Publications
Submitted publications:
Zaunseder et al., "Personalised metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases", (submitted).
Heinken et al., "APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites", (submitted).
Martinelli, F. et al, "Whole-body modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease", (submitted).
Heirendt, L., Arreckx, S., Trefois, C., Yarosz, Y., Vyas, M., Satagopam, V.P., Schneider, R., Thiele, I., Fleming, R.M.T., "ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software", arXiv:1712.05236 [cs.SE] (submitted).
Peer-reviewed publications:
2023
123. Zambrano, L.J.M., et al., "A toolbox of machine learning software to support microbiome analysis", Front. Microbiol., 14 (2023).
122. Hensen, T., Fässler, D., O’Mahony, L., Albrich, W.C., Barda, B., Garzoni, C., Kleger, G.-R., Pietsch, U., Suh, N., Hertel, J., Thiele, I., "The Effects of Hospitalisation on the Serum Metabolome in COVID-19 Patients". Metabolites, 13, 951 (2023).
121. Hertel, J., Heinken, A., Faessler, D., Thiele, I., "Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses", Cell Reports Methods (2023).
120. van der Spek, A., Stewart, I.D., Kühnel, B. et al. Circulating metabolites modulated by diet are associated with depression. Mol Psychiatry (2023).
119. Basile, A., Heinken, A., Hertel, J., Smarr, L., Li, W., Treu, L., Valle, G., Campanaro, S., Thiele, I., "Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics", Gut Microbes, 15:1 (2023).
118. Fleming, R.M.T., Haraldsdottir, H.S., Le, H.M., Vuong, P.T., Hankemeier, T., Thiele, I., "Cardinality optimisation in constraint-based modelling: Application to human metabolism", Bioinformatics, 39 (9), btad450 (2023).
117. Noecker, C., Sanchez, J., Bisanz, J.E., Escalante, V., Alexander, M., Trepka, K., Heinken, A., Liu, Y., Dodd, D., Thiele, I., DeFelice, B., Turnbaugh, P.J., "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta", PLoS Biology, 21(5), e3002125.
116. Weston, B., Thiele, I., "A nutrition algorithm to optimize feed and medium composition using genome-scale metabolic models.", Metabolic Engineering, 76, 167-178 (2023).
115. Heinken, A., Hertel, J., Acharya, G., Ravcheev, D. A., Nyga, M., Okpala, O. E., Hogan, M., Magnúsdóttir, S., Martinelli, F., Nap, B., Preciat, G., Edirisinghe, J. N., Henry, C. S., Fleming, R. M. T., Thiele, I., "Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine." Nat Biotechnol (2023). https://doi.org/10.1038/s41587-022-01628-0
114. Kindschuh, W., Baldini, F., Liu, M., Liao, J., Meydan, Y., Lee, H., Heinken, A., Thiele, I., Thaiss, C., Levy, M., Korem, T., "Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome." Nature Microbiology, 8, 246–259(2023).
2022
113. Thiele, I., Preciat, G., Fleming, R.M.T., "MetaboAnnotator: An efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions", Bioinformatics, btac596 (2022).
112. Thiele, I., Fleming, R. M. T., "Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication.", Computational and Structural Biotechnology, 4098-4109 (2022).
111. Hertel, J., Fässler, D., Heinken, A., Weiß, F. U., Rühlemann, M., Bang, C., Franke, A., Budde, K., Henning,A.-L., Petersmann, A., Völker, U., Völzke, H., Thiele, I., Grabe, H.-J., Lerch, M. M., Nauck, M., Friedrich, N., Frost, F., “NMR Metabolomics Reveal Urine Markers of Microbiome Diversity and Identify Benzoate Metabolism as a Mediator between High Microbial Alpha Diversity and Metabolic Health”, Metabolites, 12(4), 308 (2022).
110. Ternes, D., Tsenkova, M., Pozdeev, V., Meyers, M., Koncina, E., Atatri, S., Schmitz, M., Karta, J., Schmoetten, M., Heinken, A., Rodriguez, F., Delbrouck, C., Gaigneaux, A., Ginolhac, A., Nguyen, T.T.D., Grandmougin, L., Frachet Bour, A., Martin-Gallausiaux, C., Pacheco, M., Neuberger-Castillo, L., Miranda, P., Zuegel, N., Ferrand, J.-Y., Gantenbein, M., Sauter, T., Slade, D., Thiele, I., Meiser, J., Haan, S., Wilmes, P., "The gut microbial metabolite formate exacerbates colorectal cancer progression", Nature Metabolism, 4, 458–475 (2022).
109. Heinken, A., Thiele, I., "Microbiome Modelling Toolbox 2.0: Efficient, tractable modelling of microbiome communities", Bioinformatics, btac082 (2022).
2021
108. Heinken, A., Magnusdottir, S., Fleming, R.M.T., Thiele, I., "DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations", Bioinformatics, btab622 (2021).
107. Heinken, A., Basile, A., Hertel. J., Thinnes, C., Thiele, I., "Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine", Annual Review of Microbiology, 75 (2021).
106. Zhu, L., Pei, W., Thiele, I., Mahadevan, R., "Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism." PLoS Computational Biology, 17(8): e1009110 (2021).
105. Heinken, A., Basile, A., Thiele, I., "Advances in constraint-based modelling of microbial communities." Current Opinion in Systems Biology, 27: 100346 (2021).
104. Hertel, J., Heinken, A., Martinelli, F., Thiele, I., "Integration of constraint-based modelling with faecal metabolomics reveals large deleterious effects of Fusobacteria species on community butyrate production". Gut Microbes, 13(1):1-23 (2021).
103. Ben Guebila, M., Thiele, I., "Pan-organ model integration of metabolic and regulatory processes in type 1 diabetes". Nature Computational Science, 1, 348–361 (2021).
102. Mills, S., Trego, A. C., Ward, J., Castilla-Archilla, J., Hertel, J., Thiele, I., Lens, P. N. L., Ijaz, U. Z., Collins, G., "Methanogenic granule growth and development is a continual process characterized by distinct morphological features.", J. Env. Man., 286 (2021).
101. Heinken, A., Hertel, J., Thiele, I., "A systematic interrogation of the distinct metabolic potential in gut microbiomes of inflammatory bowel disease patients with dysbiosis", Systems Biology & Applications, 7, 19 (2021) .
100. Hosseinkhani, F., Heinken , A., Thiele , I., Lindenburg , P.W., Harms, A. C., Hankemeier, T. , " The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases", Gut Microbes, 13(1), 1-22 (2021).
99. Ferreira, C.R., Rahman, S., Keller, M., Zschocke, J., ICIMD Advisory Group, " An international classification of inherited metabolic disorders (ICIMD)", Journal of Inherited Metabolic Disease, 4(1) , 164-177 (2021).
98. Cheng, Y., Schlosser, P., Hertel, J., Sekula, P., Oefner, P.J., Spiekerkoetter, U., Mielke, J., Freitag, D.F., Schmidts, M., GCKD Investigators, Kronenberg, F., Eckardt, K-U., Thiele, I., Li, Y., Köttgen, A., " Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism", Nature Communications, 12(964) (2021).
2020
97. Baloni, P., Funk, C.C., Yan, J., Yurkovich, J.T., Kueider-Paisley, A., Nho, K., Heinken, A., Jia, W., Mahmoudiandehkordi, S., Louie, G., Saykin, A.J., Arnold, M., Kastenmueller, G., Griffiths, W., Thiele, I., Kaddurah-Daouk, R., Price, N.D., Alzheimer's Disease Metabolomics Consortium, "Metabolic network analysis reveals altered bile acid synthesis and cholesterol metabolism in Alzheimer’s Disease", Cell Reports Medicine, 1 (8), 100138.
96. Thiele, I., Sahoo, S., Heinken, A., Hertel, J., Heirendt, L., Aurich, M.K., Fleming, R.M.T., "Personalized whole-body models integrate metabolism, physiology, and the gut microbiome", Molecular Systems Biology, 16:e8982 (2020).
95. Baldini, F., Hertel, J., Sandt, E., Thinnes, C.C., Neuberger-Castillo, L., Pavelka, L., Betsou, F., Krüger, R., Thiele, I., "Parkinson’s disease-associated alterations of the gut microbiome can invoke disease-relevant metabolic changes", BMC Biology, 18(60) (2020).
2019
94. Hertel, J., Harms, A.C., Heinken, A., Baldini, F., Thinnes. C.C., Glaab, E., Vasco, D.A., Pietzner, M., Stewart, I.D., Wareham, N.J., Langenberg, C., Trenkwalder, C., Krüger, R., Hankemeier, T., Fleming, R.M.T., Mollenhauer, B., Ines Thiele, I., "Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease", Cell Reports (2019).
93. Poupin, N., Tremblay-Franco, M., Amiel, A., Canlet, C., Rémond, D., Debrauwer, L., Dardevet, D., Thiele, I., Aurich, M.K., Jourdan, F., Savary-Auzeloux, I., Polakof, S., "Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig". Scientific Reports, 9:12527 (2019).
92. Ravcheev, D.A, Moussu, L., Smajic, S., Thiele, I., “Comparative genomic analysis reveals novel microcompartment-associated metabolic pathways in the human gut microbiome”. Frontiers in Genetics, 7(1):75 (2019).
91. Bernabé, B.P., Thiele, I., Galdones, E., Siletz, A., Chandrasekaran, S., Woodruff, T.K., Broadbelt, J.L., Shea, L.D., "Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development", BMC Bioinformatics, 20(1), 307 (2019).
90. Heinken, A., Ravcheev, D.A., Baldini, F., Heirendt, L., Fleming, R.M.T., Thiele, I., "Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease", Microbiome, 7:75 (2019).
89. Ben Guebila, M., Thiele, I., "Predicting the gastrointestinal side effects of drugs using contextualized metabolic models", PLoS Computational Biology, 15(6):e1007100 (2019).
88. Greenhalgh, K., Ramiro-Garcia, J., Heinken, A., Ullmann, P., Bintener, T., Pires Pacheco, M., Baginska, J., Shah, P., Frachet, A., Halder, R., Fritz, J.V., Sauter, T., Thiele, I., Haan, S., Letellier, E., Wilmes, P., "Integrated in vitro and in silico modelling delineates the molecular effects of a synbiotic regimen on colorectal cancer-derived cells", Cell Reports, 27(5):1621-1632.e9 (2019).
87. Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S.N., Richelle, A., Heinken, A., Haraldsdottir, H.S., Keating, S.M., Vlasov, V., Wachowiak, J., Magnusdottir, S., Ng, C.Y., Preciat, G., Zagar, A., Chan, S.H.J., Aurich, M.K., Clancy, C.M., Modamio, J., Sauls, J.T., Noronha, A., Bordbar, A., Cousin, B., Guebila, M., Apaolaza, I., Kostromins, A., Le, H.M., Ma, D., Sun, Y., Valcarcel, L., Wang, L., Yurkovich, J.T., Vuong, P.T., El Assal, L.P., Hinton, S., Bryant, W.A., Artacho, F.J.A., Planes, F.J., Stalidzans, E., Maas, A., Vempala, S., Hucka, M., Saunders, M.A., Maranas, C.D., Lewis, N.E., Sauter, T., Palsson, B.O., Thiele, I., Fleming, R.M.T., "Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0", Nature Protocol, 14, 639-702 (2019).
86. Noronha, A., Modamio, J., Jarosz, Y., Sompairac, N., Gonzalez, G., DanÃielsdottir, A.D., Krecke, M., Merten, D., Haraldsdottir, H.S., , A., Heirendt, L., Magnusdottir, S., Ravcheev, D.A., Sahoo, S., Gawron, P., Guerard, E., Friscioni, L., Garcia, B., Prendergast, M., Rodrigues, M., Roy, A., Rouquaya, M., Wiltgen, L., Zagare, A., John, E., Krueger, M., Kuperstein, I., Zinovyev, A., Schneider, R., Fleming, R.M.T., Thiele, I., "The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease". Nucleic Acids Research, 47(D1): D614-D624 (2019). Breakthrough Article.
2018
85. Baldini, F., Heinken, A., Heirendt, L., Magnusdottir, S., Fleming, R.M.T., Thiele, I., "The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities", Bioinformatics, bty941 (2018).
84. Chen-Plotkin, A.S., Albin, R., Alcalay, R., Babcock, D., Bajaj, V., Bowman, D., Buko, A., Cedarbaum, J., Chelsky, D., Cookson, M.R., Dawson, T.M., Dewey, R., Foroud, T., Frasier, M., German, D., Gwinn, K., Huang, X., Kopil, C., Kremer, T., Lasch, S., Marek, K., Marto, J.A., Merchant, K., Mollenhauer, B., Naito, A., Potashkin, J., Reimer, A., Rosenthal, L.S., Saunders-Pullman, R., Scherzer, C.R., Sherer, T., Singleton, A., Sutherland, M., Thiele, I., van der Brug, M. Van Keuren-Jensen, K., Vaillancourt, D., Walt, D., West, A., Zhang, J., "Finding useful biomarkers for Parkinson's disease", Science Translational Medicine, 10(454): eaam6003 (2018).
83. Magnusdottir, S., Heinken, A., Fleming, R.M.T., Thiele, I., Reply to" Challenges in modeling the human gut microbiome", Nature Biotechnology, 36(8): 686 (2018).
82. Bauer, E., Thiele, I., ''From metagenomic data to personalized computational microbiotas: Predicting dietary supplements for Crohn's disease'', NPJ Systems Biology and Applications, 4(1): 27 (2018).
81. Bauer, E., Thiele, I., "From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota.", mSystems, 36, 272-281 (2018).
80. Brunk, E., Sahoo, S., Zielinski, D., Altunkaya, A., Draeger, A., Mih, N., Gatto, F., Nilsson, A., Preciat, G., Aurich, M.K., Prlic, A., Sastry, A., Danielsdottir, A.D., Heinken, A., Noronha, A., Rose, P.W., Burley, S.K., Fleming, R.M.T., Nielsen, J., Thiele, I., Palsson, B.O., "Recon3D enables a three-dimensional view of gene variation in human metabolism", Nature Biotechnology, 36(3), 272-281 (2018).
79. Magnusdottir, S., Thiele, I., "Modeling metabolism of the human gut microbiome", Current Opinion in Biotechnology, 51, 90-96 (2018).
78. Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I., Tuohy, K., ''Gut microbiota functions - Metabolism of nutrients and other food components'', European Journal of Nutrition, 57(1), 1-24 (2018).
2017
77. Ravcheev, D., Thiele, I., ''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 (2017).
76. Aurich, M K., Fleming, R.M.T., Thiele, I., ''A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines'', PLoS Computational Biology, 13(8):e1005698 (2017).
75. Thiele, I., Clancy, C.M., Heinken, A., Fleming, R.M.T., ''Quantitative systems pharmacology and the personalized drug-microbiota-diet axis'', Current Opinion in Systems Biology, 4: 43-52 (2017).
74. Preciat-Gonzalez, G.A., El Assal, L., Noronha, A., Thiele, I., Haraldsdottir, H.S., Fleming, R.M.T., ''Comparative evaluation of atom mapping algorithms for metabolic reactions: application to Recon 3D'', Journal of Cheminformatics, 9:39 (2017).
73. Bauer, E., Zimmermann, J., Baldini, F., Thiele, I., Kaleta, C., ''BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities'', PLoS Computational Biology, 13(5):e1005544 (2017).
72. Ma, D., Yang, L., Fleming, R.M.T., Thiele, I., Palsson, B.O.P., Saunders, M. A., ''Reliable and efficient solution of genome-scale models of metabolism and macromolecular expression'', Scientific Reports, 7:40863 (2017).
71. Haraldsdottir, H.S., Cousins, B., Thiele, I., Fleming, R.M.T., Vempala, S., ''CHRR: Coordinate hit-and-run with rounding for uniform sampling of constraint-based models'', Bioinformatics, 33(11):1741-1743 (2017).
70. Heirendt, L., Thiele, I., Fleming, R.M.T., ''DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia'', Bioinformatics, 33(9):1421-1423 (2017).
69. Rahman, J., Noronha, A., Thiele, I., Rahman, S., ''Leigh Map: A Novel Computational Diagnostic Resource for Mitochondrial Disease'', Annals of Neurology, 81(1):9-16 (2017).
68. Magnusdottir, S., Heinken, A., Kutt, L., Ravcheev, D.A., Bauer, E., Noronha, A., Greenhalgh, K., Jaeger, C., Baginska, J., Wilmes, P., Fleming, R.M.T., Thiele, I., ''Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota'', Nature Biotechnology, 35(1):81-89 (2017).
2016
67. Noronha, A., Danielsdottir, A.D., Gawron, P., Johannsson, F., Jonsdottir, S., Jarlsson, S., Gunnarsson, J.P., Brynjolfsson, S., Schneider, R., Thiele, I., Fleming, R.M.T., ''ReconMap: an interactive visualization of human metabolism'', Bioinformatics, 33(4):605-607 (2016).
66. Beger, D.R., Dunn, W., Schmidt, M.A., Gross, S.S., Kirwan, J.A., Cascante, M., Brennan, L., Wishart, D.S., Oresic, M., Hankemeier, T., Broadhurst, D.I., Lane, A.N., Suhre, K., Kastenmueller, G., Sumner, S.J., Thiele, I., Fiehn, O., Kaddurah-Daouk, R., ''Metabolomics enables precision medicine: A White Paper, Community Perspective'', Metabolomics, 12(10):149 (2016).
65. Dimitrov, D., Thiele, I., Ferguson, L.R.,' 'Editorial: The Human Gutome: Journey of Microbes and Health'', Frontiers in Genetics, 7:158 (2016).
64. Aurich, M.K., Fleming, R.M.T., Thiele, I., ''MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models'', Front Physiol, 7:327 (2016).
63. Fleming, R.M.T., Vlassis, N., Thiele, I., Saunders, M.A., ''Conditions for duality between fluxes and concentrations in biochemical networks'', Journal of Theoretical Biology, pii: S0022-5193(16)30167-9 (2016).
62. Ben Guebila, M., Thiele, I., ''Model-based dietary optimization for late-stage, levodopa-treated Parkinson's disease patients'', Systems Biology and Applications (2016).
61. Aurich, M.K., Thiele, I., ''Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine'', Methods in Molecular Biology, 1386:253-81 (2016).
60. Ravcheev, D.A., Thiele, I., ''Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis'', Frontiers in Microbiology, 7:128 (2016).
2015
59. Bauer, E., Laczny, C.C., Magnusdottir, S., Wilmes, P., Thiele, I., ''Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires'', Microbiome, 3:55 (2015).
58. Heinken, A., Thiele, I., ''Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework'', Gut Microbes, 6 (2), 120-130 (2015).
57. Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A.P., Chang, R.L., Dräger, A., Famili, I., Feist, A.M., Fleming, R.M.T., 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., ''Do genome-scale models need exact solvers or clearer standards?'', Molecular Systems Biology, 11 (10), 831 (2015).
56. Heinken, A., Thiele, I., ''Anoxic conditions promote species-specific mutualism between gut microbes in silico'', Applied Environmental Microbiology, 81 (12), 4049-4061 (2015).
55. Heinken, A., Thiele, I., ''Systems biology of host-microbe metabolomics'', WIREs Systems Biology and Medicine, 7(4), 195-219 (2015).
54. Magnusdottir, S., Ravcheev, D., de Crecy-Lagard, V., Thiele, I., ''Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes'', Frontiers in Genetics, 6 (2015).
2014
53. Ravcheev, D., Thiele, I., ''Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota'', Frontiers in Microbiology, 5 (2014).
52. Sahoo, S., Haraldsdottir, H., Fleming, R.M.T., Thiele, I., ''Modeling the effects of commonly used drugs on human metabolism'', FEBS Journal, 282 (2), 297-317 (2015).
51. Aurich, M.K., Paglia, G., Rolfsson, O., Hrafnsdottir, S., Magnusdottir, M., Stefaniak, M.K., Palsson, B.O., Fleming, R.M.T., Thiele, I., ''Prediction of intracellular metabolic states from extracellular metabolomic data'', Metabolomics, 11 (3), 603-619 (2015).
50. Heinken, A., Khan, M. T., Paglia, G., Rodionov, D. A., Harmsen, H. J. M., Thiele, I., ''A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe'', Journal of Bacteriology, 196(18):3289-302 (2014).
49. Thiele, I. , Vlassis, N., Fleming, R.M.T, ''FASTGAPFILL: Efficient gap filling in metabolic networks'', Bioinformatics, 30(17):2529-31 (2014).
48. Edwards, L.M., Sigurdsson, M.I., Robbins, P.A., Weale, M.E., Cavalleri, G.L., Montgomer, H.E., Thiele, I., ''Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia'', Circ Cardiovasc Genet, 7(4):407-15 (2014).
47. Sahoo, S., Aurich, M.K., Jonsson, J. J., Thiele, I., ''Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease'', Frontiers in Physiology, 5:91(2014).
46. Haraldsdottir, H.S., Thiele, I., Fleming, R.M.T., ''Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2'', Journal of Cheminformatics, 6(2) (2014).
2013
45. Sun, Y., Fleming, R.M.T., Thiele, I., Saunders, M.A., ''Robust flux balance analysis of multiscale biochemical reaction networks'', BMC Bioinformatics, 14:420 (2013).
44. Stobbe, M.D., Swertz, M.A., Thiele, I., Rengaw, T., van Kampen, A.H.C., Moerland, P.D., ''Consensus and conflict cards for metabolic pathway databases'', BMC Systems Biology, 7:50 (2013).
43. Edwards, L.M., Thiele, I., ''Applying systems biology methods to the study of human physiology in extreme environments'', Extreme Physiology and Medicine, 2:8 (2013).
42. Sahoo, S., Thiele, I., ''Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells'', Human Molecular Genetics, 22(13):2705-2722 (2013).
41. Thiele, I., Swainston, N., Fleming, R.M.T., Hoppe, A., Sahoo, S., Aurich, M.K., Haraldsdottir, H., Mo, M.L., Rolfsson, O., Stobbe, M.D., Thorleifsson, S.G., Agren, R., Boelling, 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 Novere, N., Malys, N., Mazein, A., Papin, J.A., Price, N.D., Selkov Sr., E, Sigurdsson, M.I., Simeonidis, E., Sonnenschein, N., Smallbone, K., Sorokin, A., van Beek, J.H.G.M., Weichart, D., Goryanin, I., Nielsen, J., Westerhoff, H.V., Kell, D.B., Mendes, P., Palsson, B.O., ''A community-driven global reconstruction of human metabolism'', Nature Biotechnology, 31(5):419-25 (2013).
40. Nogales, J., Gudmundsson, S., Thiele, I., ''Towards systems metabolic engineering in cyanobacteria: Opportunities and bottlenecks'', Bioengineered, 4(3):1-6 (2013).
39. Rolfsson, O., Paglia, G., Magnusdottir, M., Palsson, B.O., Thiele, I., ''Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity'', Biochemical Journal, 449(2):427-35 (2013).
38. Heinken, A., Sahoo, S., Fleming, R.M.T., Thiele, I., ''Systems-level characterization of the host-microbe metabolic symbiosis in the mammalian gut.'', Gut Microbes, 4(1):1-13 (2013).
37. Thiele, I., Heinken, A., Fleming, R.M.T. ''A systems biology approach to studying the role of microbes in human health'', Current Opinions in Biotechnology, 24(1):4-12 (2013).
2012
36. Aurich, M.K., Thiele, I., ''Contextualization procedure and modeling of monocyte specific TLR signaling'', PLoS ONE, 7(12): e49978 (2012).
35. Thiele, I., Fleming, R.M.T., Que, R., Bordbar, A., Diep, D., Palsson, B.O., ''Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage'', PLoS One, 7(9):e45635 (2012).
34. Fleming, R.M.T., Thiele, I., ''Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration'', Journal of Theoretical Biology, 314:173-181 (2012).
33. Nogales, J., Gudmunsson'An in silico re-design of the metabolism in \emph{Thermotoga , S., Thiele, I., 'maritima for increased biohydrogen production'', International Journal of Hydrogen Energy, 37(17), 12205-12218 (2012).
32. Sahoo, S., Franzson, L., Jonsson, J.J., Thiele, I., ''A compendium of inborn errors of metabolism mapped onto the human metabolic network.'', Molecular BioSystems, 8 (10), 2545 - 2558 (2012).
31. Paglia, G., Magnusdottir, M., Thorlacius, S., Sigurjonsson, O.E., Gudmundsson, S., Palsson, B.O., Thiele, I., ''Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies.'', J Chromatogr B Analyt Technol Biomed Life Sci, 898:111-20 (2012).
30. Sigurdsson, G., Fleming, R.M.T., Heinken, A., Thiele, I.,"A systems biology approach to drug targets in Pseudomonas aeruginosa Biofilm'', PLoS One, 7(4): e34337 (2012).
29. Haraldsdottir, H., Thiele, I., Fleming, R.M.T., ''Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction: Recon 1'', Biophysical Journal, 102(8):1703-1711 (2012).
28. Nogales, J., Gudmunsson, S., Knight, E.M., Palsson, B.O., Thiele, I., ''Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.'', PNAS, 109(7):2678-83 (2012).
27. Paglia, G., Hrafnsdottir, S., Magnusdottir, M., Fleming, R.M.T., Thorlacius, S., Palsson, B.O., Thiele, I., ''Monitoring metabolites consumption and secretion in cultured cells using Ultra Performance Liquid Chromatography Quadrupole-Time of Flight Mass Spectrometry (UPLC-Q-ToF-MS)'', Anal Bioanal Chem, 402(3):1183-98 (2012).
2011
26. Rolfsson, O., Palsson, B.O., Thiele, I., "The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions", BMC Systems Biology, 5:155. (2011).
25. Thorleifsson, S.G., Thiele, I.,, ''rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks'', Bioinformatics, 27(14):2009-10 (2011).
24. Schellenberger, J., Que, R., Fleming, R.M.T., Thiele, I., Orth, J.D., Feist, A.M., Zielinski, D.C., Bordbar, A., Lewis, N.E.R., Kang, J., Hydruke, D., Palsson, B.O., ''Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.'' Nature Protocols, 6, 1290-1307 (2011).
23. Thiele, I., Hyduke, D.R., Steeb, B., Fankam, G., Allen, D.K., Bazzani, S., Charusanti, P., Chen, F.C., Fleming, R.M.T., Hsiung, C.A., De Keersmaecker, S.C., 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., , D., ''A community effort towards a knowledge-base, mathematical model of the human pathogen Salmonella typhimurium LT2'', BMC Systems Biology, 5:8 (2011). Bumann
22. Fleming, R.M.T., Thiele, I., ''von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models'', Bioinformatics, 27(1):142-3 (2011).
2010
21. Sigurdsson, M.I., Jamshidi, J., Steingrimsson, E., Thiele, I., Palsson, B.O., ''A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1'', BMC Systems Biology, 4:140 (2010).
20. Gudmunsson, S., Thiele, I., ''Computationally efficient flux variability analysis'', BMC Bioinformatics, 11:489 (2010).
Integrated stoichiometric, thermodynamic and kinetic 19. Fleming, R.M.T, Thiele, I., Provan, G., Nasheuer, H.P., '''', Journal of Theoretical Biology, 264 (3): 683-692 (2010). modelling of steady state metabolism
18. Orth, J., Thiele, I. and Palsson, B.O., ''What is flux balance analysis?'', Nature Biotechnology, 28(3):245-8 (2010).
17. Thiele, I. , Palsson, B.O., ''Reconstruction annotation jamborees: A community-approach to Systems Biology'', Molecular Systems Biology, 6:361 (2010).
16. Thiele, I., Fleming, M.T., Bordbar, A., Palsson, B.O., ''Functional characterization of multiple equivalent states of Escherichia coli 's transcriptional and translational machinery.'', Biophysical Journal, 98(10): 2072-2081 (2010).
15. Thiele, I. , Palsson, B.O., ''A protocol for generating a high-quality genome-scale metabolic reconstruction.'', Nature Protocols, 5(1): 93 - 121 (2010).
2009
14. Fleming, R.M.T., Thiele, I., Nasheuer, H.P. ''Quantitative assignment of reaction directionality in constraint-based models of metabolism.'', Biophysical Chemistry, 145(2-3):47-56 (2009).
13. 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.O., Osterman, A., Godzik, A., ''Three-dimensional structural view of the central metabolic network of Thermotoga maritima.'', Science, 325(5947):1544-9 (2009). Faculty of 1000, Biology, Highlighted in Nature.
12. Manichaikul, A., Ghamsari, L., Hom, E.F.Y., Lin, C., Murray, R.R, Chang, R.L., Hao, T., Shen, Y., Chavali, A.K., Thiele, I., Yang, X., Mello, E., Hill, D.E., Vidal, M. Salehi-Ashtiani, K., Papin, J.A., ''Metabolic network analysis integrated with genome-wide transcript verification'', Nature Methods, 6: 589 - 592 (2009).
11. Feist, A.M., Herrgard, M., Thiele, I., Reed, J.L., Palsson, B.O. ''Reconstruction of biochemical networks in microbial organisms.'', Nature Reviews Microbiology, 7(2) (2009).
10. Thiele, I., Jamshidi, N., Fleming, R.M.T., Palsson, B.O.'' Genome-Scale reconstruction of the transcriptional and translational machinery in Escherichia coli: A knowledge-base, its mathematical formulation, and its functional characterization.'' PLoS Comput Biol, 5(3): e1000312 (2009).
9. Li, F., Thiele, I., Jamshidi, N., Palsson, B.O. ''Functional assessment of the TLR receptor network.'' PLoS Computational Biology, 5:e1000292(2009).
2008
8. Nogales, J., Palsson, B.O., Thiele, I. ''A genome-scale metabolic reconstruction for Pseudomonas putida KT2440: iJN746 as cell factory.'', BMC Systems Biology, 2:79 (2008).
2007
7. Yeung, M., Thiele, I., Palsson, B.O., ''Estimation of the number of extreme pathways for metabolic networks.'', BMC Bioinformatics, 8:363 (2007).
6. Duarte, N.C., Becker, S.A., Jamshidi, N., Thiele, I., Mo, M.L., Vo, T.D., Srivas, R., Palsson, B.O. ''Global reconstruction of the human metabolic network based on genomic and bibliomic data.'', PNAS, 104(6):1777-82 (2007).
2006
5. Price, N.D., Thiele, I., Palsson, B.O., ''Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of ''loop law'' thermodynamic constraints.'', Biophysical Journal, 90(11): 3919-28 (2006).
4. Reed, J.L., Famili, I., Thiele, I., Palsson, B.O., ''Towards multidimensional genome annotation.'', Nature Reviews Genetics, 7: 130-141 (2006).
2005
3. 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., e, B., McHardy, A.C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Ostermann, A., Portnoy, V., Pusch, G.D., Rodionov, D.A., Ruckert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Y., Zagnitko, O., and Vonstein, V., ''The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.'', Nucleic Acids Research, 33(17):5691-5702 (2005).
2. Thiele, I., Vo, T.D., Price, N.D. and Palsson, B.O., ''An 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): 5818-5830 (2005).
1. Thiele, I., Price, N.D., Vo, T.D. and Palsson, B.O., ''Candidate metabolic network states in human mitochondria: Impact of diabetes, ischemia, and diet.'', Journal of Biological Chemistry, 280(12):11683-11695 (2005).