Profil

THIELE Ines

Main Referenced Co-authors
FLEMING, Ronan MT  (34)
Palsson, Bernhard O. (26)
HEINKEN, Almut Katrin  (16)
NORONHA, Alberto  (8)
RAVCHEEV, Dmitry  (8)
Main Referenced Keywords
Models, Biological (18); Humans (11); Metabolic Networks and Pathways (11); Computer Simulation (10); Genome, Bacterial (8);
Main Referenced Unit & Research Centers
Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group) (21)
Luxembourg Centre for Systems Biomedicine (LCSB): Systems Biochemistry (Fleming Group) (8)
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) (2)
Luxembourg Centre for Systems Biomedicine (LCSB) (1)
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) (1)
Main Referenced Disciplines
Life sciences: Multidisciplinary, general & others (71)
Biochemistry, biophysics & molecular biology (11)
Microbiology (7)
Engineering, computing & technology: Multidisciplinary, general & others (2)
Neurology (2)

Publications (total 89)

The most downloaded
652 downloads
Ravcheev, D., & Thiele, I. (29 August 2017). Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides. Frontiers in Genetics, 8, 111. doi:10.3389/fgene.2017.00111 https://hdl.handle.net/10993/32199

The most cited

2630 citations (OpenCitations)

Orth, J. D., Thiele, I., & Palsson, B. O. (2010). What is flux balance analysis? Nature Biotechnology, 28 (3), 245-8. doi:10.1038/nbt.1614 https://hdl.handle.net/10993/13057

Marcos-Zambrano, L. J., López-Molina, V. M., Bakir-Gungor, B., Frohme, M., Karaduzovic-Hadziabdic, K., Klammsteiner, T., Ibrahimi, E., Lahti, L., Loncar-Turukalo, T., Dhamo, X., Simeon, A., Nechyporenko, A., Pio, G., Przymus, P., Sampri, A., Trajkovik, V., Lacruz-Pleguezuelos, B., Aasmets, O., Araujo, R., ... Carrillo de Santa Pau, E. (22 November 2023). A toolbox of machine learning software to support microbiome analysis. Frontiers in Microbiology, 14. doi:10.3389/fmicb.2023.1250806
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Krüger, R., Baldini, F., Thiele, I., Hertel, J., & NCER-PD Consortium. (2020). Parkinson’s disease-associated alterations of the gut microbiome predict diseaserelevant changes in metabolic functions. BMC Biology. doi:10.1186/s12915-020-00775-7
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Heinken, A. K., Ravcheev, D., Baldini, F., Heirendt, L., Fleming, R. M., & Thiele, I. (2019). Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. Microbiome. doi:10.1186/s40168-019-0689-3
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Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A. K., Haraldsdottir, H. S., Wachowiak, J., Keating, S. M., Vlasov, V., Magnusdottir, S., Ng, C. Y., Preciat, G., Zagare, A., Chan, S. H. J., Aurich, M. K., Clancy, C. M., Modamio, J., Sauls, J. T., ... Fleming, R. M. T. (2019). Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols, 14 (3), 639-702. doi:10.1038/s41596-018-0098-2
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Baldini, F., Heinken, A. K., Heirendt, L., Magnusdottir, S., Fleming, R., & Thiele, I. (2018). The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. Bioinformatics. doi:10.1093/bioinformatics/bty941
Peer reviewed

Noronha, A., Modamio Chamarro, J., Jarosz, Y., Guerard, E., Sompairac, N., Preciat Gonzalez, G. A., Danielsdottir, A. D., Krecke, M., Merten, D., Haraldsdottir, H., Heinken, A. K., Heirendt, L., Magnusdottir, S., Ravcheev, D., Sahoo, S., Gawron, P., Friscioni, L., Garcia Santa Cruz, B., Prendergast, M., ... Thiele, I. (2018). The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Research. doi:10.1093/nar/gky992
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Greenhalgh, K., Ramiro Garcia, J., Heinken, A. K., Baginska, J., Letellier, E., Halder, R., Frachet Bour, A., Ullmann, P., Thiele, I., Haan, S., & Wilmes, P. (16 February 2018). Cominatorial effect of dietary fibre and Lactobacillus rhamnosus in the context of colorectal cancer therapy [Poster presentation]. Cell Immunology symposium.

Bauer, E., & Thiele, I. (2018). From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota. mSystems. doi:10.1128/mSystems.00209-17
Peer reviewed

Magnusdottir, S., & Thiele, I. (2018). Modeling metabolism of the human gut microbiome. Current Opinion in Biotechnology. doi:10.1016/j.copbio.2017.12.005
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Brunk, E., Sahoo, S., Zielinski, D. C., Altunkaya, A., Drager, A., Mih, N., Gatto, F., Nilsson, A., Preciat Gonzalez, G. A., Aurich, M. K., Prlic, A., Sastry, A., Danielsdottir, A. D., Heinken, A. K., Noronha, A., Rose, P. W., Burley, S. K., Fleming, R. M., Nielsen, J., ... Palsson, B. O. (2018). Recon3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnology, 36 (3), 272-281. doi:10.1038/nbt.4072
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Ravcheev, D., & Thiele, I. (29 August 2017). Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides. Frontiers in Genetics, 8, 111. doi:10.3389/fgene.2017.00111
Peer Reviewed verified by ORBi

Thiele, I., Clancy, C., Heinken, A. K., & Fleming, R. M. (August 2017). Quantitative systems pharmacology and the personalized drug–microbiota–diet axis. Current Opinion in Systems Biology, 4, 43-52. doi:10.1016/j.coisb.2017.06.001
Peer reviewed

Aurich, M. K., Thiele, I., & Fleming, R. M. (2017). A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines. PLoS Computational Biology. doi:10.1371/journal.pcbi.1005698
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Preciat Gonzalez, G. A., El Assal, L., Noronha, A., Thiele, I., Haraldsdottir, H., & Fleming, R. M. (2017). Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. Journal of Cheminformatics. doi:10.1186/s13321-017-0223-1
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Bauer, E.* , Zimmermann, J.* , Baldini, F., Thiele, I., & Kaleta, C. (2017). BacArena: Individual-Based Metabolic Modeling of Heterogeneous Microbes in Complex Communities. PLoS Computational Biology. doi:10.1371/journal.pcbi.1005544
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* These authors have contributed equally to this work.

Rowland, I., Gibson, G., Heinken, A. K., Scott, K., Swann, J., Thiele, I., & Tuohy, K. (2017). Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition. doi:10.1007/s00394-017-1445-8
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Heirendt, L., Thiele, I., & Fleming, R. M. (2017). DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia. Bioinformatics. doi:10.1093/bioinformatics/btw838
Peer reviewed

Rhaman, J., Noronha, A., Thiele, I., & Rahman, S. (2017). Leigh Map: A Novel Computational Diagnostic Resource for Mitochondrial Disease. Annals of Neurology. doi:10.1002/ana.24835
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Haraldsdottir, H., Cousin, B., Thiele, I., Fleming, R. M., & Vempala, S. (2017). CHRR: Coordi- nate hit-and-run with rounding for uniform sampling of constraint-based models. Bioinformatics. doi:10.1093/bioinformatics/btx052
Peer reviewed

Ma, D., Yang, L., Fleming, R. M., Thiele, I., Palsson, B., & Saunders, M. (2017). Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression. Scientific Reports. doi:10.1038/srep40863
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Fleming, R. M., Vlassis, N., Thiele, I., & Saunders, M. (November 2016). Conditions for duality between fluxes and concentrations in biochemical networks. Journal of Theoretical Biology, 409 (21), 1-10. doi:10.1016/j.jtbi.2016.06.033
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Magnusdottir, S., Heinken, A. K., Kutt, L., Ravcheev, D., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., Fleming, R. M., & Thiele, I. (2016). Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology. doi:10.1038/nbt.3703
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Heinken, A. K., Ravcheev, D., & Thiele, I. (2016). Systems biology of bacteria-host interactions. In L. Nibali & B. Henderson (Eds.), The Human Microbiota and Chronic Disease: Dysbiosis as a Cause of Human Pathology. Hoboken, New Jersey, United States: John Wiley & Sons, i nc. doi:10.1002/9781118982907.ch7
Peer reviewed

Ben Guebila, M., & Thiele, I. (16 June 2016). Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients. NPJ Systems Biology and Applications, 2. doi:10.1038/npjsba.2016.13
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Ravcheev, D., & Thiele, I. (25 January 2016). Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis. Frontiers in Microbiology, 7 (128). doi:10.3389/fmicb.2016.00128
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Aurich, M. K., Fleming, R. M., & Thiele, I. (2016). MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models. Frontiers in Physiology. doi:10.3389/fphys.2016.00327
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Dimitrov, D., Thiele, I., & Ferguson, L. R. (2016). The Human Gutome: Journey of Microbes and Health. Frontiers in Genetics.
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Beger, D., Dunn, W., Schmidt, M., Gross, S., Kirwan, J., Cascante, M., Brennan, L., Wishart, D., Oresic, M., Hankemeier, T., Broadhurst, D., Lane, A., Suhre, K., Kastenmueller, G., Sunner, S., Thiele, I., Fiehn, O., & Kaddurah-Daouk, R. (2016). Metabolomics enables precision medicine: A White Paper, Community Perspective. Metabolomics : Official journal of the Metabolomic Society. doi:10.1007/s11306-016-1094-6
Peer reviewed

Noronha, A., Danielsdóttir, A. D., Jóhannsson, F., Jónsdóttir, S., Jarlsson, S., Gunnarsson, J. P., Brynjólfsson, S., Gawron, P., Schneider, R., Thiele, I., & Fleming, R. M. (2016). ReconMap: An interactive visualisation of human metabolism. Bioinformatics. doi:10.1093/bioinformatics/btw667
Peer reviewed

Aurich, M. K., & Thiele, I. (2015). Computational modeling of human metabolism and its application to systems biomedicine. In O. Wolkenhauer & U. Schmitz (Eds.), Systems Medicine. Springer. doi:10.1007/978-1-4939-3283-2_12

Magnusdottir, S., Ravcheev, D., de Crecy-Lagard, V., & Thiele, I. (April 2015). Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Frontiers in Genetics, 6, 148. doi:10.3389/fgene.2015.00148
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Heinken, A. K., & Thiele, I. (2015). Anoxic conditions promote species-specific mutualism between gut microbes in silico. Applied and Environmental Microbiology, 81 (12), 4049-4061. doi:10.1128/AEM.00101-15
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Heinken, A. K., & Thiele, I. (2015). Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework. Gut Microbes, 6 (2), 120-130. doi:10.1080/19490976.2015.1023494
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Aurich, M. K., Paglia, G., Rolfsson, O., Hrafnsdottir, S., Magnusdottir, M., Stefaniak, M. K., Palsson, B. O., Fleming, R. M., & Thiele, I. (2015). Prediction of intracellular metabolic states from extracellular metabolomic data. Metabolomics : Official journal of the Metabolomic Society, 11 (3), 603-619. doi:10.1007/s11306-014-0721-3
Peer reviewed

Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A. P., Chang, R. L., Dräger, A., Famili, I., Feist, A. M., Fleming, R. M., Fong, S. S., Hatzimanikatis, V., Herrgård, M. J., Holder, A., Hucka, M., Hyduke, D., Jamshidi, N., Lee, S. Y., Le Novère, N., ... Thiele, I. (2015). Do Genome-scale Models Need Exact Solvers or Clearer Standards? Molecular Systems Biology, 11 (10), 1. doi:10.15252/msb.20156157
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Heinken, A. K., & Thiele, I. (2015). Systems biology of host-microbe metabolomics. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. doi:10.1002/wsbm.1301
Peer reviewed

Bauer, E., Laczny, C. C., Magnusdottir, S., Wilmes, P., & Thiele, I. (2015). Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. Microbiome, 3 (55), 1-13. doi:10.1186/s40168-015-0121-6
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Ravcheev, D., & Thiele, I. (2014). Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota. Frontiers in Microbiology. doi:10.3389/fmicb.2014.00674
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Heinken, A. K., Khan, M. T., Paglia, G., Rodionov, D. A., Harmsen, H. J., & Thiele, I. (September 2014). A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. Journal of Bacteriology, 196 (18), 3289-3302. doi:10.1128/JB.01780-14
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Sahoo, S., Aurich, M. K., Jonsson, J., & Thiele, I. (March 2014). Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease. Frontiers in Physiology, 5, 1-24. doi:10.3389/fphys.2014.00091
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Haraldsdottir, H., Thiele, I., & Fleming, R. M. (2014). Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. Journal of Cheminformatics, 6, 2. doi:10.1186/1758-2946-6-2
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Edwards, L., Sigurdsson, M. I., Robbins, P. A., Weale, M. E., Cavalleri, G. L., Montgomery, H., & Thiele, I. (2014). Genome-Scale Methods Converge on Key Mitochondrial Genes for the Survival of Human Cardiomyocytes in Hypoxia. Circulation: Cardiovascular Genetics. doi:10.1161/CIRCGENETICS.113.000269
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Thiele, I., Vlassis, N., & Fleming, R. M. (2014). FASTGAPFILL: Efficient gap filling in metabolic networks. Bioinformatics, 30 (17), 2529-2531. doi:10.1093/bioinformatics/btu321
Peer reviewed

Sahoo, S., Haraldsdottir, H., Fleming, R. M., & Thiele, I. (2014). Modeling the effects of commonly used drugs on human metabolism. FEBS Journal. doi:10.1111/febs.13128
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Stobbe, M. D., Swertz, M. A., Thiele, I., Rengaw, T., van Kampen, A. H., & Moerland, P. D. (26 June 2013). Consensus and conflict cards for metabolic pathway databases. BMC Systems Biology, 7, 50. doi:10.1186/1752-0509-7-50
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Thiele, I., Heinken, A. K., & Fleming, R. M. (2013). A systems biology approach to studying the role of microbes in human health. Current Opinion in Biotechnology, 24 (1), 4-12. doi:10.1016/j.copbio.2012.10.001
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Rolfsson, O., Paglia, G., Magnusdottir, M., Palsson, B. O., & Thiele, I. (2013). Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity. Biochemical Journal, 449 (2), 427-435. doi:10.1042/BJ20120980
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Sahoo, S., & Thiele, I. (2013). Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells. Human Molecular Genetics, 22 (13), 2705-22. doi:10.1093/hmg/ddt119
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Nogales, J., Gudmundsson, S., & Thiele, I. (2013). Toward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks. Bioengineered, 4 (3), 158-163. doi:10.4161/bioe.22792
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Thiele, I.* , Swainston, N.* , Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., 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., ... Palsson, B. O. (2013). A community-driven global reconstruction of human metabolism. Nature Biotechnology, 31, 419-425. doi:10.1038/nbt.2488
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* These authors have contributed equally to this work.

Sun, Y., Fleming, R. M., Thiele, I., & Saunders, M. (2013). Robust flux balance analysis of multi- scale biochemical reaction networks. BMC Bioinformatics, 1 (14), 240. doi:10.1186/1471-2105-14-240
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Edwards, L., & Thiele, I. (2013). Applying systems biology methods to the study of human physiology in extreme environments. Extreme Physiology and Medicine, 2 (8). doi:10.1186/2046-7648-2-8
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Heinken, A. K., Sahoo, S., Fleming, R. M., & Thiele, I. (2013). Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes, 4 (1), 28-40. doi:10.4161/GMIC.22370
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Sigurdsson, G., Fleming, R. M., Heinken, A. K., & Thiele, I. (2012). A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm. PLoS ONE, 7 (4), 34337. doi:10.1371/journal.pone.0034337
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Aurich, M. K., & Thiele, I. (2012). Contextualization procedure and modeling of monocyte specific TLR signaling. PLoS ONE, 7 (12), 49978. doi:10.1371/journal.pone.0049978
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Paglia, G., Hrafnsdottir, S., Magnusdottir, M., Fleming, R. M., Thorlacius, S., Palsson, B. O., & Thiele, I. (2012). Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS). Analytical and Bioanalytical Chemistry, 402 (3), 1183-98. doi:10.1007/s00216-011-5556-4
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Thiele, I., Fleming, R. M., Que, R., Bordbar, A., Diep, D., & Palsson, B. O. (2012). Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS ONE, 7 (9), 45635. doi:10.1371/journal.pone.0045635
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Fleming, R. M., & Thiele, I. (2012). Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration. Journal of Theoretical Biology, 314, 173-181. doi:10.1016/j.jtbi.2012.08.021
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Haraldsdottir, H., Thiele, I., & Fleming, R. M. (2012). Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction. Biophysical Journal, 102 (8), 1703–1711. doi:10.1016/j.bpj.2012.02.032
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Nogales, J., Gudmundsson, S., Knight, E. M., Palsson, B. O., & Thiele, I. (2012). Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. Proceedings of the National Academy of Sciences of the United States of America, 109 (7), 2678-2683. doi:10.1073/pnas.1117907109
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Nogales, J. E., Gudmunsson, S., & Thiele, I. (2012). An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production. International Journal of Hydrogen Energy, 37 (17), 12205–12218. doi:10.1016/j.ijhydene.2012.06.032
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Sahoo, S., Franzson, Jonsson, J. J., & Thiele, I. (2012). A compendium of inborn errors of metabolism mapped onto the human metabolic network. Molecular Biosystems, 8 (10), 2545 - 2558. doi:10.1039/c2mb25075f
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Paglia, G., Magnusdottir, M., Thorlacius, S., Sigurjonsson, O. E., Guethmundsson, S., Palsson, B. O., & Thiele, I. (2012). Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences, 898, 111-20. doi:10.1016/j.jchromb.2012.04.026
Peer reviewed

Thiele, I., Hyduke, D. R., Steeb, B., Fankam, G., Allen, D. K., Bazzani, S., Charusanti, P., Chen, F.-C., Fleming, R. M., Hsiung, C. A., De Keersmaecker, S. C. J., Liao, Y.-C., Marchal, K., Mo, M. L., Ozdemir, E., Raghunathan, A., Reed, J. L., Shin, S.-I., Sigurbjornsdottir, S., ... Bumann, D. (2011). A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Systems Biology, 5, 8. doi:10.1186/1752-0509-5-8
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Schellenberger, J., Que, R., Fleming, R. M., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., Kang, J., Hyduke, D. R., & Palsson, B. O. (2011). Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols, 6 (9), 1290-1307. doi:10.1038/nprot.2011.308
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Rolfsson, O., Palsson, B. O., & Thiele, I. (2011). The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Systems Biology, 5, 155. doi:10.1186/1752-0509-5-155
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Fleming, R. M., & Thiele, I. (2011). von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinformatics, 27 (1), 142-3. doi:10.1093/bioinformatics/btq607
Peer reviewed

Thorleifsson, S. G., & Thiele, I. (2011). rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks. Bioinformatics, 27 (14), 2009-10. doi:10.1093/bioinformatics/btr308
Peer reviewed

Orth, J. D., Thiele, I., & Palsson, B. O. (2010). What is flux balance analysis? Nature Biotechnology, 28 (3), 245-8. doi:10.1038/nbt.1614
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Fleming, R. M., Thiele, I., Provan, G., & Nasheuer, H. P. (2010). Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. Journal of Theoretical Biology, 264 (3), 683-92. doi:10.1016/j.jtbi.2010.02.044
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Thiele, I., Fleming, R. M., Bordbar, A., Schellenberger, J., & Palsson, B. O. (2010). Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery. Biophysical Journal, 98 (10), 2072-81. doi:10.1016/j.bpj.2010.01.060
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Thiele, I., & Palsson, B. O. (2010). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protocols, 5 (1), 93-121. doi:10.1038/nprot.2009.203
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Sigurdsson, M. I., Jamshidi, N., Steingrimsson, E., Thiele, I., & Palsson, B. O. (2010). A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC Systems Biology, 4, 140. doi:10.1186/1752-0509-4-140
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Thiele, I., & Palsson, B. O. (2010). Reconstruction annotation jamborees: a community approach to systems biology. Molecular Systems Biology, 6, 361. doi:10.1038/msb.2010.15
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Gudmundsson, S., & Thiele, I. (2010). Computationally efficient flux variability analysis. BMC Bioinformatics, 11, 489. doi:10.1186/1471-2105-11-489
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Thiele, I., Jamshidi, N., Fleming, R. M., & Palsson, B. O. (2009). Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Computational Biology, 5 (3), 1000312. doi:10.1371/journal.pcbi.1000312
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Feist, A. M., Herrgard, M. J., Thiele, I., Reed, J. L., & Palsson, B. O. (2009). Reconstruction of biochemical networks in microorganisms. Nature Reviews. Microbiology, 7 (2), 129-43. doi:10.1038/nrmicro1949
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Li, F., Thiele, I., Jamshidi, N., & Palsson, B. O. (2009). Identification of potential pathway mediation targets in Toll-like receptor signaling. PLoS Computational Biology, 5 (2), 1000292. doi:10.1371/journal.pcbi.1000292
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Fleming, R. M., Thiele, I., & Nasheuer, H. P. (2009). Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Biophysical Chemistry, 145 (2-3), 47-56. doi:10.1016/j.bpc.2009.08.007
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Manichaikul, A., Ghamsari, L., Hom, E. F. Y., Lin, C., Murray, R. R., Chang, R. L., Balaji, S., Hao, T., Shen, Y., Chavali, A. K., Thiele, I., Yang, X., Fan, C., Mello, E., Hill, D. E., Vidal, M., Salehi-Ashtiani, K., & Papin, J. A. (2009). Metabolic network analysis integrated with transcript verification for sequenced genomes. Nature Methods, 6 (8), 589-592. doi:10.1038/NMETH.1348
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Zhang, Y., Thiele, I., Weekes, D., Li, Z., Jaroszewski, L., Ginalski, K., Deacon, A. M., Wooley, J., Lesley, S. A., Wilson, I. A., Palsson, B., Osterman, A., & Godzik, A. (2009). Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science, 325 (5947), 1544-1549. doi:10.1126/science.1174671
Peer Reviewed verified by ORBi

Nogales, J., Palsson, B. O., & Thiele, I. (2008). A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Systems Biology, 2, 79. doi:10.1186/1752-0509-2-79
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Yeung, M., Thiele, I., & Palsson, B. O. (2007). Estimation of the number of extreme pathways for metabolic networks. BMC Bioinformatics, 8 (1), 363. doi:10.1186/1471-2105-8-363
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Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R., & Palsson, B. O. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences of the United States of America, 104 (6), 1777-82. doi:10.1073/pnas.0610772104
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Price, N. D., Thiele, I., & Palsson, B. O. (2006). Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophysical Journal, 90 (11), 3919-28. doi:10.1529/biophysj.105.072645
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Reed, J. L., Famili, I., Thiele, I., & Palsson, B. O. (2006). Towards multidimensional genome annotation. Nature Reviews. Genetics, 7 (2), 130-41. doi:10.1038/nrg1769
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Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V., Chuang, H.-Y., Cohoon, M., de Crecy-Lagard, V., Diaz, N., Disz, T., Edwards, R., Fonstein, M., Frank, E. D., Gerdes, S., Glass, E. M., Goesmann, A., Hanson, A., Iwata-Reuyl, D., Jensen, R., Jamshidi, N., ... Vonstein, V. (2005). The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research, 33 (17), 5691-702. doi:10.1093/nar/gki866
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Thiele, I., Price, N. D., Vo, T. D., & Palsson, B. O. (2005). Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. Journal of Biological Chemistry, 280 (12), 11683-95. doi:10.1074/jbc.M409072200
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Thiele, I., Vo, T. D., Price, N. D., & Palsson, B. O. (2005). Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. Journal of Bacteriology, 187 (16), 5818-30. doi:10.1128/JB.187.16.5818-5830.2005
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