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Recon Publications

Submitted publications:

"Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism", Preciat, G., Wegrzyn, A.B., Lucumi Moreno, E., Willacey, C. C.W., Modamio, J., Monteiro, F.L., El Assal, D., Schurink, A., Oliveira, M.A.P., Zhang, Z., Cousins,B., Haraldsdóttir, H.S., Hachi, S., Zach, S., Leparc, G., Lee, Y.T.,  Hengerer,  B., Vempala, S., Saunders,  M.A., Harms, A., Glaab, E.,  Schwamborn, J.C.,  Thiele, I.,  Hankemeier, T., Fleming, R.M.T., (submitted)

Peer-reviewed publications:

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).
2018
"Recon3D enables a three-dimensional view of gene variation in human metabolism", 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., Nature Biotechnology, 36(3), 272-281 (2018). 
2017
"Comparative evaluation of atom mapping algorithms for metabolic reactions: application to Recon 3D", Preciat-Gonzalez, G.A., El Assal, L., Noronha, A., Thiele, I., Haraldsdottir, H.S., Fleming, R.M.T., Journal of Cheminformatics, 9:39 (2017).  
2016
"ReconMap: an interactive visualization of human metabolism", 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., Bioinformatics, 33(4):605-607 (2016). 
2015
"Modeling the effects of commonly used drugs on human metabolism", Sahoo, S., Haraldsdottir, H., Fleming, R.M.T., Thiele, I., FEBS Journal, 282 (2), 297-317 (2015). 
2014
2015
"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).  
2013
"A community-driven global reconstruction of human metabolism", 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., Nature Biotechnology, 31(5):419-25 (2013).
2012
2020
"Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction: Recon 1", Haraldsdottir, H., Thiele, I., Fleming, R.M.T., Biophysical Journal, 102(8):1703-1711 (2012).
2018
2017
2016
2007
2011
"The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions", Rolfsson, O., Palsson, B.O., Thiele, I., BMC Systems Biology, 5:155. (2011).
2010
"A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1", Sigurdsson, M.I., Jamshidi, J., Steingrimsson, E., Thiele, I., Palsson, B.O., BMC Systems Biology, 4:140 (2010). 
2007
"Global reconstruction of the human metabolic network based on genomic and bibliomic data.", Duarte, N.C., Becker, S.A., Jamshidi, N., Thiele, I., Mo, M.L., Vo, T.D., Srivas, R., Palsson, B.O., PNAS, 104(6):1777-82 (2007).
2014
2013
2012
2011
2010
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