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Emulation of Quantitative Systems Pharmacology models to accelerate virtual population inference in immuno-oncology

Methods (San Diego, Calif.), 2024-03, Vol.223, p.118-126

2024

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Mitochondrial Metabolism in the Spotlight: Maintaining Balanced RNAP III Activity Ensures Cellular Homeostasis

International journal of molecular sciences, 2023-10, Vol.24 (19), p.14763

2023

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Mechanistic Models of COVID-19: Insights into Disease Progression, Vaccines, and Therapeutics

International journal of antimicrobial agents, 2022-07, Vol.60 (1), p.106606-106606, Article 106606

2022

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Slow protein fluctuations explain the emergence of growth phenotypes and persistence in clonal bacterial populations

PloS one, 2013-01, Vol.8 (1), p.e54272-e54272

2013

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Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

PloS one, 2015-10, Vol.10 (10), p.e0139507-e0139507

2015

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The genetic requirements for fast and slow growth in mycobacteria

PloS one, 2009-04, Vol.4 (4), p.e5349-e5349

2009

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The prognostic significance of specific HOX gene expression patterns in ovarian cancer

International journal of cancer, 2016-10, Vol.139 (7), p.1608-1617

2016

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MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models

PloS one, 2012-12, Vol.7 (12), p.e51511-e51511

2012

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Systems-based approaches to probing metabolic variation within the Mycobacterium tuberculosis complex

PloS one, 2013-09, Vol.8 (9), p.e75913

2013

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Integration of Omics Data Sources to Inform Mechanistic Modeling of Immune‐Oncology Therapies: A Tutorial for Clinical Pharmacologists

Clinical pharmacology and therapeutics, 2020-04, Vol.107 (4), p.858-870

2020

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Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification

Microbial cell factories, 2010-11, Vol.9 (1), p.88-88, Article 88

2010

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GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism

Genome biology, 2007-01, Vol.8 (5), p.R89-R89

2007

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Mycobacterium leprae genomes from a British medieval leprosy hospital: towards understanding an ancient epidemic

BMC genomics, 2014-04, Vol.15 (1), p.270-270

2014

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Learn–confirm in model‐informed drug development: Assessing an immunogenicity quantitative systems pharmacology platform

CPT: pharmacometrics and systems pharmacology, 2023-02, Vol.12 (2), p.139-143

2023

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Quantitative Systems Pharmacology Approaches for Immuno‐Oncology: Adding Virtual Patients to the Development Paradigm

Clinical pharmacology and therapeutics, 2021-03, Vol.109 (3), p.605-618

2021

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Lipid metabolism and Type VII secretion systems dominate the genome scale virulence profile of Mycobacterium tuberculosis in human dendritic cells

BMC genomics, 2015-05, Vol.16 (1), p.372-372, Article 372

2015

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Diverse control of metabolism and other cellular processes in Streptomyces coelicolor by the PhoP transcription factor: genome-wide identification of in vivo targets

Nucleic acids research, 2012-10, Vol.40 (19), p.9543

2012

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Application of quantitative systems pharmacology to guide the optimal dosing of COVID‐19 vaccines

CPT: pharmacometrics and systems pharmacology, 2021-10, Vol.10 (10), p.1130-1133

2021

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Generation of 2,000 breast cancer metabolic landscapes reveals a poor prognosis group with active serotonin production

Scientific reports, 2016-01, Vol.6 (1), p.19771-19771, Article 19771

2016

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Bridging the Gap between Stochastic and Deterministic Regimes in the Kinetic Simulations of the Biochemical Reaction Networks

Biophysical journal, 2004-03, Vol.86 (3), p.1357-1372

2004

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QSP Designer: Quantitative systems pharmacology modeling with modular biological process map notation and multiple language code generation

CPT: pharmacometrics and systems pharmacology, 2023-07, Vol.12 (7), p.889-903

2023

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SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

Bioinformatics, 2011-02, Vol.27 (3), p.433-434

2011

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Systems biology approaches for studying the pathogenesis of non-alcoholic fatty liver disease

World journal of gastroenterology : WJG, 2014-11, Vol.20 (41), p.15070-15078

2014

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Genome-wide analysis of the role of the antibiotic biosynthesis regulator AbsA2 in Streptomyces coelicolor A3(2)

PloS one, 2019-04, Vol.14 (4), p.e0200673-e0200673

2019

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Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization

BMC genomics, 2010-12, Vol.11 (1), p.682-682, Article 682

2010

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Emulation of Quantitative Systems Pharmacology models to accelerate virtual population inference in immuno-oncology

Mitochondrial Metabolism in the Spotlight: Maintaining Balanced RNAP III Activity Ensures Cellular Homeostasis

Mechanistic Models of COVID-19: Insights into Disease Progression, Vaccines, and Therapeutics

Slow protein fluctuations explain the emergence of growth phenotypes and persistence in clonal bacterial populations

Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

The genetic requirements for fast and slow growth in mycobacteria

The prognostic significance of specific HOX gene expression patterns in ovarian cancer

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models

Systems-based approaches to probing metabolic variation within the Mycobacterium tuberculosis complex

Integration of Omics Data Sources to Inform Mechanistic Modeling of Immune‐Oncology Therapies: A Tutorial for Clinical Pharmacologists

Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification

GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism

Mycobacterium leprae genomes from a British medieval leprosy hospital: towards understanding an ancient epidemic

Learn–confirm in model‐informed drug development: Assessing an immunogenicity quantitative systems pharmacology platform

Quantitative Systems Pharmacology Approaches for Immuno‐Oncology: Adding Virtual Patients to the Development Paradigm

Lipid metabolism and Type VII secretion systems dominate the genome scale virulence profile of Mycobacterium tuberculosis in human dendritic cells

Diverse control of metabolism and other cellular processes in Streptomyces coelicolor by the PhoP transcription factor: genome-wide identification of in vivo targets

Application of quantitative systems pharmacology to guide the optimal dosing of COVID‐19 vaccines

Generation of 2,000 breast cancer metabolic landscapes reveals a poor prognosis group with active serotonin production

Bridging the Gap between Stochastic and Deterministic Regimes in the Kinetic Simulations of the Biochemical Reaction Networks

QSP Designer: Quantitative systems pharmacology modeling with modular biological process map notation and multiple language code generation

SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

Systems biology approaches for studying the pathogenesis of non-alcoholic fatty liver disease

Genome-wide analysis of the role of the antibiotic biosynthesis regulator AbsA2 in Streptomyces coelicolor A3(2)

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization

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