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

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A biochemically-interpretable machine learning classifier for microbial GWAS 由 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 由 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 由 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 由 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 由 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 由 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. 由 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 由 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 由 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 由 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 由 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 由 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 由 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. 由 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 由 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. 由 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 由 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 由 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 由 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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