Jonathan M Monk (Jonathan Monk)

Publication Activity (10 Years)

Years Active: 2019-2023
Publications (10 Years): 13

Top Topics

Genetic Diversity

Pseudomonas Aeruginosa

Antimicrobial Resistance

Machine Learning

Top Venues

PLoS computational biology

Proceedings of the National Academy of Sciences of the United States of America

Nature communications

Genome research

This page only lists publications with an associated author ORCID identifier.

Publications

Edward Alexander Catoiu, Patrick V Phaneuf, Jonathan M Monk, Bernhard O Palsson
Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks. Proceedings of the National Academy of Sciences of the United States of America 120 (15) (2023)
Jason C Hyun, Jonathan M Monk, Richard Szubin, Ying Hefner, Bernhard O Palsson
Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species. Nature communications 14 (1) (2023)
Ben Vezina, Lousie M Judd, Fiona K McDougall, Wayne S J Boardman, Michelle L Power, Jane Hawkey, Sylvain Brisse, Jonathan M Monk, Kathryn E Holt, Kelly L Wyres
Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies. Environmental microbiology 24 (9) (2022)
Jonathan M Monk
Genome-scale metabolic network reconstructions of diverse Escherichia strains reveal strain-specific adaptations. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 377 (1861) (2022)
Charles J Norsigian, Heather A Danhof, Colleen K Brand, Firas S Midani, Jared T Broddrick, Tor C Savidge, Robert A Britton, Bernhard O Palsson, Jennifer K Spinler, Jonathan M Monk
Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power. Proceedings of the National Academy of Sciences of the United States of America 119 (18) (2022)
Jane Hawkey, Ben Vezina, Jonathan M Monk, Lousie M Judd, Taylor Harshegyi, Sebastián López-Fernández, Carla Rodrigues, Sylvain Brisse, Kathryn E Holt, Kelly L Wyres
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality. Genome research 32 (5) (2022)
Akanksha Rajput, Yara Seif, Kumari Sonal Choudhary, Christopher Dalldorf, Saugat Poudel, Jonathan M Monk, Bernhard O Palsson
Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens. mSystems 6 (1) (2021)
Colton J Lloyd, Jonathan M Monk, Laurence Yang, Ali Ebrahim, Bernhard O Palsson
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. PLoS computational biology 17 (6) (2021)
Jane Hawkey, Jonathan M Monk, Helen Billman-Jacobe, Bernhard O Palsson, Kathryn E Holt
Impact of insertion sequences on convergent evolution of Shigella species. PLoS genetics 16 (7) (2020)
Erol S Kavvas, Laurence Yang, Jonathan M Monk, David Heckmann, Bernhard O Palsson
A biochemically-interpretable machine learning classifier for microbial GWAS. Nature communications 11 (1) (2020)
Charles J Norsigian, Heather A Danhof, Colleen K Brand, Numan Oezguen, Firas S Midani, Bernhard O Palsson, Tor C Savidge, Robert A Britton, Jennifer K Spinler, Jonathan M Monk
Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence. NPJ systems biology and applications 6 (1) (2020)
Jason C Hyun, Erol S Kavvas, Jonathan M Monk, Bernhard O Palsson
Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. PLoS computational biology 16 (3) (2020)
Jinyuan Yan, Henri Estanbouli, Chen Liao, Wook Kim, Jonathan M Monk, Rayees Rahman, Mini Kamboj, Bernhard O Palsson, Wei-Gang Qiu, Joao B Xavier
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PLoS computational biology 15 (12) (2019)