Publications

2017

Ravcheev, D., & Thiele, I. (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.
Aurich, M. K., Thiele, I., & Fleming, R. M. (2017, August). A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines. PLoS Computational Biology.
Thiele, I., Clancy, C., Heinken, A. K., & Fleming, R. M. (2017). Quantitative systems pharmacology and the personalized drug–microbiota–diet axis. Current Opinion in Systems Biology, 4, 43-52.
Magnusdottir, S. (2017). Development and analysis of individual-based gut microbiome metabolic models. Unpublished doctoral thesis, University of Luxembourg, ​Esch-sur-Alzette, ​​Luxembourg.
Jury: Thiele, I. (Promotor), Wilmes, P., Fleming, R. M., Lacroix, C., & Planes, F.
Preciat Gonzalez, G. A., El Assal, L., Noronha, A., Thiele, I., Haraldsdottir, H., & Fleming, R. M. (2017, June 14). Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. Journal of Cheminformatics.
Bauer, E.* , Zimmermann, J.* , Baldini, F., Thiele, I., & Kaleta, C. (2017, May 22). BacArena: Individual-Based Metabolic Modeling of Heterogeneous Microbes in Complex Communities. PLoS Computational Biology.
* These authors have contributed equally to this work.
Rowland, I., Gibson, G., Heinken, A. K., Scott, K., Swann, J., Thiele, I., & Tuohy, K. (2017, April 09). Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition.
Heirendt, L., Thiele, I., & Fleming, R. M. (2017, January 16). DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia. Bioinformatics.
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.
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.
Rhaman, J., Noronha, A., Thiele, I., & Rahman, S. (2017). Leigh Map: A Novel Computational Diagnostic Resource for Mitochondrial Disease. Annals of Neurology.

2016

Fleming, R. M., Vlassis, N., Thiele, I., & Saunders, M. (2016). Conditions for duality between fluxes and concentrations in biochemical networks. Journal of Theoretical Biology, 409(21), 1-10.
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, November). Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology.
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, USA: John Wiley & Sons, i nc.
Ben Guebila, M., & Thiele, I. (2016). Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients. NPJ Systems Biology and Applications, 2.
Ravcheev, D., & Thiele, I. (2016). Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis. Frontiers in Microbiology, 7(128).
Aurich, M. K., Fleming, R. M., & Thiele, I. (2016). MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models. Frontiers in Physiology.
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.
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.

2015

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.
Magnusdottir, S., Ravcheev, D., de Crecy-Lagard, V., & Thiele, I. (2015). Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Frontiers in Genetics, 6, 148.
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.
Bauer, E., Laczny, 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.
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., Lerman, J. A., Lewis, N. E., Ma, D., Mahadevan, R., Maranas, C., Nagarajan, H., Navid, A., Nielsen, J., Nielsen, L. K., Nogales, J., Noronha, A., Pal, C., Palsson, B. O., Papin, J. A., Patil, K. R., Price, N. D., Reed, J. L., Saunders, M., Senger, R. S., Sonnenschein, N., Sun, Y., & Thiele, I. (2015). Do Genome-scale Models Need Exact Solvers or Clearer Standards? Molecular Systems Biology, 11(10), 1.
Feng, Y., Kumar, R., Ravcheev, D., & Zhang, H. (2015). Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism. MicrobiologyOpen, 4, 644–659.
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.
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.
Heinken, A. K., & Thiele, I. (2015). Systems biology of host-microbe metabolomics. Wiley Interdisciplinary Reviews. Systems Biology and Medicine.
Zhang, H., Ravcheev, D., Hu, D., Zhang, F., Gong, X., Hao, L., Cao, M., Rodionov, D. A., Wang, C., & Feng, Y. (2015). Two novel regulators of N-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections. MicrobiologyOpen, 4(6), 983-1000.

2014

Ravcheev, D., & Thiele, I. (2014, December). Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota. Frontiers in Microbiology.
Heinken, A. K., Khan, M. T., Paglia, G., Rodionov, D. A., Harmsen, H. J., & Thiele, I. (2014). A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. Journal of Bacteriology, 196(18), 3289-3302.
Sahoo, S., Aurich, M. K., Jonsson, J., & Thiele, I. (2014). Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease. Frontiers in Physiology, 5, 1-24.
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.
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.
Sahoo, S., Haraldsdottir, H., Fleming, R. M., & Thiele, I. (2014). Modeling the effects of commonly used drugs on human metabolism. FEBS Journal.
Thiele, I., Vlassis, N., & Fleming, R. M. (2014). FASTGAPFILL: Efficient gap filling in metabolic networks. Bioinformatics, 30(17), 2529-2531.

2013

Stobbe, M. D., Swertz, M. A., Thiele, I., Rengaw, T., van Kampen, A. H., & Moerland, P. D. (2013). Consensus and conflict cards for metabolic pathway databases. BMC Systems Biology, 7, 50.
Edwards, L., & Thiele, I. (2013). Applying systems biology methods to the study of human physiology in extreme environments. Extreme Physiology & Medicine, 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.
Nogales, J., Gudmundsson, S., & Thiele, I. (2013). Toward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks. Bioengineered, 4(3), 158-163.
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.
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.
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.
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.
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., 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. S., Sigurdsson, M. I., Simeonidis, E., 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. (2013). A community-driven global reconstruction of human metabolism. Nature Biotechnology, 31, 419-425.
* These authors have contributed equally to this work.

2012

Aurich, M. K., & Thiele, I. (2012). Contextualization procedure and modeling of monocyte specific TLR signaling. PLoS ONE, 7(12), 49978.
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.
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.
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.
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.
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.
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 & Life Sciences, 898, 111-20.
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.
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.
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.

2011

Fleming, R. M., & Thiele, I. (2011). von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinformatics (Oxford, England), 27(1), 142-3.
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.
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.
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., Steinmann, J., Sudarsan, S., Swainston, N., Thijs, I. M., Zengler, K., Palsson, B. O., Adkins, J. N., & 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.
Thorleifsson, S. G., & Thiele, I. (2011). rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks. Bioinformatics (Oxford, England), 27(14), 2009-10.

2010

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.
Gudmundsson, S., & Thiele, I. (2010). Computationally efficient flux variability analysis. BMC Bioinformatics, 11, 489.
Orth, J. D., Thiele, I., & Palsson, B. O. (2010). What is flux balance analysis? Nature Biotechnology, 28(3), 245-8.
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.
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.
Thiele, I., & Palsson, B. O. (2010). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protocols, 5(1), 93-121.
Thiele, I., & Palsson, B. O. (2010). Reconstruction annotation jamborees: a community approach to systems biology. Molecular Systems Biology, 6, 361.

2009

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

2008

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.

2007

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.
Yeung, M., Thiele, I., & Palsson, B. O. (2007). Estimation of the number of extreme pathways for metabolic networks. BMC Bioinformatics, 8(1), 363.

2006

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.
Reed, J. L., Famili, I., Thiele, I., & Palsson, B. O. (2006). Towards multidimensional genome annotation. Nature Reviews. Genetics, 7(2), 130-41.

2005

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., Krause, L., Kubal, M., Larsen, N., Linke, B., McHardy, A. C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Osterman, A., Portnoy, V., Pusch, G. D., Rodionov, D. A., Ruckert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Y., Zagnitko, O., & 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.
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.
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.