Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity by Jason C. Hyun, Jonathan M. Monk, Bernhard O. Palsson

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

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

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Improved Dried Blood Spot-Based Metabolomics: A Targeted, Broad-Spectrum, Single-Injection Method by Kefeng Li, Jane C. Naviaux, Jonathan M. Monk, Lin Wang, Robert K. Naviaux

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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

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Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species by Jason C. Hyun, Jonathan M. Monk, Richard Szubin, Ying Hefner, Bernhard O. Palsson

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Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets by Omkar S. Mohite, Colton J. Lloyd, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson

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Impact of insertion sequences on convergent evolution of Shigella species. by Jane Hawkey, Jonathan M Monk, Helen Billman-Jacobe, Bernhard Palsson, Kathryn E Holt

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Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess by Monika Kumaraswamy, Alison Coady, Richard Szubin, Thomas CS Martin, Bernhard Palsson, Victor Nizet, Jonathan M. Monk

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Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes by Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang, Bernhard O. Palsson

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High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies by Jared T. Broddrick, Richard Szubin, Charles J. Norsigian, Jonathan M. Monk, Bernhard O. Palsson, Mary N. Parenteau

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Decomposition of the pangenome matrix reveals a structure in gene distribution in the Escherichia coli species by Siddharth M. Chauhan, Omid Ardalani, Jason C. Hyun, Jonathan M. Monk, Patrick V. Phaneuf, Bernhard O. Palsson

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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

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High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917 by Max van ‘t Hof, Omkar S. Mohite, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson, Morten O. A. Sommer

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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

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Estimated Roles of the Carrier and the Bacterial Strain When Methicillin-Resistant Staphylococcus aureus Decolonization Fails: a Case-Control Study by Mona Katrine Alberthe Holm, Kristina Melbardis Jørgensen, Kristian Bagge, Peder Worning, Michael Pedersen, Henrik Westh, Jonathan M. Monk, Mette Damkjær Bartels

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Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. by Jinyuan Yan, Henri Estanbouli, Chen Liao, Wook Kim, Jonathan M Monk, Rayees Rahman, Mini Kamboj, Bernhard O Palsson, Weigang Qiu, Joao B Xavier

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Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase–Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates by Charles J. Norsigian, Heba Attia, Richard Szubin, Aymen S. Yassin, Aymen S. Yassin, Bernhard Ø. Palsson, Ramy K. Aziz, Ramy K. Aziz, Jonathan M. Monk

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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

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Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models by Ben Vezina, Stephen C Watts, Jane Hawkey, Helena B Cooper, Louise M Judd, Adam WJ Jenney, Jonathan M Monk, Kathryn E Holt, Kelly L Wyres

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