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Software and Toolbox Publications

Submitted publications:

"ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software", Heirendt, L., Arreckx, S., Trefois, C., Yarosz, Y., Vyas, M., Satagopam, V.P., Schneider, R., Thiele, I., Fleming, R.M.T., arXiv:1712.05236 [cs.SE] (submitted). 

Peer-reviewed publications:

2023
2022
2021
2020
2019
2018
2022
2023
2020
2021
2017
2019
"A toolbox of machine learning software to support microbiome analysis", Zambrano, L.J.M., et al., Front. Microbiol., 14 (2023). 
"MetaboAnnotator: An efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions", Thiele, I., Preciat, G., Fleming, R.M.T., Bioinformatics, btac596 (2022).
"Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine", Heinken, A., Basile, A., Hertel. J., Thinnes, C., Thiele, I., Annual Review of Microbiology, 75 (2021).
"Advances in constraint-based modelling of microbial communities.", Heinken, A., Basile, A., Thiele, I., Current Opinion in Systems Biology, 27: 100346 (2021).
"Cardinality optimisation in constraint-based modelling: Application to human metabolism", Fleming, R.M.T., Haraldsdottir, H.S., Le, H.M., Vuong, P.T., Hankemeier, T., Thiele, I., Bioinformatics, 39 (9), btad450 (2023).
"Microbiome Modelling Toolbox 2.0: Efficient, tractable modelling of microbiome communities", Heinken, A., Thiele, I., Bioinformatics, btac082 (2022).
"MEMOTE for standardized genome-scale metabolic model testing", C. Lieven, M.E. Beber, B.G. Olivier, F.T. Bergmann, M. Ataman, P. Babaei, L.M. Blank, S. Chauhan, K. Correia, C. Diener, A, Drager, B.E. Ebert, J.N. Edirisinghe, J.P. Faria, A.M. Feist, G. Fengos, R.M.T. Fleming, B. Garcia-Jimenez, V. Hatzimanikatis, Wout Van Helvoirt, C. S. Henry, H. Hermjakob, M. J. Herrgård, A. Kaafarani, H. U. Kim, Z. King, S. Klamt, E. Klipp, J. J. Koehorst, M. König, M. Lakshmanan, D.Y. Lee, S. Y. Lee, S. Lee, N. E. Lewis, F. Liu, H. Ma, D. Machado, R. Mahadevan, P. Maia, A. Mardinoglu, G. L. Medlock, J. M. Monk, J. Nielsen, L. K. Nielsen, J. Nogales, I. Nookaew, B. O. Palsson, J. A. Papin, K. R. Patil, M. Poolman, N. D. Price, O. Resendis-Antonio, A. Richelle, I. Rocha, B. J. Sánchez, P. J. Schaap, R. S. M. Sheriff, S. Shoaie, N. Sonnenschein, B. Teusink, P. Vilaça, J. O. Vik, J. A.H. Wodke, J. C. Xavier, Q. Yuan, M. Zakhartsev, C. Zhang,  Nature biotechnology 38 (3), 272-276, (2020)
"Personalized whole-body models integrate metabolism, physiology, and the gut microbiome", Thiele, I., Sahoo, S., Heinken, A., Hertel, J., Heirendt, L., Aurich, M.K., Fleming, R.M.T., , Molecular Systems Biology, 16:e8982 (2020).
"Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0", 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., Nature Protocol, 14, 639-702 (2019). 
"The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities", Baldini, F., Heinken, A., Heirendt, L., Magnusdottir, S., Fleming, R.M.T., Thiele, I., Bioinformatics, bty941 (2018). 
"From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota.", Bauer, E., Thiele, I., mSystems, 36, 272-281 (2018).
"Modeling metabolism of the human gut microbiome", Magnusdottir, S., Thiele, I., Current Opinion in Biotechnology, 51, 90-96 (2018).  
2017
"Quantitative systems pharmacology and the personalized drug-microbiota-diet axis", Thiele, I., Clancy, C.M., Heinken, A., Fleming, R.M.T., Current Opinion in Systems Biology, 4: 43-52 (2017).
"CHRR: Coordinate hit-and-run with rounding for uniform sampling of constraint-based models", Haraldsdottir, H.S., Cousins, B., Thiele, I., Fleming, R.M.T., Vempala, S., Bioinformatics, 33(11):1741-1743 (2017). 
2016
"MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models", Aurich, M.K., Fleming, R.M.T., Thiele, I., Front Physiol, 7:327 (2016). 
2015
"Do genome-scale models need exact solvers or clearer standards?", 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., HerrgÃ¥rd, 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., Molecular Systems Biology, 11 (10), 831 (2015). 
"FASTGAPFILL: Efficient gap filling in metabolic networks", Thiele, I. , Vlassis, N., Fleming, R.M.T, Bioinformatics, 30(17):2529-31 (2014).  
2014
"Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2", Haraldsdottir, H.S., Thiele, I., Fleming, R.M.T., Journal of Cheminformatics, 6(2) (2014).  
2011
"rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks", Thorleifsson, S.G., Thiele, I., Bioinformatics, 27(14):2009-10 (2011).
"Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.", 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., Nature Protocols, 6, 1290-1307 (2011).
"von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models", Fleming, R.M.T., Thiele, I., Bioinformatics, 27(1):142-3 (2011).
2018
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2016
2015
2014
2011

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