Thermodynamically constrained steady state solution space of the E. coli metabolic network. - Ronan M. T. Fleming; Aaron Golden; Heinz-Peter Nasheuer (BMC Syst. Biol., 2007)

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)

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

Consistent Estimation of Gibbs Energy Using Component Contributions. - Elad Noor; Hulda S. Haraldsdóttir; Ron Milo; Ronan M. T. Fleming (PLoS Comput. 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)

Globally convergent algorithms for finding zeros of duplomonotone mappings. - Francisco J. Aragón Artacho; Ronan M. T. Fleming (Optim. Lett., 2015)

Non-rigid estimation of cell motion in calcium time-lapse images. - Siham Hachi; Edinson Lucumi Moreno; An-Sofie Desmet; Pieter Vanden Berghe; Ronan M. T. Fleming (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2016)

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks. - Hulda S. Haraldsdóttir; Ronan M. T. Fleming (PLoS Comput. Biol., 2016)

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)

Accelerating the DC algorithm for smooth functions. - Francisco J. Aragón Artacho; Ronan M. T. Fleming; Phan Tu Vuong (Math. Program., 2018)

Local convergence of the Levenberg-Marquardt method under Hölder metric subregularity. - Masoud Ahookhosh; Francisco J. Aragón Artacho; Ronan M. T. Fleming; Phan Tu Vuong (Adv. Comput. Math., 2019)

Community-driven roadmap for integrated disease maps. - Marek Ostaszewski; Stephan Gebel; Inna Kuperstein; Alexander Mazein; Andrei Yu. Zinovyev; Ugur Dogrusoz; Jan Hasenauer; Ronan M. T. Fleming; Nicolas Le Novère; Piotr Gawron; Thomas S. Ligon; Anna Niarakis; et al. (Briefings Bioinform., 2019)

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)

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer. - Nicolas Sompairac; Jennifer Modamio; Emmanuel Barillot; Ronan M. T. Fleming; Andrei Yu. Zinovyev; Inna Kuperstein (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)

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)

Finding zeros of Hölder metrically subregular mappings via globally convergent Levenberg-Marquardt methods. - Masoud Ahookhosh; Ronan M. T. Fleming; Phan Tu Vuong (Optim. Methods Softw., 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)

Constraint-based modeling of bioenergetic differences between synaptic and non-synaptic components of dopaminergic neurons in Parkinson's disease. - Xi Luo; Diana C. El Assal; Yanjun Liu; Samira Ranjbar; Ronan M. T. Fleming (Frontiers Comput. Neurosci., 2025)