Ines Thiele

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Bernhard PalssonUCSDVerified email at eng.ucsd.edu
Ronan M.T. FlemingAssoc. Prof., National University of Ireland, Galway, & Asst. Prof., Leiden UniversityVerified email at lacdr.leidenuniv.nl
Almut HeinkenUniversity of LorraineVerified email at univ-lorraine.fr
Stefania MagnusdottirPhD Student, University of LuxembourgVerified email at uni.lu
Adam FeistUCSD / DTUVerified email at ucsd.edu
Thomas HankemeierProfessor of Analytical Biosciences, Leiden UniversityVerified email at lacdr.leidenuniv.nl
Nathan E LewisAssociate Professor, University of California, San DiegoVerified email at ucsd.edu
Nathan D. PriceCSO, Thorne HealthTech; Professor, Institute for Systems BiologyVerified email at systemsbiology.org
Gabi KastenmüllerHelmholtz Zentrum München - German Research Center for Environmental HealthVerified email at helmholtz-muenchen.de
Oliver FiehnUC DavisVerified email at ucdavis.edu
Karen P. ScottSenior Research Fellow, Rowett Institute of Nutrition and Health, University of AberdeenVerified email at abdn.ac.uk
Markus HerrgardCTO, BioInnovation InstituteVerified email at novo.dk
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 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
Michael SaundersProfessor of Operations Research, Stanford UniversityVerified email at stanford.edu
Valerie de Crecy-LagardMicrobiology and Cell Science, University of FloridaVerified email at ufl.edu
David BroadhurstProfessor, Data Science & Biostatistics, School of Science, Edith Cowan UniversityVerified email at ecu.edu.au

Ines Thiele

National University of Ireland, Galway

Verified email at nuigalway.ie

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


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
What is flux balance analysis? JD Orth, I Thiele, BØ Palsson Nature biotechnology 28 (3), 245-248, 2010	3394	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	2074	2005
A protocol for generating a high-quality genome-scale metabolic reconstruction I Thiele, BØ Palsson Nature protocols 5 (1), 93-121, 2010	1663	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	1530	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), 1290-1307, 2011	1517	2011
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	1263	2018
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	1052	2013
Reconstruction of biochemical networks in microorganisms AM Feist, MJ Herrgård, I Thiele, JL Reed, BØ Palsson Nature Reviews Microbiology 7 (2), 129-143, 2009	1023	2009
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	601	2019
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	486	2017
Towards multidimensional genome annotation JL Reed, I Famili, I Thiele, BO Palsson Nature Reviews Genetics 7 (2), 130-141, 2006	439	2006
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	432	2015
Metabolomics enables precision medicine:“a white paper, community perspective” RD Beger, W Dunn, MA Schmidt, SS Gross, JA Kirwan, M Cascante, ... Metabolomics 12 (9), 1-15, 2016	415*	2016
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	379	2018
Computationally efficient flux variability analysis S Gudmundsson, I Thiele BMC bioinformatics 11 (1), 1-3, 2010	326	2010
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	319	2012
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	286	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	278	2005
Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its … I Thiele, N Jamshidi, RMT Fleming, BØ Palsson PLoS computational biology 5 (3), e1000312, 2009	230	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	214	2013

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