![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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. |
![]() ![]() | 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 ![]() |
![]() ![]() | Bauer, E., & THIELE, I. (2018). From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota. mSystems. doi:10.1128/mSystems.00209-17 ![]() |
![]() ![]() | MAGNUSDOTTIR, S., & THIELE, I. (2018). Modeling metabolism of the human gut microbiome. Current Opinion in Biotechnology. doi:10.1016/j.copbio.2017.12.005 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() * 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | Dimitrov, D., THIELE, I., & Ferguson, L. R. (2016). The Human Gutome: Journey of Microbes and Health. Frontiers in Genetics. ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | HEINKEN, A. K., & THIELE, I. (2015). Systems biology of host-microbe metabolomics. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. doi:10.1002/wsbm.1301 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() * 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | Gudmundsson, S., & THIELE, I. (2010). Computationally efficient flux variability analysis. BMC Bioinformatics, 11, 489. doi:10.1186/1471-2105-11-489 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
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 ![]() |
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 ![]() |
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 ![]() |
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 ![]() |
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 ![]() |
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 ![]() |
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 ![]() |
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 ![]() |