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List of works by Jonathan M Monk

A biochemically-interpretable machine learning classifier for microbial GWAS

scientific article published on 22 May 2020

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

scientific article published on 09 January 2019

A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

scientific article published on 20 December 2019

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

scientific article published on 22 April 2019

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

scientific article published on 03 July 2019

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

scientific article published on 26 April 2019

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

scientific article published on 19 May 2016

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

scientific article published on 10 June 2016

Constraint-based models predict metabolic and associated cellular functions.

scientific article published on 16 January 2014

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.

scientific article

Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology

scientific article published on 04 October 2018

Genome-scale metabolic modeling reveals key features of a minimal gene set

scientific article published on 01 July 2021

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

scientific article

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

scientific article published in Nature Communications

High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

scientific article published on 11 November 2019

Impact of insertion sequences on convergent evolution of Shigella species

scientific article published on 09 July 2020

Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences.

scientific article published in January 2018

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

scientific article published in Nature Communications

Machine learning in computational biology to accelerate high-throughput protein expression.

scientific article published on 07 April 2017

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens

scientific article published on 02 March 2020

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

scientific article published on 30 October 2018

Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC

scientific article published on 23 September 2015

Model-driven discovery of underground metabolic functions in Escherichia coli

scientific article

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

scientific article published on 21 September 2016

Predicting Antimicrobial Resistance and Associated Genomic Features from Whole-Genome Sequencing

scientific article published on 30 January 2019

Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media

scientific article published on 17 December 2019

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus

scientific article published on 16 October 2019

Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence

scientific article published on 20 October 2020

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

scientific article

Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

scientific article published on 4 November 2015

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection

scientific article published on 20 December 2019

The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli.

scientific article published on 4 November 2016

Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice

article published in the Proceedings of the National Academy of Sciences of the United States of America

Using Genome-scale Models to Predict Biological Capabilities

scientific article

Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network

scientific journal article

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

scientific article published on 18 February 2016

iML1515, a knowledgebase that computes Escherichia coli traits.

scientific article published in October 2017

ssbio: A Python Framework for Structural Systems Biology

scientific article published on 12 February 2018

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