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

Nature communications, 2018-10, Vol.9 (1), p.4306-9, Article 4306

2018

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Is the kinetome conserved?

Molecular systems biology, 2022-02, Vol.18 (2), p.e10782-n/a

2022

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

Nature communications, 2018-09, Vol.9 (1), p.3771-12, Article 3771

2018

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Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

Scientific reports, 2017-04, Vol.7 (1), p.46249-46249, Article 46249

2017

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Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

Nucleic acids research, 2018-11, Vol.46 (20), p.10682

2018

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Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo

Nucleic acids research, 2021-09, Vol.49 (17), p.9696

2021

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The quantitative metabolome is shaped by abiotic constraints

Nature communications, 2021-05, Vol.12 (1), p.3178-3178, Article 3178

2021

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Community standards to facilitate development and address challenges in metabolic modeling

Molecular systems biology, 2020-08, Vol.16 (8), p.e9235-n/a

2020

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MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

PLoS computational biology, 2021-01, Vol.17 (1), p.e1008208-e1008208

2021

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Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

BMC genomics, 2020-07, Vol.21 (1), p.514-514, Article 514

2020

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Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks

The Journal of biological chemistry, 2017-12, Vol.292 (48), p.19556-19564

2017

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Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Cell reports (Cambridge), 2020-04, Vol.31 (4), p.107577-107577, Article 107577

2020

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Visualizing metabolic network dynamics through time-series metabolomic data

BMC bioinformatics, 2020-04, Vol.21 (1), p.130-130, Article 130

2020

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Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells

PLoS computational biology, 2017-03, Vol.13 (3), p.e1005424-e1005424

2017

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Genome-scale metabolic model of the rat liver predicts effects of diet restriction

Scientific reports, 2019-07, Vol.9 (1), p.9807-12, Article 9807

2019

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Temperature Dependence of Platelet Metabolism

Metabolites, 2024-01, Vol.14 (2), p.91

2024

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The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures

Frontiers in microbiology, 2018-05, Vol.9, p.1082-1082

2018

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A framework towards digital twins for type 2 diabetes

Frontiers in digital health, 2024, Vol.6, p.1336050-1336050

2024

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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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Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials

PLoS computational biology, 2018-08, Vol.14 (8), p.e1006356

2018

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Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Cell reports (Cambridge), 2021-06, Vol.35 (11), p.109287-109287, Article 109287

2021

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BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Nucleic acids research, 2020-01, Vol.48 (D1), p.D402

2020

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Poliovirus Vaccination Induces a Humoral Immune Response That Cross Reacts With SARS-CoV-2

Frontiers in medicine, 2021-08, Vol.8, p.710010-710010

2021

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Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model Reconstruction

Frontiers in cell and developmental biology, 2021-06, Vol.9, p.642681-642681

2021

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Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine

Frontiers in bioengineering and biotechnology, 2020-03, Vol.8, p.239

2020

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

Is the kinetome conserved?

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

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo

The quantitative metabolome is shaped by abiotic constraints

Community standards to facilitate development and address challenges in metabolic modeling

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Visualizing metabolic network dynamics through time-series metabolomic data

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells

Genome-scale metabolic model of the rat liver predicts effects of diet restriction

Temperature Dependence of Platelet Metabolism

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures

A framework towards digital twins for type 2 diabetes

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

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Poliovirus Vaccination Induces a Humoral Immune Response That Cross Reacts With SARS-CoV-2

Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model Reconstruction

Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine

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