Ronan M. T. Fleming

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 18

Top Topics

Metabolic Networks

Top Venues

J. Cheminformatics

PLoS Comput. Biol.

Publications

Ronan M. T. Fleming, Hulda S. Haraldsdóttir, Le Hoai Minh, Phan Tu Vuong, Thomas Hankemeier, Ines Thiele
Cardinality optimization in constraint-based modelling: application to human metabolism. Bioinform. 39 (9) (2023)
Masoud Ahookhosh, Ronan M. T. Fleming, Phan Tu Vuong
Finding zeros of Hölder metrically subregular mappings via globally convergent Levenberg-Marquardt methods. Optim. Methods Softw. 37 (1) (2022)
Ines Thiele, German A. Preciat Gonzalez, Ronan M. T. Fleming
MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions. Bioinform. 38 (20) (2022)
Almut Heinken, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations. Bioinform. 37 (21) (2021)
Masoud Ahookhosh, Francisco J. Aragón Artacho, Ronan M. T. Fleming, Phan Tu Vuong
Local convergence of the Levenberg-Marquardt method under Hölder metric subregularity. Adv. Comput. Math. 45 (5) (2019)
Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Yu. Zinovyev, Inna Kuperstein
Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer. BMC Bioinform. (4) (2019)
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, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider
Community-driven roadmap for integrated disease maps. Briefings Bioinform. 20 (2) (2019)
Federico Baldini, Almut Heinken, Laurent Heirendt, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele
The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. Bioinform. 35 (13) (2019)
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, Stefanía Magnúsdóttir, Dmitry A. Ravcheev, Swagatika Sahoo, Piotr Gawron, Lucia Friscioni, Beatriz Garcia, Mabel Prendergast, Alberto Puente, Mariana Rodrigues, Akansha Roy, Mouss Rouquaya, Luca Wiltgen, Alise Zagare, Elisabeth John, Maren Krueger, Inna Kuperstein, Andrei Yu. Zinovyev, Reinhard Schneider, Ronan M. T. Fleming, Ines Thiele
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 47 (Database-Issue) (2019)
Francisco J. Aragón Artacho, Ronan M. T. Fleming, Phan Tu Vuong
Accelerating the DC algorithm for smooth functions. Math. Program. 169 (1) (2018)
Hulda S. Haraldsdóttir, Ben Cousins, Ines Thiele, Ronan M. T. Fleming, Santosh S. Vempala
CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models. Bioinform. 33 (11) (2017)
Laurent Heirendt, Ines Thiele, Ronan M. T. Fleming
DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia. Bioinform. 33 (9) (2017)
Laurent Heirendt, Sylvain Arreckx, Christophe Trefois, Yohan Yarosz, Maharshi Vyas, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele, Ronan M. T. Fleming
ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software. CoRR (2017)
Maike K. Aurich, Ronan M. T. Fleming, Ines Thiele
A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines. PLoS Comput. Biol. 13 (8) (2017)
German A. Preciat Gonzalez, Lemmer R. P. El Assal, Alberto Noronha, Ines Thiele, Hulda S. Haraldsdóttir, Ronan M. T. Fleming
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. J. Cheminformatics 9 (1) (2017)
Alberto Noronha, Anna Dröfn Daníelsdóttir, Piotr Gawron, Freyr Jóhannsson, Soffía Jónsdóttir, Sindri Jarlsson, Jón Pétur Gunnarsson, Sigurður Brynjólfsson, Reinhard Schneider, Ines Thiele, Ronan M. T. Fleming
ReconMap: an interactive visualization of human metabolism. Bioinform. 33 (4) (2017)
Hulda S. Haraldsdóttir, Ronan M. T. Fleming
Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks. PLoS Comput. Biol. 12 (11) (2016)
Siham Hachi, Edinson Lucumi Moreno, An-Sofie Desmet, Pieter Vanden Berghe, Ronan M. T. Fleming
Non-rigid estimation of cell motion in calcium time-lapse images. Medical Imaging: Biomedical Applications in Molecular, Structural, and Functional Imaging (2016)
Francisco J. Aragón Artacho, Ronan M. T. Fleming
Globally convergent algorithms for finding zeros of duplomonotone mappings. Optim. Lett. 9 (3) (2015)
Ines Thiele, Nikos Vlassis, Ronan M. T. Fleming
fastGapFill: efficient gap filling in metabolic networks. Bioinform. 30 (17) (2014)
Hulda S. Haraldsdóttir, Ines Thiele, Ronan M. T. Fleming
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. J. Cheminformatics 6 (1) (2014)
Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, Ronan M. T. Fleming
Consistent Estimation of Gibbs Energy Using Component Contributions. PLoS Comput. Biol. 9 (7) (2013)
Yuekai Sun, Ronan M. T. Fleming, Ines Thiele, Michael A. Saunders
Robust flux balance analysis of multiscale biochemical reaction networks. BMC Bioinform. 14 (2013)
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, Kathleen Marchal, Monica L. Mo, Emre Özdemir, Anu Raghunathan, Jennifer L. Reed, Sook-Il Shin, Sara Sigurbjörnsdóttir, Jonas Steinmann, Suresh Sudarsan, Neil Swainston, Inge M. Thijs, Karsten Zengler, Bernhard O. Palsson, Joshua N. Adkins, Dirk Bumann
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst. Biol. 5 (2011)
Ronan M. T. Fleming, Ines Thiele
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinform. 27 (1) (2011)
Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard O. Palsson
's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization. PLoS Comput. Biol. 5 (3) (2009)
Ronan M. T. Fleming, Aaron Golden, Heinz-Peter Nasheuer
Thermodynamically constrained steady state solution space of the E. coli metabolic network. BMC Syst. Biol. 1 (S-1) (2007)