Search Results - Jonathan M Monk

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  1. 1

    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

    Published in BMC Genomics (2022-01-01)
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  2. 2

    Rapid resistance development to three antistaphylococcal therapies in antibiotic-tolerant staphylococcus aureus bacteremia. by Christopher R Miller, Jonathan M Monk, Richard Szubin, Andrew D Berti

    Published in PLoS ONE (2021-01-01)
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  3. 3

    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

    Published in Nature Communications (2023-11-01)
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  4. 4

    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

    Published in Synthetic and Systems Biotechnology (2022-09-01)
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  5. 5

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

    Published in PLoS Genetics (2020-07-01)
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  6. 6

    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

    Published in Current Research in Microbial Sciences (2023-01-01)
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  7. 7

    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

    Published in Frontiers in Microbiology (2020-11-01)
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  8. 8

    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

    Published in mSphere (2025-01-01)
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  9. 9

    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

    Published in Microbiology Spectrum (2022-10-01)
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  10. 10

    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

    Published in PLoS Computational Biology (2019-12-01)
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  11. 11

    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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  12. 12

    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

    Published in eLife (2023-10-01)
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  13. 13

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

    Published in mSystems (2022-12-01)
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  14. 14

    Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species by Joshua Mueller, Jayanth Krishnan, Qixing Wei, Ying Hefner, Jonathan M. Monk, Hans Verkler, Juan D. Tibocha-Bonilla, Anthony Ayala, Bernhard O. Palsson, Adam M. Feist, Wei Niu

    Published in mSystems (2026-04-01)
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  15. 15

    Metabolic network analysis of pre-ASD newborns and 5-year-old children with autism spectrum disorder by Sai Sachin Lingampelly, Jane C. Naviaux, Luke S. Heuer, Jonathan M. Monk, Kefeng Li, Lin Wang, Lori Haapanen, Chelsea A. Kelland, Judy Van de Water, Robert K. Naviaux

    Published in Communications Biology (2024-05-01)
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  16. 16

    Metabolic and behavioral features of acute hyperpurinergia and the maternal immune activation mouse model of autism spectrum disorder. by Zarazuela Zolkipli-Cunningham, Jane C Naviaux, Tomohiro Nakayama, Charlotte M Hirsch, Jonathan M Monk, Kefeng Li, Lin Wang, Thuy P Le, Simone Meinardi, Donald R Blake, Robert K Naviaux

    Published in PLoS ONE (2021-01-01)
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  17. 17

    Rev1 deficiency induces a metabolic shift in MEFs that can be manipulated by the NAD+ precursor nicotinamide riboside by Sharath Anugula, Zhiquan Li, Yuan Li, Alexander Hendriksen, Peter Bjarn Christensen, Lin Wang, Jonathan M. Monk, Niels de Wind, Vilhelm A. Bohr, Claus Desler, Robert K. Naviaux, Lene Juel Rasmussen

    Published in Heliyon (2023-06-01)
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  18. 18

    Genome‐scale metabolic modeling reveals key features of a minimal gene set by Jean‐Christophe Lachance, Dominick Matteau, Joëlle Brodeur, Colton J Lloyd, Nathan Mih, Zachary A King, Thomas F Knight, Adam M Feist, Jonathan M Monk, Bernhard O Palsson, Pierre‐Étienne Jacques, Sébastien Rodrigue

    Published in Molecular Systems Biology (2021-07-01)
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  19. 19

    Metabolic features of treatment-refractory major depressive disorder with suicidal ideation by Lisa A. Pan, Jane C. Naviaux, Lin Wang, Kefeng Li, Jonathan M. Monk, Sai Sachin Lingampelly, Anna Maria Segreti, Kaitlyn Bloom, Jerry Vockley, Mark A. Tarnopolsky, David N. Finegold, David G. Peters, Robert K. Naviaux

    Published in Translational Psychiatry (2023-12-01)
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  20. 20

    Mathematical models to study the biology of pathogens and the infectious diseases they cause by Joao B. Xavier, Jonathan M. Monk, Saugat Poudel, Charles J. Norsigian, Anand V. Sastry, Chen Liao, Jose Bento, Marc A. Suchard, Mario L. Arrieta-Ortiz, Eliza J.R. Peterson, Nitin S. Baliga, Thomas Stoeger, Felicia Ruffin, Reese A.K. Richardson, Catherine A. Gao, Thomas D. Horvath, Anthony M. Haag, Qinglong Wu, Tor Savidge, Michael R. Yeaman

    Published in iScience (2022-04-01)
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