| 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), 4306, 2018 | 192 | 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), 3771, 2018 | 131 | 2018 |
| A biochemically-interpretable machine learning classifier for microbial GWAS ES Kavvas, L Yang, JM Monk, D Heckmann, BO Palsson Nature communications 11 (1), 2580, 2020 | 81 | 2020 |
| Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens JC Hyun, ES Kavvas, JM Monk, BO Palsson PLoS computational biology 16 (3), e1007608, 2020 | 70 | 2020 |
| 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, 1-15, 2018 | 61 | 2018 |
| 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, 1-10, 2018 | 52 | 2018 |
| Independent component analysis recovers consistent regulatory signals from disparate datasets AV Sastry, A Hu, D Heckmann, S Poudel, E Kavvas, BO Palsson PLoS computational biology 17 (2), e1008647, 2021 | 42 | 2021 |
| 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 | 42 | 2018 |
| Evaluation of rate law approximations in bottom-up kinetic models of metabolism B Du, DC Zielinski, ES Kavvas, A Dräger, J Tan, Z Zhang, KE Ruggiero, ... BMC systems biology 10, 1-15, 2016 | 40 | 2016 |
| The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures KS Choudhary, N Mih, J Monk, E Kavvas, JT Yurkovich, G Sakoulas, ... Frontiers in microbiology 9, 1082, 2018 | 38 | 2018 |
| ssbio: a Python framework for structural systems biology N Mih, E Brunk, K Chen, E Catoiu, A Sastry, E Kavvas, JM Monk, Z Zhang, ... Bioinformatics 34 (12), 2155-2157, 2018 | 36 | 2018 |
| Systems Biology and Pangenome of Salmonella O-Antigens Y Seif, JM Monk, H Machado, E Kavvas, BO Palsson MBio 10 (4), 10.1128/mbio. 01247-19, 2019 | 26 | 2019 |
| Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli MM Matson, MM Cepeda, A Zhang, AE Case, ES Kavvas, X Wang, ... Metabolic Engineering 69, 50-58, 2022 | 20 | 2022 |
| Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nat Commun 9: 4306 ES Kavvas, E Catoiu, N Mih, JT Yurkovich, Y Seif, N Dillon, D Heckmann, ... | 17 | 2018 |
| Experimental evolution reveals unifying systems-level adaptations but diversity in driving genotypes ES Kavvas, CP Long, A Sastry, S Poudel, MR Antoniewicz, Y Ding, ... Msystems 7 (6), e00165-22, 2022 | 16 | 2022 |
| Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nat Commun 9: 3771 Y Seif, E Kavvas, JC Lachance, JT Yurkovich, SP Nuccio, X Fang, ... | 15 | 2018 |
| Systems biology and pangenome of Y Seif, JM Monk, H Machado, E Kavvas, BO Palsson Salmonella, 2019 | 11 | 2019 |
| Laboratory evolution of multiple E. coli strains reveals unifying principles of adaptation but diversity in driving genotypes ES Kavvas, M Antoniewicz, C Long, Y Ding, JM Monk, BO Palsson, ... bioRxiv, 2020.05. 19.104992, 2020 | 7 | 2020 |
| Matrix factorization recovers consistent regulatory signals from disparate datasets AV Sastry, A Hu, D Heckmann, S Poudel, E Kavvas, BO Palsson bioRxiv, 2020.04. 26.061978, 2020 | 6 | 2020 |
| Systems biology and pangenome of Salmonella O-antigens. mBio. 2019; 10: e01247-19 Y Seif, JM Monk, H Machado, E Kavvas, BO Palsson | 3 | |
Jonathan MonkUC San DiegoE-mailová adresa ověřena na: ucsd.edu