List of works - Ines Thiele

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

scientific article

A community-driven global reconstruction of human metabolism. ⬇️

scientific article

A compendium of inborn errors of metabolism mapped onto the human metabolic network

scientific article

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.

scientific article

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

scientific article (publication date: 16 September 2008)

A protocol for generating a high-quality genome-scale metabolic reconstruction

scientific article

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines

scientific article published on 14 August 2017

A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm

scientific article

A systems biology approach to studying the role of microbes in human health.

scientific article published on 25 October 2012

An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production

article

Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico

scientific article published on 3 April 2015

Applying systems biology methods to the study of human physiology in extreme environments

scientific article published on 22 March 2013

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

scientific article

Bringing Genomes to Life: The Use of Genome-Scale In Silico Models

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.

scientific article

Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.

scientific article published on 30 November 2004

Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.

scientific article

Cardinality optimization in constraint-based modelling: application to human metabolism

scientific article published in September 2023

Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides

scientific article published on 29 August 2017

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

scientific article published on 14 June 2017

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

scientific article

Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine

scientific article published on January 2016

Computationally efficient flux variability analysis

scientific article

Conditions for duality between fluxes and concentrations in biochemical networks

scientific article published on 23 June 2016

Consensus and conflict cards for metabolic pathway databases

scientific article

Contextualization procedure and modeling of monocyte specific TLR signaling

scientific article

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

scientific article published on 01 March 2019

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

scientific article published on 30 January 2012

DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia.

scientific article

Do genome-scale models need exact solvers or clearer standards?

scientific article published on 14 October 2015

Editorial: The Human Gutome: Nutrigenomics of Host-Microbiome Interactions

scientific article published on 6 September 2016

Erratum to: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.

scientific article published on 4 July 2016

Estimation of the number of extreme pathways for metabolic networks

scientific article

Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants

scientific article

Finding useful biomarkers for Parkinson's disease

article

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

scientific article published on 27 March 2018

From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease

scientific article published on 01 August 2018

Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery

scientific article

Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe

scientific article

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

scientific article

Genome-Scale Reconstruction, Modeling, and Simulation of E. coli℉s Metabolic Network

scholarly article published 2009

Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia

scientific article

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

scientific article

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

scientific article published on 9 February 2016

Global reconstruction of the human metabolic network based on genomic and bibliomic data ⬇️

scientific article

Gut microbiota functions: metabolism of nutrients and other food components

scientific article published on 9 April 2017

Identification of potential pathway mediation targets in Toll-like receptor signaling

scientific article

Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity

scientific article published in 2013

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism

scientific article (publication date: 7 June 2010)

Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism

scientific article published on 05 August 2021

Intracellular metabolite profiling of platelets: Evaluation of extraction processes and chromatographic strategies

scientific article published on 30 April 2012

Leigh map: A novel computational diagnostic resource for mitochondrial disease

scientific article published on 15 December 2016

Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration

scientific article published on 28 August 2012

Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease

scientific article published on 11 March 2014

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

scientific article published on 03 August 2016

Metabolic network analysis integrated with transcript verification for sequenced genomes.

scientific article

Metabolomics enables precision medicine: "A White Paper, Community Perspective"

scientific article

Model-based dietary optimization for late-stage, levodopa-treated, Parkinson's disease patients

scientific article

Modeling metabolism of the human gut microbiome

scientific article published on 16 December 2017

Modeling the effects of commonly used drugs on human metabolism

scientific article published on 21 November 2014

Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).

scientific article

Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage

scientific article

Personalized metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases

scientific article published in June 2024

Personalized whole-body models integrate metabolism, physiology, and the gut microbiome

scientific article published on 01 May 2020

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

scientific article published on 30 November 2015

Predicting gastrointestinal drug effects using contextualized metabolic models

scientific article published on 26 June 2019

Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells

scientific article published on 13 March 2013

Prediction of intracellular metabolic states from extracellular metabolomic data

scientific article

Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.

scientific article published in April 2012

Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli

scientific article

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

scientific article (publication date: 4 August 2011)

Quantitative systems pharmacology and the personalized drug-microbiota-diet axis

scientific article published on 01 August 2017

Recon3D enables a three-dimensional view of gene variation in human metabolism.

scientific article published on 19 February 2018

ReconMap: an interactive visualization of human metabolism

scientific article

Reconstruction annotation jamborees: a community approach to systems biology

scientific article published on April 2010

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

scientific article published on 18 January 2017

Replication Protein A, the Main Eukaryotic Single-Stranded DNA Binding Protein, a Focal Point in Cellular DNA Metabolism

scientific article published on 2 January 2024

Reply to "Challenges in modeling the human gut microbiome"

scientific article published on 01 August 2018

Robust flux balance analysis of multiscale biochemical reaction networks.

scientific article

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

scientific article published on 15 May 2019

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

scientific article

Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota

scientific article

Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework

scientific article published on January 2015

Systems biology of host-microbe metabolomics

scientific article published on 30 April 2015

Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut

scientific article published on 28 September 2012

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

article

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

scientific article

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

scientific article

Three-dimensional structural view of the central metabolic network of Thermotoga maritima

scientific article

Toward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks

scientific article (publication date: 2013)

Towards multidimensional genome annotation

scientific article

What is flux balance analysis?

scientific article

XomicsToModel: Multiomics data integration and generation of thermodynamically consistent metabolic models

scientific article

fastGapFill: efficient gap filling in metabolic networks

scientific article

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks

scientific article published on 19 May 2011

von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models

scientific article

List of works by Ines Thiele

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

A community-driven global reconstruction of human metabolism. ⬇️

A compendium of inborn errors of metabolism mapped onto the human metabolic network

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

A protocol for generating a high-quality genome-scale metabolic reconstruction

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines

A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm

A systems biology approach to studying the role of microbes in human health.

An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production

Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico

Applying systems biology methods to the study of human physiology in extreme environments

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

Bringing Genomes to Life: The Use of Genome-Scale In Silico Models

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.

Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.

Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.

Cardinality optimization in constraint-based modelling: application to human metabolism

Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine

Computationally efficient flux variability analysis

Conditions for duality between fluxes and concentrations in biochemical networks

Consensus and conflict cards for metabolic pathway databases

Contextualization procedure and modeling of monocyte specific TLR signaling

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia.

Do genome-scale models need exact solvers or clearer standards?

Editorial: The Human Gutome: Nutrigenomics of Host-Microbiome Interactions

Erratum to: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.

Estimation of the number of extreme pathways for metabolic networks

Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants

Finding useful biomarkers for Parkinson's disease

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease

Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery

Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

Genome-Scale Reconstruction, Modeling, and Simulation of E. coli℉s Metabolic Network

Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

Global reconstruction of the human metabolic network based on genomic and bibliomic data ⬇️

Gut microbiota functions: metabolism of nutrients and other food components

Identification of potential pathway mediation targets in Toll-like receptor signaling

Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism

Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism

Intracellular metabolite profiling of platelets: Evaluation of extraction processes and chromatographic strategies

Leigh map: A novel computational diagnostic resource for mitochondrial disease

Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration

Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

Metabolic network analysis integrated with transcript verification for sequenced genomes.

Metabolomics enables precision medicine: "A White Paper, Community Perspective"

Model-based dietary optimization for late-stage, levodopa-treated, Parkinson's disease patients

Modeling metabolism of the human gut microbiome

Modeling the effects of commonly used drugs on human metabolism

Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).

Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage

Personalized metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases

Personalized whole-body models integrate metabolism, physiology, and the gut microbiome

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

Predicting gastrointestinal drug effects using contextualized metabolic models

Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells

Prediction of intracellular metabolic states from extracellular metabolomic data

Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.

Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Quantitative systems pharmacology and the personalized drug-microbiota-diet axis

Recon3D enables a three-dimensional view of gene variation in human metabolism.

ReconMap: an interactive visualization of human metabolism

Reconstruction annotation jamborees: a community approach to systems biology

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

Replication Protein A, the Main Eukaryotic Single-Stranded DNA Binding Protein, a Focal Point in Cellular DNA Metabolism

Reply to "Challenges in modeling the human gut microbiome"

Robust flux balance analysis of multiscale biochemical reaction networks.