Ines Thiele

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 17

Top Topics

Saccharomyces Cerevisiae

Interactive Visual

Sequence Similarity

Top Venues

PLoS Comput. Biol.

J. Cheminformatics

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)
Almut Heinken, Ines Thiele
Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities. Bioinform. 38 (8) (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)
Marouen Ben Guebila, Ines Thiele
Dynamic flux balance analysis of whole-body metabolism for type 1 diabetes. Nat. Comput. Sci. 1 (5) (2021)
Leo Zhu, William Pei, Ines Thiele, Radhakrishnan Mahadevan
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. 17 (8) (2021)
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)
Marouen Ben Guebila, Ines Thiele
Predicting gastrointestinal drug effects using contextualized metabolic models. PLoS Comput. Biol. 15 (6) (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)
Beatriz Peñalver Bernabé, Ines Thiele, Eugene Galdones, Anaar Siletz, Sriram Chandrasekaran, Teresa K. Woodruff, Linda J. Broadbelt, Lonnie D. Shea
Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. BMC Bioinform. 20 (1) (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)
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)
Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities. PLoS Comput. Biol. 13 (5) (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)
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)
Yuekai Sun, Ronan M. T. Fleming, Ines Thiele, Michael A. Saunders
Robust flux balance analysis of multiscale biochemical reaction networks. BMC Bioinform. 14 (2013)
Miranda D. Stobbe, Morris A. Swertz, Ines Thiele, Trebor Rengaw, Antoine H. C. van Kampen, Perry D. Moerland
Consensus and conflict cards for metabolic pathway databases. BMC Syst. Biol. 7 (2013)
Stefan Gretar Thorleifsson, Ines Thiele
works. Bioinform. 27 (14) (2011)
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)
Ottar Rolfsson, Bernhard Ø. Palsson, Ines Thiele
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst. Biol. 5 (2011)
Steinn Gudmundsson, Ines Thiele
Computationally efficient flux variability analysis. BMC Bioinform. 11 (2010)
Martin I. Sigurdsson, Neema Jamshidi, Eiríkur Steingrímsson, Ines Thiele, Bernhard Ø. Palsson
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC Syst. Biol. 4 (2010)
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)
Fan Li, Ines Thiele, Neema Jamshidi, Bernhard O. Palsson
Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling. PLoS Comput. Biol. 5 (2) (2009)
Juan Nogales, Bernhard Ø. Palsson, Ines Thiele
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst. Biol. 2 (2008)
Matthew Yeung, Ines Thiele, Bernhard O. Palsson
Estimation of the number of extreme pathways for metabolic networks. BMC Bioinform. 8 (2007)