Ines Thiele

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Citations	18562	10602
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Co-authors

Bernhard PalssonUCSDVerified email at eng.ucsd.edu
Ronan M.T. FlemingAssistant Professor, Systems Biochemistry Group, Division of Systems Biomedicine and PharmacologyVerified email at lacdr.leidenuniv.nl
Almut HeinkenNational University of Ireland, GalwayVerified email at nuigalway.ie
Stefania MagnusdottirPhD Student, University of LuxembourgVerified email at uni.lu
Adam FeistUCSD / DTUVerified email at ucsd.edu
Nathan E LewisAssociate Professor, University of California, San DiegoVerified email at ucsd.edu
Nathan D. PriceCo-CEO Onegevity; Professor, Institute for Systems BiologyVerified email at systemsbiology.org
Gabi KastenmüllerHelmholtz Zentrum München - German Research Center for Environmental HealthVerified email at helmholtz-muenchen.de
Markus HerrgardCTO, BioInnovation InstituteVerified email at novo.dk
Thomas HankemeierProfessor of Analytical Biosciences, Leiden UniversityVerified email at lacdr.leidenuniv.nl
Karen P. ScottSenior Research Fellow, Rowett Institute of Nutrition and Health, University of AberdeenVerified email at abdn.ac.uk
Michael SaundersProfessor of Operations Research, Stanford UniversityVerified email at stanford.edu
Heinz P. NasheuerProfessor, Dr. rer. nat., NUI Galway, Biochemistry - School of Natural SciencesVerified email at nuigalway.ie
David BroadhurstProfessor, Biostatistics & Clinical Data Science, School of Science, Edith Cowan UniversityVerified email at ecu.edu.au
Marta CascanteUniversitat de BarcelonaVerified email at ub.edu
Warwick DunnUniversity of Birmingham, UKVerified email at bham.ac.uk
David WishartProfessor, Depts. of Computing Science and Biological Sciences - University of AlbertaVerified email at ualberta.ca
Matej OrešičProfessor of Medical Sciences (Systems Medicine), Örebro University & Turku Bioscience CentreVerified email at oru.se
Lorraine BrennanUCDVerified email at ucd.ie
Oliver FiehnUC DavisVerified email at ucdavis.edu

Ines Thiele

National University of Ireland, Galway

Verified email at nuigalway.ie

constraint-based modeling multiscale modeling human metabolism gut microbiome gut-brain-axis


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What is flux balance analysis? JD Orth, I Thiele, BØ Palsson Nature biotechnology 28 (3), 245-248, 2010	2795	2010
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes R Overbeek, T Begley, RM Butler, JV Choudhuri, HY Chuang, M Cohoon, ... Nucleic acids research 33 (17), 5691-5702, 2005	1873	2005
A protocol for generating a high-quality genome-scale metabolic reconstruction I Thiele, BØ Palsson Nature protocols 5 (1), 93, 2010	1426	2010
Global reconstruction of the human metabolic network based on genomic and bibliomic data NC Duarte, SA Becker, N Jamshidi, I Thiele, ML Mo, TD Vo, R Srivas, ... Proceedings of the National Academy of Sciences 104 (6), 1777-1782, 2007	1416	2007
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0 J Schellenberger, R Que, RMT Fleming, I Thiele, JD Orth, AM Feist, ... Nature protocols 6 (9), 1290, 2011	1389	2011
Reconstruction of biochemical networks in microorganisms AM Feist, MJ Herrgård, I Thiele, JL Reed, BØ Palsson Nature Reviews Microbiology 7 (2), 129-143, 2009	968	2009
A community-driven global reconstruction of human metabolism I Thiele, N Swainston, RMT Fleming, A Hoppe, S Sahoo, MK Aurich, ... Nature biotechnology 31 (5), 419-425, 2013	957	2013
Gut microbiota functions: metabolism of nutrients and other food components I Rowland, G Gibson, A Heinken, K Scott, J Swann, I Thiele, K Tuohy European journal of nutrition 57 (1), 1-24, 2018	623	2018
Towards multidimensional genome annotation JL Reed, I Famili, I Thiele, BO Palsson Nature Reviews Genetics 7 (2), 130-141, 2006	424	2006
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota S Magnúsdóttir, A Heinken, L Kutt, DA Ravcheev, E Bauer, A Noronha, ... Nature biotechnology 35 (1), 81, 2017	324	2017
Metabolomics enables precision medicine:“a white paper, community perspective” RD Beger, W Dunn, MA Schmidt, SS Gross, JA Kirwan, M Cascante, ... Metabolomics 12 (9), 149, 2016	314*	2016
Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis J Nogales, S Gudmundsson, EM Knight, BO Palsson, I Thiele Proceedings of the National Academy of Sciences 109 (7), 2678-2683, 2012	283	2012
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0 L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ... Nature protocols 14 (3), 639-702, 2019	281	2019
Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes S Magnúsdóttir, D Ravcheev, V de Crécy-Lagard, I Thiele Frontiers in genetics 6, 148, 2015	280	2015
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single-and double-deletion mutants I Thiele, TD Vo, ND Price, BØ Palsson Journal of bacteriology 187 (16), 5818-5830, 2005	273	2005
Computationally efficient flux variability analysis S Gudmundsson, I Thiele BMC bioinformatics 11 (1), 489, 2010	262	2010
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory J Nogales, B Palsson, I Thiele BMC systems biology 2 (1), 79, 2008	254	2008
Recon3D enables a three-dimensional view of gene variation in human metabolism E Brunk, S Sahoo, DC Zielinski, A Altunkaya, A Dräger, N Mih, F Gatto, ... Nature biotechnology 36 (3), 272, 2018	224	2018
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization I Thiele, N Jamshidi, RMT Fleming, BØ Palsson PLoS Comput Biol 5 (3), e1000312, 2009	211	2009
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut A Heinken, S Sahoo, RMT Fleming, I Thiele Gut microbes 4 (1), 28-40, 2013	190	2013

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