  | 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  Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
  | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi* 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | Dimitrov, D., Thiele, I., & Ferguson, L. R. (2016). The Human Gutome: Journey of Microbes and Health. Frontiers in Genetics. Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer reviewed |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi* 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | Gudmundsson, S., & Thiele, I. (2010). Computationally efficient flux variability analysis. BMC Bioinformatics, 11, 489. doi:10.1186/1471-2105-11-489 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
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 Peer Reviewed verified by ORBi |
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 Peer Reviewed verified by ORBi |
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 Peer Reviewed verified by ORBi |
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 Peer Reviewed verified by ORBi |
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 Peer Reviewed verified by ORBi |
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 Peer Reviewed verified by ORBi |
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 Peer Reviewed verified by ORBi |