbio: a Python framework for structural systems biology
- Nathan Mih, Elizabeth Brunk, Ke Chen, …, Jonathan M Monk, Zhen Zhang, Bernhard O Palsson
- Bioinformatics, 10.1093/bioinformatics/bty077
Evaluation of rate law approximations in bottom-up kinetic models of metabolism
- Bin Du, Daniel C Zielinski, Erol S Kavvas, …, Kayla E Ruggiero, Garri A Arzumanyan, Bernhard O Palsson
- None, 10.1186/s12918-016-0283-2