Lista de obras - Jonathan M Monk - Dominio Público Uruguay

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

artículo científico publicado en 2019

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

artículo científico publicado en 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

artículo científico publicado en 2019

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

artículo científico publicado en 2016

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

artículo científico publicado en 2016

Constraint-based models predict metabolic and associated cellular functions.

artículo científico

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

artículo científico publicado en 2018

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

artículo científico publicado en 2021

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

artículo científico publicado en 2013

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

artículo científico publicado en 2018

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.

artículo científico publicado en 2018

MEMOTE for standardized genome-scale metabolic model testing

artículo científico publicado en 2020

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

artículo científico publicado en 2018

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

artículo científico

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

artículo científico publicado en 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

artículo científico publicado en 2018

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

artículo científico publicado en 2015

Model-driven discovery of underground metabolic functions in Escherichia coli

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2020

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2019

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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado en 2016

iML1515, a knowledgebase that computes Escherichia coli traits.

artículo científico publicado en 2017

ssbio: A Python Framework for Structural Systems Biology

artículo científico publicado en 2018

Lista de obras de Jonathan M Monk

A biochemically-interpretable machine learning classifier for microbial GWAS

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

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

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

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

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

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

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

Constraint-based models predict metabolic and associated cellular functions.

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

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

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

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

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

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

Impact of insertion sequences on convergent evolution of Shigella species

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

MEMOTE for standardized genome-scale metabolic model testing

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

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

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

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

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

Model-driven discovery of underground metabolic functions in Escherichia coli

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

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

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

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

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

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

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

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

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

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

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

Using Genome-scale Models to Predict Biological Capabilities

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

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

iML1515, a knowledgebase that computes Escherichia coli traits.

ssbio: A Python Framework for Structural Systems Biology