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Ines Thiele

Ines Thiele

Associate professor in Systems Biomedicine

Academic Area(s) Biochemistry, biophysics & molecular biology / Biotechnology / Microbiology / Multidisciplinary, general & others
Research Topics Constraint-based Modeling, Multiscale Modeling, Human Metabolism, Gut Microbiome, Rare Metabolic Diseases
Faculty or Centre Luxembourg Centre for Systems Biomedicine
Postal Address Campus Belval, Université du Luxembourg
7, Avenue des Hauts Fourneaux
L-4362 Esch-sur-Alzette
Campus Office BioTech I, 2.10
Telephone (+352) 46 66 44 6647
Speaks English, French, German
Research Stays in Iceland, USA

Principal Investigator in the Molecular Systems Physiology group (Thiele Lab) & EMBO Young Investigator.

FNR ATTRACT Fellows in Biomedicine (Video)

Last updated on: Wednesday, 05 August 2015

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In press

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Rowland, I; Gibson, G; Heinken, Almut Katrin; Scott, K; Swann, J; Thiele, Ines; Tuohy, K

in European Journal of Nutrition (in press)

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See detailBacArena: Individual-Based Metabolic Modeling of Heterogeneous Microbes in Complex Communities
Bauer, Eugen; Zimmermann, Johannes; Baldini, Federico; Thiele, Ines; Kaleta, Christoph

in PLoS Computational Biology (2017)

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See detailCHRR: Coordi- nate hit-and-run with rounding for uniform sampling of constraint-based models
Haraldsdottir, Hulda; Cousin, B; Thiele, Ines; Fleming, Ronan MT; Vempala, S

in Bioinformatics (2017)

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See detailDistributedFBA.jl: High-level, high-performance flux balance analysis in Julia.
Heirendt, Laurent; Thiele, Ines; Fleming, Ronan MT

in Bioinformatics (2017)

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See detailReliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
Ma, Ding; Yang, Laurence; Fleming, Ronan MT; Thiele, Ines; Palsson, Bernhard; Saunders, Michael

in Scientific Reports (2017)

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See detailLeigh Map: A Novel Computational Diagnostic Resource for Mitochondrial Disease
Rhaman, Joyeeta; Noronha, Alberto; Thiele, Ines; Rahman, Shamima

in Annals of Neurology (2017)

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See detailMetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models
Aurich, Maike Kathrin; Fleming, Ronan MT; Thiele, Ines

in Frontiers in Physiology (2016)

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See detailMetabolomics enables precision medicine: A White Paper, Community Perspective
Beger, DR; Dunn, W; Schmidt, MA; Gross, SS; Kirwan, JA; Cascante, M; Brennan, L; Wishart, DS; Oresic, M; Hankemeier, T; Broadhurst, DI; Lane, AN; Suhre, K; Kastenmueller, G; Sunner, SJ; Thiele, Ines; Fiehn, O; Kaddurah-Daouk, R

in Metabolomics : Official journal of the Metabolomic Society (2016)

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See detailModel-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients
Ben Guebila, Marouen; Thiele, Ines

in NPJ Systems Biology and Applications (2016), 2

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See detailThe Human Gutome: Journey of Microbes and Health
Dimitrov, Dimiter; Thiele, Ines; Ferguson, Lynnette Robin

in Frontiers in Genetics (2016)

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See detailConditions for duality between fluxes and concentrations in biochemical networks
Fleming, Ronan MT; Vlassis, Nikos; Thiele, Ines; Saunders, Michael

in Journal of Theoretical Biology (2016), 409(21), 1-10

See detailSystems biology of bacteria-host interactions
Heinken, Almut Katrin; Ravcheev, Dmitry; Thiele, Ines

in Nibali, Luigi; Henderson, Brian (Eds.) The Human Microbiota and Chronic Disease: Dysbiosis as a Cause of Human Pathology (2016)

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See detailGeneration of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Magnusdottir, Stefania; Heinken, Almut Katrin; Kutt, Laura; Ravcheev, Dmitry; Bauer, Eugen; Noronha, Alberto; Greenhalgh, Kacy; Jäger, Christian; Baginska, Joanna; Wilmes, Paul; Fleming, Ronan MT; Thiele, Ines

in Nature Biotechnology (2016)

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See detailReconMap: An interactive visualisation of human metabolism
Noronha, Alberto; Danielsdóttir, Anna Dröfn; Jóhannsson, Freyr; Jónsdóttir, Soffia; Jarlsson, Sindri; Gunnarsson, Jón Pétur; Brynjólfsson, Sigurður; Gawron, Piotr; Schneider, Reinhard; Thiele, Ines; Fleming, Ronan MT

in Bioinformatics (2016)

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See detailGenomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis
Ravcheev, Dmitry; Thiele, Ines

in Frontiers in Microbiology (2016), 7(128),

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See detailPrediction of intracellular metabolic states from extracellular metabolomic data
Aurich, Maike Kathrin; Paglia, Guiseppe; Rolfsson, Ottar; Hrafnsdottir, Sigrun; Magnusdottir, Manuela; Stefaniak, Madgalena K.; Palsson, Bernhard O.; Fleming, Ronan MT; Thiele, Ines

in Metabolomics : Official journal of the Metabolomic Society (2015), 11(3), 603-619

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See detailComputational modeling of human metabolism and its application to systems biomedicine
Aurich, Maike Kathrin; Thiele, Ines

in Wolkenhauer, Olaf; Schmitz, Ulf (Eds.) Systems Medicine (2015)

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See detailPhenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires
Bauer, Eugen; Laczny, Cédric; Magnusdottir, Stefania; Wilmes, Paul; Thiele, Ines

in Microbiome (2015), 3(55), 1-13

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See detailDo Genome-scale Models Need Exact Solvers or Clearer Standards?
Ebrahim, Ali; Almaas, Eivind; Bauer, Eugen; Bordbar, Aarash; Burgard, Anthony P.; Chang, Roger L.; Dräger, Andreas; Famili, Iman; Feist, Adam M.; Fleming, Ronan MT; Fong, Stephen S.; Hatzimanikatis, Vassily; Herrgård, Markus J.; Holder, Allen; Hucka, Michael; Hyduke, Daniel; Jamshidi, Neema; Lee, Sang Yup; Le Novère, Nicolas; Lerman, Joshua A.; Lewis, Nathan E.; Ma, Ding; Mahadevan, Radhakrishnan; Maranas, Costas; Nagarajan, Harish; Navid, Ali; Nielsen, Jens; Nielsen, Lars K.; Nogales, Juan; Noronha, Alberto; Pal, Csaba; Palsson, Bernhard O.; Papin, Jason A.; Patil, Kiran R.; Price, Nathan D.; Reed, Jennifer L.; Saunders, Michael; Senger, Ryan S.; Sonnenschein, Nikolaus; Sun, Yuekai; Thiele, Ines

in Molecular Systems Biology (2015), 11(10), 1

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See detailAnoxic conditions promote species-specific mutualism between gut microbes in silico
Heinken, Almut Katrin; Thiele, Ines

in Applied and Environmental Microbiology (2015), 81(12), 4049-4061

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See detailSystems biology of host-microbe metabolomics
Heinken, Almut Katrin; Thiele, Ines

in Wiley Interdisciplinary Reviews. Systems Biology and Medicine (2015)

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See detailSystematic prediction of health-relevant human-microbial co-metabolism through a computational framework
Heinken, Almut Katrin; Thiele, Ines

in Gut Microbes (2015), 6(2), 120-130

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See detailSystematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes
Magnusdottir, Stefania; Ravcheev, Dmitry; de Crecy-Lagard, Valerie; Thiele, Ines

in Frontiers in Genetics (2015), 6

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See detailGenome-Scale Methods Converge on Key Mitochondrial Genes for the Survival of Human Cardiomyocytes in Hypoxia
Edwards, Lindsay; Sigurdsson, Martin I; Robbins, Peter A; Weale, Michael E; Cavalleri, Gianpiero L; Montgomery, Hugh; Thiele, Ines

in Circulation: Cardiovascular Genetics (2014)

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See detailA functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe
Heinken, Almut Katrin; Khan, M Tanweer; Paglia, Giuseppe; Rodionov, Dmitry A; Harmsen, Hermie JM; Thiele, Ines

in Journal of Bacteriology (2014), 196(18), 3289-3302

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See detailMembrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease
Sahoo, Swagatika; Aurich, Maike Kathrin; Jonsson, Jon; Thiele, Ines

in Frontiers in Physiology (2014), 5

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See detailModeling the effects of commonly used drugs on human metabolism
Sahoo, Swagatika; Haraldsdottir, Hulda; Fleming, Ronan MT; Thiele, Ines

in FEBS Journal (2014)

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See detailFASTGAPFILL: Efficient gap filling in metabolic networks
Thiele, Ines; Vlassis, Nikos; Fleming, Ronan MT

in Bioinformatics (2014), 30(17), 2529-2531

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See detailApplying systems biology methods to the study of human physiology in extreme environments
Edwards, Lindsay; Thiele, Ines

in Extreme Physiology & Medicine (2013), 2(8),

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See detailSystems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut.
Heinken, Almut Katrin; Sahoo, Swagatika; Fleming, Ronan MT; Thiele, Ines

in Gut microbes (2013), 4(1), 28-40

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See detailToward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks.
Nogales, Juan; Gudmundsson, Steinn; Thiele, Ines

in Bioengineered (2013), 4(3), 158-163

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See detailInferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.
Rolfsson, Ottar; Paglia, Giuseppe; Magnusdottir, Manuela; Palsson, Bernhard O.; Thiele, Ines

in Biochemical Journal (2013), 449(2), 427-435

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See detailPredicting the impact of diet and enzymopathies on human small intestinal epithelial cells
Sahoo, Swagatika; Thiele, Ines

in Human Molecular Genetics (2013), 22(13), 2705-22

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See detailConsensus and conflict cards for metabolic pathway databases.
Stobbe, Miranda D.; Swertz, Morris A.; Thiele, Ines; Rengaw, Trebor; van Kampen, Antoine Hc; Moerland, Perry D.

in BMC Systems Biology (2013), 7

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See detailRobust flux balance analysis of multi- scale biochemical reaction networks
Sun, Y; Fleming, Ronan MT; Thiele, Ines; Saunders, MA

in BMC Bioinformatics (2013), 1(14), 240

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See detailA systems biology approach to studying the role of microbes in human health.
Thiele, Ines; Heinken, Almut Katrin; Fleming, Ronan MT

in Current Opinion in Biotechnology (2013), 24(1), 4-12

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See detailA community-driven global reconstruction of human metabolism.
Thiele, Ines; Swainston, N.; Fleming, Ronan MT; Hoppe, A.; Sahoo, Swagatika; Aurich, Maike Kathrin; Haraldsdottir, Hulda; Mo, M. L.; Rolfsson, O.; Stobbe, M. D.; Thorleifsson, S. G.; Agren, R.; Bölling, C.; Bordel, S.; Chavali, A. K.; Dobson, P.; Dunn, W. B.; Endler, L.; Hala, D.; Hucka, M.; Hull, D.; Jameson, D.; Jamshidi, N.; Jonsson, J. J.; Juty, N.; Keating, S.; Nookaew, I.; Le Novère, N.; Malys, N.; Mazein, A.; Papin, J. A.; Price, N. D.; Selkov, E. Sr; Sigurdsson, M. I.; Simeonidis, Evangelos; Sonnenschein, N.; Smallbone, K.; Sorokin, A.; van Beek, J. H.; Weichart, D.; Goryanin, I.; Nielsen, J.; Westerhoff, H. V.; Kell, D. B.; Mendes, P.; Palsson, B. O.

in Nature Biotechnology (2013), 31

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See detailContextualization procedure and modeling of monocyte specific TLR signaling.
Aurich, Maike Kathrin; Thiele, Ines

in PLoS ONE (2012), 7(12), 49978

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See detailQuantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction
Haraldsdottir, Hulda; Thiele, Ines; Fleming, Ronan MT

in Biophysical Journal (2012), 102(8), 17031711

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See detailAn in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production
Nogales, Juan E; Gudmunsson, Steinn; Thiele, Ines

in International Journal of Hydrogen Energy (2012), 37(17), 1220512218

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See detailDetailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.
Nogales, Juan; Gudmundsson, Steinn; Knight, Eric M.; Palsson, Bernhard O.; Thiele, Ines

in Proceedings of the National Academy of Sciences of the United States of America (2012), 109(7), 2678-2683

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See detailMonitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).
Paglia, Giuseppe; Hrafnsdottir, Sigrun; Magnusdottir, Manuela; Fleming, Ronan MT; Thorlacius, Steinunn; Palsson, Bernhard O.; Thiele, Ines

in Analytical and Bioanalytical Chemistry (2012), 402(3), 1183-98

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See detailIntracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies.
Paglia, Giuseppe; Magnusdottir, Manuela; Thorlacius, Steinunn; Sigurjonsson, Olafur E.; Guethmundsson, Sveinn; Palsson, Bernhard O.; Thiele, Ines

in Journal of Chromatography. B : Analytical Technologies in the Biomedical & Life Sciences (2012), 898

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See detailA compendium of inborn errors of metabolism mapped onto the human metabolic network
Sahoo, Swagatika; Franzson; Jonsson, Jon J; Thiele, Ines

in Molecular Biosystems (2012), 8(10), 2545-2558

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See detailA systems biology approach to drug targets in Pseudomonas aeruginosa biofilm.
Sigurdsson, Gunnar; Fleming, Ronan MT; Heinken, Almut Katrin; Thiele, Ines

in PLoS ONE (2012), 7(4), 34337

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See detailMultiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.
Thiele, Ines; Fleming, Ronan MT; Que, Richard; Bordbar, Aarash; Diep, Dinh; Palsson, Bernhard O.

in PLoS ONE (2012), 7(9), 45635

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See detailvon Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.
Fleming, Ronan MT; Thiele, Ines

in Bioinformatics (Oxford, England) (2011), 27(1), 142-3

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See detailThe human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.
Rolfsson, Ottar; Palsson, Bernhard O.; Thiele, Ines

in BMC Systems Biology (2011), 5

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See detailQuantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
Schellenberger, Jan; Que, Richard; Fleming, Ronan MT; Thiele, Ines; Orth, Jeffrey D.; Feist, Adam M.; Zielinski, Daniel C.; Bordbar, Aarash; Lewis, Nathan E.; Rahmanian, Sorena; Kang, Joseph; Hyduke, Daniel R.; Palsson, Bernhard O.

in Nature Protocols (2011), 6(9), 1290-1307

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See detailA community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.
Thiele, Ines; Hyduke, Daniel R.; Steeb, Benjamin; Fankam, Guy; Allen, Douglas K.; Bazzani, Susanna; Charusanti, Pep; Chen, Feng-Chi; Fleming, Ronan MT; Hsiung, Chao A.; De Keersmaecker, Sigrid C. J.; Liao, Yu-Chieh; Marchal, Kathleen; Mo, Monica L.; Ozdemir, Emre; Raghunathan, Anu; Reed, Jennifer L.; Shin, Sook-Il; Sigurbjornsdottir, Sara; Steinmann, Jonas; Sudarsan, Suresh; Swainston, Neil; Thijs, Inge M.; Zengler, Karsten; Palsson, Bernhard O.; Adkins, Joshua N.; Bumann, Dirk

in BMC Systems Biology (2011), 5

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See detailrBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks.
Thorleifsson, Stefan Gretar; Thiele, Ines

in Bioinformatics (Oxford, England) (2011), 27(14), 2009-10

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See detailIntegrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.
Fleming, Ronan MT; Thiele, Ines; Provan, G.; Nasheuer, H. P.

in Journal of Theoretical Biology (2010), 264(3), 683-92

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See detailComputationally efficient flux variability analysis
Gudmundsson, Steinn; Thiele, Ines

in BMC Bioinformatics (2010), 11

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See detailWhat is flux balance analysis?
Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard O.

in Nature Biotechnology (2010), 28(3), 245-8

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See detailA detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
Sigurdsson, Martin I.; Jamshidi, Neema; Steingrimsson, Eirikur; Thiele, Ines; Palsson, Bernhard O.

in BMC Systems Biology (2010), 4

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See detailFunctional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.
Thiele, Ines; Fleming, Ronan MT; Bordbar, Aarash; Schellenberger, Jan; Palsson, Bernhard O.

in Biophysical Journal (2010), 98(10), 2072-81

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See detailReconstruction annotation jamborees: a community approach to systems biology.
Thiele, Ines; Palsson, Bernhard O.

in Molecular Systems Biology (2010), 6

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See detailA protocol for generating a high-quality genome-scale metabolic reconstruction.
Thiele, Ines; Palsson, Bernhard O.

in Nature Protocols (2010), 5(1), 93-121

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See detailReconstruction of biochemical networks in microorganisms.
Feist, Adam M.; Herrgard, Markus J.; Thiele, Ines; Reed, Jennie L.; Palsson, Bernhard O.

in Nature Reviews. Microbiology (2009), 7(2), 129-43

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See detailQuantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli.
Fleming, Ronan MT; Thiele, Ines; Nasheuer, H. P.

in Biophysical Chemistry (2009), 145(2-3), 47-56

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See detailIdentification of potential pathway mediation targets in Toll-like receptor signaling.
Li, Fan; Thiele, Ines; Jamshidi, Neema; Palsson, Bernhard O.

in PLoS Computational Biology (2009), 5(2), 1000292

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See detailMetabolic network analysis integrated with transcript verification for sequenced genomes.
Manichaikul, Ani; Ghamsari, Lila; Hom, Erik F. Y.; Lin, Chenwei; Murray, Ryan R.; Chang, Roger L.; Balaji, S.; Hao, Tong; Shen, Yun; Chavali, Arvind K.; Thiele, Ines; Yang, Xinping; Fan, Changyu; Mello, Elizabeth; Hill, David E.; Vidal, Marc; Salehi-Ashtiani, Kourosh; Papin, Jason A.

in Nature Methods (2009), 6(8), 589-592

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See detailGenome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.
Thiele, Ines; Jamshidi, Neema; Fleming, Ronan MT; Palsson, Bernhard O.

in PLoS Computational Biology (2009), 5(3), 1000312

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See detailThree-dimensional structural view of the central metabolic network of Thermotoga maritima.
Zhang, Ying; Thiele, Ines; Weekes, Dana; Li, Zhanwen; Jaroszewski, Lukasz; Ginalski, Krzysztof; Deacon, Ashley M.; Wooley, John; Lesley, Scott A.; Wilson, Ian A.; Palsson, Bernhard; Osterman, Andrei; Godzik, Adam

in Science (New York, N.Y.) (2009), 325(5947), 1544-1549

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See detailA genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.
Nogales, Juan; Palsson, Bernhard O.; Thiele, Ines

in BMC Systems Biology (2008), 2

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See detailGlobal reconstruction of the human metabolic network based on genomic and bibliomic data.
Duarte, Natalie C.; Becker, Scott A.; Jamshidi, Neema; Thiele, Ines; Mo, Monica L.; Vo, Thuy D.; Srivas, Rohith; Palsson, Bernhard O.

in Proceedings of the National Academy of Sciences of the United States of America (2007), 104(6), 1777-82

See detailEstimation of the number of extreme pathways for metabolic networks.
Yeung, Matthew; Thiele, Ines; Palsson, Bernard O.

in BMC Bioinformatics (2007), 8(1), 363

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See detailCandidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.
Price, Nathan D.; Thiele, Ines; Palsson, Bernhard O.

in Biophysical Journal (2006), 90(11), 3919-28

See detailTowards multidimensional genome annotation.
Reed, Jennifer L.; Famili, Iman; Thiele, Ines; Palsson, Bernhard O.

in Nature Reviews. Genetics (2006), 7(2), 130-41

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See detailThe subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Overbeek, Ross; Begley, Tadhg; Butler, Ralph M.; Choudhuri, Jomuna V.; Chuang, Han-Yu; Cohoon, Matthew; de Crecy-Lagard, Valerie; Diaz, Naryttza; Disz, Terry; Edwards, Robert; Fonstein, Michael; Frank, Ed D.; Gerdes, Svetlana; Glass, Elizabeth M.; Goesmann, Alexander; Hanson, Andrew; Iwata-Reuyl, Dirk; Jensen, Roy; Jamshidi, Neema; Krause, Lutz; Kubal, Michael; Larsen, Niels; Linke, Burkhard; McHardy, Alice C.; Meyer, Folker; Neuweger, Heiko; Olsen, Gary; Olson, Robert; Osterman, Andrei; Portnoy, Vasiliy; Pusch, Gordon D.; Rodionov, Dmitry A.; Ruckert, Christian; Steiner, Jason; Stevens, Rick; Thiele, Ines; Vassieva, Olga; Ye, Yuzhen; Zagnitko, Olga; Vonstein, Veronika

in Nucleic Acids Research (2005), 33(17), 5691-702

See detailCandidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.
Thiele, Ines; Price, Nathan D.; Vo, Thuy D.; Palsson, Bernhard O.

in Journal of Biological Chemistry (2005), 280(12), 11683-95

See detailExpanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.
Thiele, Ines; Vo, Thuy D.; Price, Nathan D.; Palsson, Bernhard O.

in Journal of Bacteriology (2005), 187(16), 5818-30

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