I. Thiele

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Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an In Silico Genome-Scale Characterization of Single- and Double-Deletion Mutants

B. Palsson, N. Price, I. Thiele, 2005, Journal of bacteriology.

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

Monica L. Mo, B. Palsson, S. Becker, 2007, Proceedings of the National Academy of Sciences.

A community-driven global reconstruction of human metabolism

Ronan M. T. Fleming, Jason A. Papin, Sarah M. Keating, 2013, Nature Biotechnology.

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

Ronan M. T. Fleming, M. Saunders, B. Palsson, 2016, Scientific Reports.

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

Ronan M. T. Fleming, B. Palsson, R. Fleming, 2012, PloS one.

Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0.

Francisco J. Planes, Ronan M. T. Fleming, Sarah M. Keating, 2017, 1710.04038.

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

Daniel C. Zielinski, Maike K. Aurich, Anand V. Sastry, 2018 .

Systems biology of bacteria-host interactions

I. Thiele, A. Heinken, D. Ravcheev, 2016 .

Systems biology of host–microbe metabolomics

I. Thiele, A. Heinken, 2015, Wiley interdisciplinary reviews. Systems biology and medicine.

Reconstruction annotation jamborees: a community approach to systems biology

Ines Thiele, Bernhard Ø Palsson, B. Palsson, 2010, Molecular systems biology.

Reconstruction of biochemical networks in microorganisms

Adam M. Feist, Markus J. Herrgård, B. Palsson, 2009, Nature Reviews Microbiology.

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

I. Thiele, Eugen Bauer, 2018, mSystems.

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

Ronan M. T. Fleming, Ines Thiele, Almut Heinken, 2013, Current opinion in biotechnology.

Towards multidimensional genome annotation

B. Palsson, J. Reed, I. Famili, 2006, Nature Reviews Genetics.

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

Ronan M. T. Fleming, R. Fleming, I. Thiele, 2009, Biophysical chemistry.

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe

H. Harmsen, I. Thiele, A. Heinken, 2014, Journal of bacteriology.

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

B. Palsson, E. M. Knight, I. Thiele, 2012, Proceedings of the National Academy of Sciences.

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

B. Palsson, I. Thiele, Ines Thiele, 2010 .

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

Ronan M. T. Fleming, Hulda S. Haraldsdóttir, R. Fleming, 2012, Biophysical journal.

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.

Ronan M. T. Fleming, G. Provan, R. Fleming, 2010, Journal of theoretical biology.

Quadruple-precision solution of genome-scale models of Metabolism and macromolecular Expression

Ronan M. T. Fleming, M. Saunders, B. Palsson, 2016, 1606.00054.

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

Naryttza N. Diaz, Rick L. Stevens, R. Overbeek, 2005, Nucleic acids research.

Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism

E. L. Moreno, S. Vempala, M. Saunders, 2021, bioRxiv.

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

Ronan M. T. Fleming, Maike K. Aurich, R. Fleming, 2020, Molecular systems biology.

Candidate Metabolic Network States in Human Mitochondria

B. Palsson, N. Price, I. Thiele, 2005, Journal of Biological Chemistry.

Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells.

Maria Pires Pacheco, P. Wilmes, I. Thiele, 2019, Cell Reports.

Resource Integrated In Vitro and In S ilico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells Graphical

Maria Pires Pacheco, P. Wilmes, I. Thiele, 2019 .

A Systems Biology Approach to Drug Targets in Pseudomonas aeruginosa Biofilm

Ronan M. T. Fleming, R. Fleming, I. Thiele, 2012, PloS one.

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

V. de Crécy-Lagard, I. Thiele, Stefanía Magnúsdóttir, 2015, Front. Genet..

Metabolic network analysis integrated with transcript verification for sequenced genomes

Jason A. Papin, Roger L. Chang, Erik F. Y. Hom, 2009, Nature Methods.

Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism

Avlant Nilsson, Ronan M. T. Fleming, Elizabeth Brunk, 2018, Nature Biotechnology.

Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions

Maike K. Aurich, P. May, P. Wilmes, 2020, BMC Biology.

Parkinson’s disease-associated alterations of the gut microbiome can invoke disease-relevant metabolic changes

R. Krüger, I. Thiele, F. Betsou, 2019, bioRxiv.

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

Ronan M. T. Fleming, Eugen Bauer, Ines Thiele, 2016, Nature Biotechnology.

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

Ronan M. T. Fleming, Adam M. Feist, Jason A. Papin, 2015, Molecular systems biology.

Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine.

Ines Thiele, Maike K. Aurich, Maike K Aurich, 2016, Methods in molecular biology.

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

Ines Thiele, Maike K. Aurich, Swagatika Sahoo, 2014, Front. Physiol..

Prediction of intracellular metabolic states from extracellular metabolomic data

Ronan M. T. Fleming, Ines Thiele, Bernhard Ø. Palsson, 2014, Metabolomics.

Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

Ines Thiele, Adam Godzik, Ashley M Deacon, 2009, Science.

Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease

R. Fleming, R. Krüger, T. Hankemeier, 2019, Cell Reports.

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

Ines Thiele, Almut Heinken, I. Thiele, 2015, Gut microbes.

Integration of constraint-based modelling with faecal metabolomics reveals large deleterious effects of Fusobacteria species on community butyrate production

I. Thiele, A. Heinken, J. Hertel, 2020, bioRxiv.

Modeling metabolism of the human gut microbiome.

Ines Thiele, Stefanía Magnúsdóttir, I. Thiele, 2018, Current opinion in biotechnology.

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

I. Thiele, D. Ravcheev, 2016, Front. Microbiol..

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

Ronan M. T. Fleming, Ines Thiele, Swagatika Sahoo, 2013, Gut microbes.

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

Ronan M. T. Fleming, R. Fleming, I. Thiele, 2019, Microbiome.

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

R. Fleming, I. Thiele, Reinhard Schneider, 2018, bioRxiv.

Comparative genomic analysis of the human gut microbiome reveals a broad distribution of metabolic pathways for the degradation of host-synthetized mucin glycans

I. Thiele, D. Ravcheev, 2017, 1703.10524.

AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities

Ronan M. T. Fleming, Janaka N. Edirisinghe, R. Fleming, 2020, bioRxiv.

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

I. Thiele, L. Ferguson, D. Dimitrov, 2016, Front. Genet..

Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome

I. Thiele, D. Ravcheev, S. Smajic, 2019, Front. Genet..

Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig

Maike K. Aurich, F. Jourdan, I. Thiele, 2019, Scientific Reports.

Title : “ Genome-scale methods converge on key mitochondrial genes 1 for the survival of human cardiomyocytes in hypoxia . ”

I. Thiele, P. Robbins, G. Cavalleri, 2018 .

Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer’s Disease

Cory C. Funk, James T. Yurkovich, Xianlin Han, 2020, Cell reports. Medicine.

Pan-organ model integration of metabolic and regulatory processes in type 1 diabetes

I. Thiele, Marouen Ben Guebila, 2019, bioRxiv.

Identifying differences in bile acid pathways for cholesterol clearance in Alzheimer’s disease using metabolic networks of human brain regions

Cory C. Funk, James T. Yurkovich, N. Price, 2019 .

Creation and analysis of biochemical constraint-based models : the COBRA Toolbox v 3 . 0 26 th February 2018

Francisco J. Planes, Ronan M. T. Fleming, Maike K. Aurich, 2018 .

Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells.

Maria Pires Pacheco, P. Wilmes, I. Thiele, 2019, Cell reports.

Systems biology illuminates alternative metabolic niches in the human gut microbiome

I. Thiele, P. Turnbaugh, A. Heinken, 2022, bioRxiv.

Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease

Ronan M. T. Fleming, R. Fleming, R. Krüger, 2019, Cell reports.

Metabolic systems biology

B. Palsson, N. Jamshidi, I. Thiele, 2009, Encyclopedia of Complexity and Systems Science.

Genomic analysis of the respiration the microbiota of human intestine

I. Thiele, D. Ravcheev, 2015 .

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

R. Fleming, I. Thiele, Laurent Heirendt, 2017, Bioinformatics.

MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions

Ronan M. T. Fleming, R. Fleming, I. Thiele, 2022, Bioinform..

Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities

I. Thiele, A. Heinken, 2022, Bioinform..

Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism

Ronan M. T. Fleming, E. L. Moreno, Hulda S. Haraldsdóttir, 2021, bioRxiv.

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

Ines Thiele, Swagatika Sahoo, I. Thiele, 2012, Molecular bioSystems.

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

Ines Thiele, Marouen Ben Guebila, I. Thiele, 2016, npj Systems Biology and Applications.

Dynamic flux balance analysis of whole-body metabolism for type 1 diabetes

I. Thiele, Marouen Ben Guebila, Marouen Ben Guebila, 2021, Nature Computational Science.

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

Anne Richelle, Iñigo Apaolaza, Lin Wang, 2019, Nature Protocols.

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

Ronan M. T. Fleming, Ines Thiele, R. Fleming, 2017, Current opinion in systems biology.

Modeling the effects of commonly used drugs on human metabolism

Ronan M. T. Fleming, Ines Thiele, Swagatika Sahoo, 2015, The FEBS journal.

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

Ines Thiele, Swagatika Sahoo, I. Thiele, 2013, Human molecular genetics.

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

Ronan M. T. Fleming, Aarash Bordbar, Adam M. Feist, 2007, Nature Protocols.

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

Ronan M. T. Fleming, Ines Thiele, Maike K. Aurich, 2017, PLoS Comput. Biol..

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

Ronan M. T. Fleming, Ines Thiele, Maike K. Aurich, 2016, Front. Physiol..

Genome-Scale Methods Converge on Key Mitochondrial Genes for the Survival of Human Cardiomyocytes in Hypoxia

Ines Thiele, Michael E. Weale, Peter A. Robbins, 2014, Circulation. Cardiovascular genetics.

What is flux balance analysis?

Jeffrey D Orth, Bernhard Ø Palsson, Ines Thiele, 2010, Nature Biotechnology.

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

Adam M. Feist, Bernhard O. Palsson, Ines Thiele, 2009 .

MetabolicSystems Biology: A Constraint-Based Approach

Nathan E. Lewis, N. Jamshidi, I. Thiele, 2008 .

Genome-Scale In Silico Models

I. Thiele, Ø. Bernhard, 2007 .

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

Bernhard O. Palsson, Ines Thiele, B. Palsson, 2007 .

A nutrition algorithm to optimize feed and medium composition using genome-scale metabolic models.

I. Thiele, B. Weston, 2023, Metabolic engineering.

Metabolomics enables precision medicine: “A White Paper, Community Perspective”

Matej Oresic, David S. Wishart, Richard D. Beger, 2016, Metabolomics.

An international classification of inherited metabolic disorders (ICIMD)

Robert W. Taylor, A. Ballabio, E. Bertini, 2020, Journal of inherited metabolic disease.

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

Ines Thiele, Óttar Rolfsson, Bernhard Ø Palsson, 2013, The Biochemical journal.

Gut microbiota functions: metabolism of nutrients and other food components

I. Thiele, A. Heinken, I. Rowland, 2017, European Journal of Nutrition.

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

Ines Thiele, Dmitry A. Ravcheev, I. Thiele, 2014, Front. Microbiol..

Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism

Daniel F. Freitag, F. Kronenberg, P. Oefner, 2021, Nature Communications.

Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development

Ines Thiele, Linda J. Broadbelt, Beatriz Peñalver Bernabé, 2019, BMC Bioinformatics.

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

Bernhard O. Palsson, Ines Thiele, Ottar Rolfsson, 2011, BMC Systems Biology.

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

Bernhard O. Palsson, Ines Thiele, Neema Jamshidi, 2010, BMC Systems Biology.

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

Bernhard O. Palsson, Ines Thiele, Juan Nogales, 2008, BMC Systems Biology.

Predicting gastrointestinal drug effects using contextualized metabolic models

Ines Thiele, Marouen Ben Guebila, I. Thiele, 2019, PLoS Comput. Biol..

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

Ines Thiele, Dmitry A. Ravcheev, I. Thiele, 2017, Front. Genet..

Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of Fusobacterium spp. on community butyrate production

I. Thiele, A. Heinken, J. Hertel, 2021, Gut microbes.

Causal inference on microbiome-metabolome relations via in silico in vivo association pattern analyses

I. Thiele, A. Heinken, J. Hertel, 2021, bioRxiv.

Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions

Ronan M. T. Fleming, Maike K. Aurich, P. May, 2020, BMC Biology.

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

Johannes Zimmermann, Eugen Bauer, Federico Baldini, 2017, PLoS Comput. Biol..

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

Federico Baldini, Ines Thiele, Laurent Heirendt, 2018, bioRxiv.

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

Santosh S. Vempala, Ronan M. T. Fleming, Ines Thiele, 2017, Bioinform..

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

Piotr Gawron, Inna Kuperstein, Ronan M. T. Fleming, 2018, bioRxiv.

Finding useful biomarkers for Parkinson’s disease

A. Singleton, D. Vaillancourt, D. German, 2018, Science Translational Medicine.

DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

Ronan M. T. Fleming, Ines Thiele, Almut Heinken, 2021, Bioinform..

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

Ronan M. T. Fleming, R. Fleming, I. Thiele, 2019, Microbiome.

Computationally efficient flux variability analysis

Ines Thiele, Steinn Gudmundsson, I. Thiele, 2010, BMC Bioinformatics.

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

Ines Thiele, Almut Heinken, I. Thiele, 2015, Applied and Environmental Microbiology.

Reply to "Challenges in modeling the human gut microbiome"

Ronan M. T. Fleming, Ines Thiele, Ronan M T Fleming, 2018, Nature Biotechnology.

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

Eugen Bauer, Ines Thiele, Paul Wilmes, 2015, Microbiome.

ReconMap: an interactive visualization of human metabolism

Piotr Gawron, Ronan M. T. Fleming, Reinhard Schneider, 2016, Bioinform..

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

Ronan M. T. Fleming, Bernhard O. Palsson, Ines Thiele, 2009, PLoS Comput. Biol..

The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases

T. Hankemeier, I. Thiele, A. Heinken, 2021, Gut microbes.

Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling

Bernhard O. Palsson, Ines Thiele, Neema Jamshidi, 2009, PLoS Comput. Biol..

Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication

Ronan M. T. Fleming, R. Fleming, I. Thiele, 2022, bioRxiv.

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

Eugen Bauer, Ines Thiele, I. Thiele, 2018, npj Systems Biology and Applications.

Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals

Ronan M. T. Fleming, Federico Baldini, Ines Thiele, 2017, bioRxiv.

Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis

I. Thiele, A. Heinken, J. Hertel, 2021, NPJ systems biology and applications.

Systematic interrogation of the distinct metabolic potential in gut microbiomes of inflammatory bowel disease patients with dysbiosis

I. Thiele, A. Heinken, 2019, bioRxiv.

From metagenomic data to personalized computational microbiotas: Predicting dietary supplements for Crohn's disease

I. Thiele, Eugen Bauer, 2017, 1709.06007.

Contextualization Procedure and Modeling of Monocyte Specific TLR Signaling

Ines Thiele, Maike K. Aurich, I. Thiele, 2012, PloS one.

Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies.

Ines Thiele, Bernhard Ø Palsson, B. Palsson, 2012, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

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

Aarash Bordbar, Ines Thiele, Jan Schellenberger, 2010, Biophysical journal.

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

Kathleen Marchal, Ronan M. T. Fleming, Neil Swainston, 2011, BMC Systems Biology.

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

Ronan M. T. Fleming, Ines Thiele, R. Fleming, 2011, Bioinform..

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

Ines Thiele, Juan Nogales, Steinn Gudmundsson, 2012 .

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

Ronan M. T. Fleming, Ines Thiele, Bernhard Ø. Palsson, 2011, Analytical and Bioanalytical Chemistry.

Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine.

I. Thiele, A. Heinken, J. Hertel, 2021, Annual review of microbiology.

When metabolism meets physiology: Harvey and Harvetta

Ronan M. T. Fleming, Ines Thiele, Maike K. Aurich, 2018, bioRxiv.

Leigh map: A novel computational diagnostic resource for mitochondrial disease

Ines Thiele, Alberto Noronha, Shamima Rahman, 2017, Annals of neurology.

Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Cholesterol Metabolism in Alzheimer’s Disease

Cory C. Funk, James T. Yurkovich, N. Price, 2020, SSRN Electronic Journal.

Conditions for duality between fluxes and concentrations in biochemical networks.

Ronan M. T. Fleming, Ines Thiele, Nikos Vlassis, 2015, Journal of theoretical biology.

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

Bernhard Ø Palsson, Nathan D Price, Ines Thiele, 2006, Biophysical journal.

fastGapFill: efficient gap filling in metabolic networks

Ronan M. T. Fleming, Ines Thiele, Nikos Vlassis, 2014, Bioinform..

Prediction of intracellular metabolic states from extracellular metabolomic data

Ronan M. T. Fleming, Maike K. Aurich, B. Palsson, 2014, Metabolomics.

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

C. Laczny, P. Wilmes, I. Thiele, 2015, Microbiome.

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

Ines Thiele, Stefan Gretar Thorleifsson, I. Thiele, 2011, Bioinform..

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

Ronan M. T. Fleming, Ines Thiele, Hulda S. Haraldsdóttir, 2014, Journal of Cheminformatics.

Consensus and conflict cards for metabolic pathway databases

Antoine H. C. van Kampen, Morris A. Swertz, Ines Thiele, 2013, BMC Systems Biology.

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

B. Palsson, I. Thiele, 2010, Nature Protocols.

Robust flux balance analysis of multiscale biochemical reaction networks

Michael A. Saunders, Ronan M. T. Fleming, Ines Thiele, 2013, BMC Bioinformatics.

A Systems Biology Approach to the Evolution of Codon Use Pattern

B. Palsson, R. Fleming, A. Bordbar, 2011 .

A Genome-scale Metabolic Reconstruction of Pseudomonas Putida Kt2440: Ijn746 as a Cell Factory

B. Palsson, I. Thiele, Juan Nogales, 2008 .

Estimation of the number of extreme pathways for metabolic networks

Bernhard O. Palsson, Ines Thiele, Matthew Yeung, 2007, BMC Bioinformatics.

COBRA Toolbox 2.0

Ronan M. T. Fleming, Aarash Bordbar, Adam M. Feist, 2011 .

Bioinformatics Applications Note Systems Biology Rbionet: a Cobra Toolbox Extension for Reconstructing High-quality Biochemical Networks

I. Thiele, S. G. Thorleifsson, 2022 .

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

Ronan M. T. Fleming, I. Thiele, R M T Fleming, 2011, Journal of theoretical biology.

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

Ronan M. T. Fleming, R. Fleming, T. Hankemeier, 2021, bioRxiv.

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

Ronan M. T. Fleming, Ines Thiele, Alberto Noronha, 2017, Journal of Cheminformatics.

Thermotoga maritima of Three-Dimensional Structural View of the Central Metabolic Network

Ines Thiele, Ying Zhang, Adam Godzik, 2011 .

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

Ines Thiele, Radhakrishnan Mahadevan, William Pei, 2021, PLoS Comput. Biol..

Reconstruction of biochemical networks in microorganisms

Adam M. Feist, Markus J. Herrgård, B. Palsson, 2009, Nature Reviews Microbiology.

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

B. Palsson, I. Thiele, Juan Nogales, 2008, BMC Systems Biology.

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

Ronan M. T. Fleming, Adam M. Feist, Daniel C. Zielinski, 2007, Nature Protocols.

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

B. Palsson, E. M. Knight, I. Thiele, 2012, Proceedings of the National Academy of Sciences.

A Systems Biology Approach to the Evolution of Codon Use Pattern

Ronan M. T. Fleming, B. Palsson, A. Bordbar, 2011 .

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

Sarah M. Keating, Maike K. Aurich, H. S. Hinton, 2019, Nature Protocols.

Metabolomics enables precision medicine: “A White Paper, Community Perspective”

Michael A. Schmidt, O. Fiehn, D. Wishart, 2016, Metabolomics.

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

C. Laczny, P. Wilmes, I. Thiele, 2016, Microbiome.

Metabolic systems biology

Bernhard O. Palsson, Nathan E. Lewis, Ines Thiele, 2009, Encyclopedia of Complexity and Systems Science.

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

Ines Thiele, Lindsay M Edwards, I. Thiele, 2013, Extreme Physiology and Medicine.