Ronan M. T. Fleming

28 papers Journal 27Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Constraint-based modeling of bioenergetic differences between synaptic and non-synaptic components of dopaminergic neurons in Parkinson's disease.
Frontiers Comput. Neurosci.
Xi Luo, Diana C. El Assal, Yanjun Liu, Samira Ranjbar, Ronan M. T. Fleming
2023 J jnl
Cardinality optimization in constraint-based modelling: application to human metabolism.
Bioinform.
Ronan M. T. Fleming, Hulda S. Haraldsdóttir, Le Hoai Minh, Phan Tu Vuong, Thomas Hankemeier, Ines Thiele
2022 J jnl
Finding zeros of Hölder metrically subregular mappings via globally convergent Levenberg-Marquardt methods.
Optim. Methods Softw.
Masoud Ahookhosh, Ronan M. T. Fleming, Phan Tu Vuong
2022 J jnl
MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions.
Bioinform.
Ines Thiele, German A. Preciat Gonzalez, Ronan M. T. Fleming
2021 J jnl
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations.
Bioinform.
Almut Heinken, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele
2019 J jnl
Community-driven roadmap for integrated disease maps.
Briefings Bioinform.
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
2019 J jnl
Local convergence of the Levenberg-Marquardt method under Hölder metric subregularity.
Adv. Comput. Math.
Masoud Ahookhosh, Francisco J. Aragón Artacho, Ronan M. T. Fleming, Phan Tu Vuong
2019 J jnl
Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer.
BMC Bioinform.
Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Yu. Zinovyev, Inna Kuperstein
2019 J jnl
The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities.
Bioinform.
Federico Baldini, Almut Heinken, Laurent Heirendt, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele
2019 J jnl
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease.
Nucleic Acids Res.
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 Santa Cruz, 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
2018 J jnl
Accelerating the DC algorithm for smooth functions.
Math. Program.
Francisco J. Aragón Artacho, Ronan M. T. Fleming, Phan Tu Vuong
2017 J jnl
A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines.
PLoS Comput. Biol.
Maike K. Aurich, Ronan M. T. Fleming, Ines Thiele
2017 J jnl
ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software.
CoRR
Laurent Heirendt, Sylvain Arreckx, Christophe Trefois, Yohan Yarosz, Maharshi Vyas, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele, Ronan M. T. Fleming
2017 J jnl
CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.
Bioinform.
Hulda S. Haraldsdóttir, Ben Cousins, Ines Thiele, Ronan M. T. Fleming, Santosh S. Vempala
2017 J jnl
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.
J. Cheminformatics
German A. Preciat Gonzalez, Lemmer R. P. El Assal, Alberto Noronha, Ines Thiele, Hulda S. Haraldsdóttir, Ronan M. T. Fleming
2017 J jnl
DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia.
Bioinform.
Laurent Heirendt, Ines Thiele, Ronan M. T. Fleming
2017 J jnl
ReconMap: an interactive visualization of human metabolism.
Bioinform.
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
2016 J jnl
Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks.
PLoS Comput. Biol.
Hulda S. Haraldsdóttir, Ronan M. T. Fleming
2016 — conf
Non-rigid estimation of cell motion in calcium time-lapse images.
Biomedical Applications in Molecular, Structural, and Functional Imaging
Siham Hachi, Edinson Lucumi Moreno, An-Sofie Desmet, Pieter Vanden Berghe, Ronan M. T. Fleming
2015 J jnl
Globally convergent algorithms for finding zeros of duplomonotone mappings.
Optim. Lett.
Francisco J. Aragón Artacho, Ronan M. T. Fleming
2014 J jnl
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2.
J. Cheminformatics
Hulda S. Haraldsdóttir, Ines Thiele, Ronan M. T. Fleming
2014 J jnl
fastGapFill: efficient gap filling in metabolic networks.
Bioinform.
Ines Thiele, Nikos Vlassis, Ronan M. T. Fleming
2013 J jnl
Consistent Estimation of Gibbs Energy Using Component Contributions.
PLoS Comput. Biol.
Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, Ronan M. T. Fleming
2013 J jnl
Robust flux balance analysis of multiscale biochemical reaction networks.
BMC Bioinform.
Yuekai Sun, Ronan M. T. Fleming, Ines Thiele, Michael A. Saunders
2011 J jnl
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.
BMC Syst. Biol.
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
2011 J jnl
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.
Bioinform.
Ronan M. T. Fleming, Ines Thiele
2009 J jnl
Genome-Scale Reconstruction of
PLoS Comput. Biol.
Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard O. Palsson
2007 J jnl
Thermodynamically constrained steady state solution space of the E. coli metabolic network.
BMC Syst. Biol.
Ronan M. T. Fleming, Aaron Golden, Heinz-Peter Nasheuer