Ronan M. T. Fleming

According to our database, Ronan M. T. Fleming authored at least 27 papers between 2007 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

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., September, 2023

2022

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

Ines Thiele, German A. Preciat Gonzalez, Ronan M. T. Fleming

Bioinform., October, 2022

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

2021

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

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, 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

Nucleic Acids Res., 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 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

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, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider

Briefings Bioinform., 2019

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

2018

Accelerating the DC algorithm for smooth functions.

Francisco J. Aragón Artacho, Ronan M. T. Fleming, Phan Tu Vuong

Math. Program., 2018

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

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

ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software.

Laurent Heirendt, Sylvain Arreckx, Christophe Trefois, Yohan Yarosz, Maharshi Vyas, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele, Ronan M. T. Fleming

CoRR, 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, Ines Thiele, Ronan M. T. Fleming

Bioinform., 2017

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

Laurent Heirendt, Ines Thiele, Ronan M. T. Fleming

Bioinform., 2017

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

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

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

Proceedings of the Medical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging, San Diego, California, United States, 27 February, 2016

2015

Globally convergent algorithms for finding zeros of duplomonotone mappings.

Francisco J. Aragón Artacho, Ronan M. T. Fleming

Optim. Lett., 2015

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

fastGapFill: efficient gap filling in metabolic networks.

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

Bioinform., 2014

2013

Consistent Estimation of Gibbs Energy Using Component Contributions.

Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, Ronan M. T. Fleming

PLoS Comput. Biol., 2013

Robust flux balance analysis of multiscale biochemical reaction networks.

Yuekai Sun, Ronan M. T. Fleming, Ines Thiele, Michael A. Saunders

BMC Bioinform., 2013

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, 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

BMC Syst. Biol., 2011

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

Ronan M. T. Fleming, Ines Thiele

Bioinform., 2011

2009

Genome-Scale Reconstruction of <i>Escherichia coli</i>'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

2007

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