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Ines Thiele
Researcher at National University of Ireland, Galway
Publications - 159
Citations - 23484
Ines Thiele is an academic researcher from National University of Ireland, Galway. The author has contributed to research in topics: Microbiome & Metabolic network. The author has an hindex of 55, co-authored 146 publications receiving 19437 citations. Previous affiliations of Ines Thiele include University of California, San Diego & National University of Ireland.
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Journal ArticleDOI
What is flux balance analysis
TL;DR: This primer covers the theoretical basis of the approach, several practical examples and a software toolbox for performing the calculations.
Journal ArticleDOI
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Ross Overbeek,Tadhg P. Begley,Ralph Butler,Jomuna V. Choudhuri,Han-Yu Chuang,Matthew P. Cohoon,Valérie de Crécy-Lagard,Naryttza N. Diaz,Terry Disz,Robert D. Edwards,Robert D. Edwards,Michael Fonstein,Ed D. Frank,Svetlana Gerdes,Elizabeth M. Glass,Alexander Goesmann,Andrew C. Hanson,Dirk Iwata-Reuyl,Roy A. Jensen,Neema Jamshidi,Lutz Krause,Michael Kubal,Niels Bent Larsen,Burkhard Linke,Alice C. McHardy,Folker Meyer,Heiko Neuweger,Gary J. Olsen,Robert Olson,Andrei L. Osterman,Vasiliy A. Portnoy,Gordon D. Pusch,Dmitry A. Rodionov,Christian Rückert,Jason Steiner,Rick Stevens,Rick Stevens,Ines Thiele,Olga Vassieva,Yuzhen Ye,Olga Zagnitko,Veronika Vonstein +41 more
TL;DR: The subsystem approach is described, the first release of the growing library of populated subsystems is offered, and the SEED is the first annotation environment that supports this model of annotation.
Journal ArticleDOI
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Jan Schellenberger,Richard Que,Ronan M. T. Fleming,Ines Thiele,Jeffrey D. Orth,Adam M. Feist,Daniel C. Zielinski,Aarash Bordbar,Nathan E. Lewis,Sorena Rahmanian,Joseph Kang,Daniel R. Hyduke,Bernhard O. Palsson +12 more
TL;DR: The constraint-based reconstruction and analysis toolbox as discussed by the authors is a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraintbased approach and allows predictive computations of both steady-state and dynamic optimal growth behavior, the effects of gene deletions, comprehensive robustness analyses, sampling the range of possible cellular metabolic states and the determination of network modules.
Journal ArticleDOI
A protocol for generating a high-quality genome-scale metabolic reconstruction.
TL;DR: This protocol provides a helpful manual for all stages of the reconstruction process and presents a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction.
Journal ArticleDOI
Global reconstruction of the human metabolic network based on genomic and bibliomic data
Natalie C. Duarte,Scott A Becker,Neema Jamshidi,Ines Thiele,Monica L. Mo,Thuy D. Vo,Rohith Srivas,Bernhard O. Palsson +7 more
TL;DR: The reconstruction process is described and it is demonstrated how the resulting genome-scale (or global) network can be used for the discovery of missing information, for the formulation of an in silico model, and as a structured context for analyzing high-throughput biological data sets.