Ines Thiele

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Ronan M.T. FlemingAssoc. Prof., School of Medicine, University of Galway.Verified email at universityofgalway.ie
Almut HeinkenUniversity of LorraineVerified email at univ-lorraine.fr
Stefania MagnusdottirPhD Student, University of LuxembourgVerified email at uni.lu
Thomas HankemeierProfessor of Analytical Biosciences, Leiden UniversityVerified email at lacdr.leidenuniv.nl
Adam FeistUC San Diego (UCSD) / Technical University of Denmark (DTU)Verified email at ucsd.edu
Nathan E LewisGRA Eminent Scholar and Professor, University of GeorgiaVerified email at uga.edu
Gabi KastenmüllerHelmholtz Zentrum München - German Research Center for Environmental HealthVerified email at helmholtz-muenchen.de
Nathan D. PriceProfessor, Buck Institute for Research on AgingVerified email at buckinstitute.org
Karen P. ScottSenior Research Fellow, Rowett Institute of Nutrition and Health, University of AberdeenVerified email at abdn.ac.uk
Oliver FiehnUC DavisVerified email at ucdavis.edu
David BroadhurstProfessor, Biosystems Data Science, School of Science, Edith Cowan UniversityVerified email at ecu.edu.au
Marta CascanteUniversitat de BarcelonaVerified email at ub.edu
Warwick DunnDepartment of Biochemistry and Systems Biology, ISMIB, University of LiverpoolVerified email at liverpool.ac.uk
David S. WishartProfessor, Depts. of Computing Science and Biological Sciences - University of AlbertaVerified email at ualberta.ca
Matej OrešičProfessor of Medicine (Systems Medicine), Örebro University & University of TurkuVerified email at oru.se
Lorraine BrennanUCDVerified email at ucd.ie
Markus HerrgardCTO, BioInnovation InstituteVerified email at bii.dk
Michael SaundersProfessor of Operations Research, Stanford UniversityVerified email at stanford.edu
Valérie de Crécy-LagardDistinguished Professor, Microbiology and Cell Science Dpt, University of FloridaVerified email at ufl.edu
Heinz P. NasheuerProfessor, Dr. rer. nat., University of Galway, School of Biological and Chemical SciencesVerified email at nuigalway.ie

Ines Thiele

University of Galway

Verified email at universityofgalway.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	4455	2010
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, 1-24, 2018	2759	2018
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	2350	2005
A protocol for generating a high-quality genome-scale metabolic reconstruction I Thiele, BØ Palsson Nature protocols 5 (1), 93-121, 2010	2078	2010
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), 1290-1307, 2011	1696	2011
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	1692	2007
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	1234	2013
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	1208	2019
Reconstruction of biochemical networks in microorganisms AM Feist, MJ Herrgård, I Thiele, JL Reed, BØ Palsson Nature Reviews Microbiology 7 (2), 129-143, 2009	1123	2009
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	816	2015
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), 81-89, 2017	799	2017
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), 272-281, 2018	727	2018
Metabolomics enables precision medicine:“a white paper, community perspective” RD Beger, W Dunn, MA Schmidt, SS Gross, JA Kirwan, M Cascante, ... Metabolomics 12, 1-15, 2016	619*	2016
Computationally efficient flux variability analysis S Gudmundsson, I Thiele BMC bioinformatics 11, 1-3, 2010	455	2010
Towards multidimensional genome annotation JL Reed, I Famili, I Thiele, BO Palsson Nature Reviews Genetics 7 (2), 130-141, 2006	453	2006
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	365	2012
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease A Noronha, J Modamio, Y Jarosz, E Guerard, N Sompairac, G Preciat, ... Nucleic acids research 47 (D1), D614-D624, 2019	360	2019
Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease A Heinken, DA Ravcheev, F Baldini, L Heirendt, RMT Fleming, I Thiele Microbiome 7, 1-18, 2019	326*	2019
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	318	2008
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	293	2005

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