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ORCIDRonan M. T. Fleming
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2020 – today
- 2023
[j25]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)- 2022
- [j24]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): 4831-4832 (2022) - [j23]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): 113-149 (2022) - 2021
- [j22]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): 3974-3975 (2021)
2010 – 2019
- 2019
- [j21]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): 2771-2806 (2019) - [j20]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): 659-670 (2019) - [j19]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): 2332-2334 (2019) - [j18]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. 20-S(4): 140:1-140:14 (2019) - [j17]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:
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 47(Database-Issue): D614-D624 (2019) - 2018
- [j16]Francisco J. Aragón Artacho, Ronan M. T. Fleming, Phan Tu Vuong:
Accelerating the DC algorithm for smooth functions. Math. Program. 169(1): 95-118 (2018) - 2017
- [j15]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): 605-607 (2017) - [j14]Laurent Heirendt, Ines Thiele, Ronan M. T. Fleming:
DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia. Bioinform. 33(9): 1421-1423 (2017) - [j13]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): 1741-1743 (2017) - [j12]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): 39:1-39:15 (2017) - [j11]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) - [i1]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 abs/1712.05236 (2017) - 2016
- [j10]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) - [c1]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. Biomedical Applications in Molecular, Structural, and Functional Imaging 2016: 97880A - 2015
- [j9]Francisco J. Aragón Artacho, Ronan M. T. Fleming:
Globally convergent algorithms for finding zeros of duplomonotone mappings. Optim. Lett. 9(3): 569-584 (2015) - 2014
- [j8]Ines Thiele, Nikos Vlassis, Ronan M. T. Fleming:
fastGapFill: efficient gap filling in metabolic networks. Bioinform. 30(17): 2529-2531 (2014) - [j7]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): 2 (2014) - 2013
- [j6]Yuekai Sun, Ronan M. T. Fleming, Ines Thiele, Michael A. Saunders:
Robust flux balance analysis of multiscale biochemical reaction networks. BMC Bioinform. 14: 240 (2013) - [j5]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) - 2011
- [j4]Ronan M. T. Fleming, Ines Thiele:
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinform. 27(1): 142-143 (2011) - [j3]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: 8 (2011)
2000 – 2009
- 2009
- [j2]Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard O. Palsson:
Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization. PLoS Comput. Biol. 5(3) (2009) - 2007
- [j1]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): P15 (2007)
Coauthor Index
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