Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens von Hyun, Jason C, Kavvas, Erol S, Monk, Jonathan M, Palsson, Bernhard O

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A biochemically-interpretable machine learning classifier for microbial GWAS von Kavvas, Erol S., Yang, Laurence, Monk, Jonathan M., Heckmann, David, Palsson, Bernhard O.

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Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance von Kavvas, Erol S., Catoiu, Edward, Mih, Nathan, Yurkovich, James T., Seif, Yara, Dillon, Nicholas, Heckmann, David, Anand, Amitesh, Yang, Laurence, Nizet, Victor, Monk, Jonathan M., Palsson, Bernhard O.

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Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits von Seif, Yara, Kavvas, Erol, Lachance, Jean-Christophe, Yurkovich, James T., Nuccio, Sean-Paul, Fang, Xin, Catoiu, Edward, Raffatellu, Manuela, Palsson, Bernhard O., Monk, Jonathan M.

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Independent component analysis recovers consistent regulatory signals from disparate datasets von Sastry, Anand V., Hu, Alyssa, Heckmann, David, Poudel, Saugat, Kavvas, Erol, Palsson, Bernhard O.

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Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli von Matson, Morgan M., Cepeda, Mateo M., Zhang, Angela, Case, Anna E., Kavvas, Erol S., Wang, Xiaokang, Carroll, Austin L., Tagkopoulos, Ilias, Atsumi, Shota

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Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions von Kavvas, Erol S, Seif, Yara, Yurkovich, James T, Norsigian, Charles, Poudel, Saugat, Greenwald, William W, Ghatak, Sankha, Palsson, Bernhard O, Monk, Jonathan M

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iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE von Norsigian, Charles J, Kavvas, Erol, Seif, Yara, Palsson, Bernhard O, Monk, Jonathan M

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Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes von Kavvas, Erol S, Long, Christopher P, Sastry, Anand, Poudel, Saugat, Antoniewicz, Maciek R, Ding, Yang, Mohamed, Elsayed T, Szubin, Richard, Monk, Jonathan M, Feist, Adam M, Palsson, Bernhard O

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The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures von Choudhary, Kumari S, Mih, Nathan, Monk, Jonathan, Kavvas, Erol, Yurkovich, James T, Sakoulas, George, Palsson, Bernhard O

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Evaluation of rate law approximations in bottom-up kinetic models of metabolism von Du, Bin, Zielinski, Daniel C, Kavvas, Erol S, Dräger, Andreas, Tan, Justin, Zhang, Zhen, Ruggiero, Kayla E, Arzumanyan, Garri A, Palsson, Bernhard O

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Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens von Hyun, Jason C., Kavvas, Erol S., Monk, Jonathan M., Palsson, Bernhard O.

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ssbio: a Python framework for structural systems biology von Mih, Nathan, Brunk, Elizabeth, Chen, Ke, Catoiu, Edward, Sastry, Anand, Kavvas, Erol, Monk, Jonathan M, Zhang, Zhen, Palsson, Bernhard O

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Systems Biology and Pangenome of Salmonella O-Antigens von Seif, Yara, Monk, Jonathan M, Machado, Henrique, Kavvas, Erol, Palsson, Bernhard O

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Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa von Fang, Xin, Monk, Jonathan M, Mih, Nathan, Du, Bin, Sastry, Anand V, Kavvas, Erol, Seif, Yara, Smarr, Larry, Palsson, Bernhard O

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Systems Biology and Pangenome of italic toggle="yes">Salmonella /italic> O-Antigens von Yara Seif, Jonathan M. Monk, Henrique Machado, Erol Kavvas, Bernhard O. Palsson

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Supplementary Figure 2 von Kavvas, Erol

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Supplementary Figure 3 von Kavvas, Erol

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Supplementary Figure 4 von Kavvas, Erol

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Supplementary Figure 1 von Kavvas, Erol

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