Ines Thiele

32 papers Journal 31
YearRankTypeTitle / Venue / Authors
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
MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions.
Bioinform.
Ines Thiele, German A. Preciat Gonzalez, Ronan M. T. Fleming
2022 J jnl
Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities.
Bioinform.
Almut Heinken, Ines Thiele
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
2021 J jnl
Dynamic flux balance analysis of whole-body metabolism for type 1 diabetes.
Nat. Comput. Sci.
Marouen Ben Guebila, Ines Thiele
2021 J jnl
Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism.
PLoS Comput. Biol.
Leo Zhu, William Pei, Ines Thiele, Radhakrishnan Mahadevan
2019 J jnl
Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development.
BMC Bioinform.
Beatriz Peñalver Bernabé, Ines Thiele, Eugene Galdones, Anaar Siletz, Sriram Chandrasekaran, Teresa K. Woodruff, Linda J. Broadbelt, Lonnie D. Shea
2019 J jnl
Predicting gastrointestinal drug effects using contextualized metabolic models.
PLoS Comput. Biol.
Marouen Ben Guebila, Ines Thiele
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
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
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities.
PLoS Comput. Biol.
Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta
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
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
Consensus and conflict cards for metabolic pathway databases.
BMC Syst. Biol.
Miranda D. Stobbe, Morris A. Swertz, Ines Thiele, Trebor Rengaw, Antoine H. C. van Kampen, Perry D. Moerland
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
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.
BMC Syst. Biol.
Ottar Rolfsson, Bernhard Ø. Palsson, Ines Thiele
2011 J jnl
rBioNet: A COBRA toolbox extension for
Bioinform.
Stefan Gretar Thorleifsson, Ines Thiele
2011 J jnl
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.
Bioinform.
Ronan M. T. Fleming, Ines Thiele
2010 J jnl
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.
BMC Syst. Biol.
Martin I. Sigurdsson, Neema Jamshidi, Eiríkur Steingrímsson, Ines Thiele, Bernhard Ø. Palsson
2010 J jnl
Computationally efficient flux variability analysis.
BMC Bioinform.
Steinn Gudmundsson, Ines Thiele
2009 J jnl
Genome-Scale Reconstruction of
PLoS Comput. Biol.
Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard O. Palsson
2009 J jnl
Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling.
PLoS Comput. Biol.
Fan Li, Ines Thiele, Neema Jamshidi, Bernhard O. Palsson
2009 — ch.
Metabolic Systems Biology.
Encyclopedia of Complexity and Systems Science
Nathan E. Lewis, Neema Jamshidi, Ines Thiele, Bernhard O. Palsson
2008 J jnl
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.
BMC Syst. Biol.
Juan Nogales, Bernhard Ø. Palsson, Ines Thiele
2007 J jnl
Estimation of the number of extreme pathways for metabolic networks.
BMC Bioinform.
Matthew Yeung, Ines Thiele, Bernhard O. Palsson