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Reconstructing organisms in silico: genome-scale models and their emerging applications

Nature reviews. Microbiology, 2020-12, Vol.18 (12), p.731-743

2020

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COBRAme: A computational framework for genome-scale models of metabolism and gene expression

PLoS computational biology, 2018-07, Vol.14 (7), p.e1006302-e1006302

2018

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Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

PLoS computational biology, 2019-12, Vol.15 (12), p.e1007525-e1007525

2019

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Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Nature communications, 2018-12, Vol.9 (1), p.5252-10, Article 5252

2018

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iML1515, a knowledgebase that computes Escherichia coli traits

Nature biotechnology, 2017-10, Vol.35 (10), p.904-908

2017

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

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006971-e1006971

2019

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Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

Applied and environmental microbiology, 2017-07, Vol.83 (13)

2017

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Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Proceedings of the National Academy of Sciences - PNAS, 2020-09, Vol.117 (37), p.23182-23190

2020

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Next-generation genome-scale models for metabolic engineering

Current opinion in biotechnology, 2015-12, Vol.35, p.23-29

2015

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Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen

PLoS computational biology, 2019-03, Vol.15 (3), p.e1006848

2019

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Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

PLoS computational biology, 2021-06, Vol.17 (6), p.e1007817-e1007817

2021

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Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities

Proceedings of the National Academy of Sciences - PNAS, 2017-09, Vol.114 (38), p.10286-10291

2017

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DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

BMC systems biology, 2019-01, Vol.13 (1), p.2-2, Article 2

2019

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Cellular responses to reactive oxygen species are predicted from molecular mechanisms

Proceedings of the National Academy of Sciences - PNAS, 2019-07, Vol.116 (28), p.14368-14373

2019

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The genetic basis for adaptation of model-designed syntrophic co-cultures

PLoS computational biology, 2019-03, Vol.15 (3), p.e1006213-e1006213

2019

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

Molecular systems biology, 2021-07, Vol.17 (7), p.e10099-n/a

2021

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Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298

mBio, 2024-10, Vol.15 (10), p.e0087324

2024

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solveME: fast and reliable solution of nonlinear ME models

BMC bioinformatics, 2016-09, Vol.17 (1), p.391-391, Article 391

2016

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Principles of proteome allocation are revealed using proteomic data and genome-scale models

Scientific reports, 2016-11, Vol.6 (1), p.36734-36734, Article 36734

2016

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

Proceedings of the National Academy of Sciences - PNAS, 2015-08, Vol.112 (34), p.10810-10815

2015

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Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets

Synthetic and systems biotechnology, 2022-09, Vol.7 (3), p.900-910

2022

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Predicting stress response and improved protein overproduction in Bacillus subtilis

NPJ systems biology and applications, 2022-12, Vol.8 (1), p.50-50, Article 50

2022

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Antigen receptor repertoire profiling from RNA-seq data

Nature biotechnology, 2017-10, Vol.35 (10), p.908-911

2017

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Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

PLoS computational biology, 2021-06, Vol.17 (6)

2021

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Predicting stress response and improved protein overproduction in Bacillus subtilis

NPJ systems biology and applications, 2022-12, Vol.8 (1)

2022

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Reconstructing organisms in silico: genome-scale models and their emerging applications

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

iML1515, a knowledgebase that computes Escherichia coli traits

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

Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Next-generation genome-scale models for metabolic engineering

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

The genetic basis for adaptation of model-designed syntrophic co-cultures

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

Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298

solveME: fast and reliable solution of nonlinear ME models

Principles of proteome allocation are revealed using proteomic data and genome-scale models

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

Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets

Predicting stress response and improved protein overproduction in Bacillus subtilis

Antigen receptor repertoire profiling from RNA-seq data

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Predicting stress response and improved protein overproduction in Bacillus subtilis

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