Estimation of the number of extreme pathways for metabolic networks. - Matthew Yeung; Ines Thiele; Bernhard O. Palsson (BMC Bioinform., 2007)

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. - Juan Nogales; Bernhard Ø. Palsson; Ines Thiele (BMC Syst. Biol., 2008)

Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling. - Fan Li 002; Ines Thiele; Neema Jamshidi; Bernhard O. Palsson (PLoS Comput. Biol., 2009)

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization. - Ines Thiele; Neema Jamshidi; Ronan M. T. Fleming; Bernhard O. Palsson (PLoS Comput. Biol., 2009)

Metabolic Systems Biology. - Nathan E. Lewis; Neema Jamshidi; Ines Thiele; Bernhard O. Palsson (Encyclopedia of Complexity and Systems Science, 2009)

Computationally efficient flux variability analysis. - Steinn Gudmundsson; Ines Thiele (BMC Bioinform., 2010)

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. - Martin I. Sigurdsson; Neema Jamshidi; Eiríkur Steingrímsson; Ines Thiele; Bernhard Ø. Palsson (BMC Syst. Biol., 2010)

von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. - Ronan M. T. Fleming; Ines Thiele (Bioinform., 2011)

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks. - Stefan Gretar Thorleifsson; Ines Thiele (Bioinform., 2011)

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. - Ottar Rolfsson; Bernhard Ø. Palsson; Ines Thiele (BMC Syst. Biol., 2011)

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. - Ines Thiele; Daniel R. Hyduke; Benjamin Steeb; Guy Fankam; Douglas K. Allen; Susanna Bazzani; Pep Charusanti; Feng-Chi Chen; Ronan M. T. Fleming; Chao A. Hsiung; Sigrid C. J. De Keersmaecker; Yu-Chieh Liao; et al. (BMC Syst. Biol., 2011)

Robust flux balance analysis of multiscale biochemical reaction networks. - Yuekai Sun; Ronan M. T. Fleming; Ines Thiele; Michael A. Saunders (BMC Bioinform., 2013)

Consensus and conflict cards for metabolic pathway databases. - Miranda D. Stobbe; Morris A. Swertz; Ines Thiele; Trebor Rengaw; Antoine H. C. van Kampen; Perry D. Moerland (BMC Syst. Biol., 2013)

fastGapFill: efficient gap filling in metabolic networks. - Ines Thiele; Nikos Vlassis; Ronan M. T. Fleming (Bioinform., 2014)

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. - Hulda S. Haraldsdóttir; Ines Thiele; Ronan M. T. Fleming (J. Cheminformatics, 2014)

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models. - Hulda S. Haraldsdóttir; Ben Cousins; Ines Thiele; Ronan M. T. Fleming; Santosh S. Vempala (Bioinform., 2017)

DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia. - Laurent Heirendt; Ines Thiele; Ronan M. T. Fleming (Bioinform., 2017)

ReconMap: an interactive visualization of human metabolism. - Alberto Noronha; Anna Dröfn Daníelsdóttir; Piotr Gawron; Freyr Jóhannsson; Soffía Jónsdóttir; Sindri Jarlsson; Jón Pétur Gunnarsson; Sigurður Brynjólfsson; Reinhard Schneider 002; Ines Thiele; Ronan M. T. Fleming (Bioinform., 2017)

ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software. - Laurent Heirendt; Sylvain Arreckx; Christophe Trefois; Yohan Yarosz; Maharshi Vyas; Venkata P. Satagopam; Reinhard Schneider 002; Ines Thiele; Ronan M. T. Fleming (CoRR, 2017)

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. - German A. Preciat Gonzalez; Lemmer R. P. El Assal; Alberto Noronha; Ines Thiele; Hulda S. Haraldsdóttir; Ronan M. T. Fleming (J. Cheminformatics, 2017)

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines. - Maike K. Aurich; Ronan M. T. Fleming; Ines Thiele (PLoS Comput. Biol., 2017)

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities. - Eugen Bauer; Johannes Zimmermann; Federico Baldini; Ines Thiele; Christoph Kaleta (PLoS Comput. Biol., 2017)

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. - Federico Baldini; Almut Heinken; Laurent Heirendt; Stefanía Magnúsdóttir; Ronan M. T. Fleming; Ines Thiele (Bioinform., 2019)

Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. - Beatriz Peñalver Bernabé; Ines Thiele; Eugene Galdones; Anaar Siletz; Sriram Chandrasekaran; Teresa K. Woodruff; Linda J. Broadbelt; Lonnie D. Shea (BMC Bioinform., 2019)

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. - Alberto Noronha; Jennifer Modamio; Yohan Jarosz; Elisabeth Guerard; Nicolas Sompairac; German A. Preciat Gonzalez; Anna Dröfn Daníelsdóttir; Max Krecke; Diane Merten; Hulda S. Haraldsdóttir; Almut Heinken; Laurent Heirendt; et al. (Nucleic Acids Res., 2019)

Predicting gastrointestinal drug effects using contextualized metabolic models. - Marouen Ben Guebila; Ines Thiele (PLoS Comput. Biol., 2019)

DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations. - Almut Heinken; Stefanía Magnúsdóttir; Ronan M. T. Fleming; Ines Thiele (Bioinform., 2021)

Dynamic flux balance analysis of whole-body metabolism for type 1 diabetes. - Marouen Ben Guebila; Ines Thiele (Nat. Comput. Sci., 2021)

Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism. - Leo Zhu; William Pei; Ines Thiele; Radhakrishnan Mahadevan (PLoS Comput. Biol., 2021)

Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities. - Almut Heinken; Ines Thiele (Bioinform., 2022)

MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions. - Ines Thiele; German A. Preciat Gonzalez; Ronan M. T. Fleming (Bioinform., 2022)

Cardinality optimization in constraint-based modelling: application to human metabolism. - Ronan M. T. Fleming; Hulda S. Haraldsdóttir; Le Hoai Minh; Phan Tu Vuong; Thomas Hankemeier; Ines Thiele (Bioinform., 2023)