Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome

Autor: Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike K Aurich, Ronan MT Fleming

Publikováno v: Molecular Systems Biology, Vol 16, Iss 5, Pp 1-24 (2020)

Abstract Comprehensive molecular‐level models of human metabolism have been generated on a cellular level. However, models of whole‐body metabolism have not been established as they require new methodological approaches to integrate molecular and

Externí odkaz: https://doaj.org/article/a552db6e045340a5a96cd800271a386b

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome

Autor: Ronan M. T. Fleming, Maike K. Aurich, Almut Heinken, Ines Thiele, Laurent Heirendt, Johannes Hertel, Swagatika Sahoo

Publikováno v: Molecular Systems Biology, Vol 16, Iss 5, Pp n/a-n/a (2020)
Molecular Systems Biology, 16(5), e8982. WILEY
Molecular Systems Biology

Comprehensive molecular‐level models of human metabolism have been generated on a cellular level. However, models of whole‐body metabolism have not been established as they require new methodological approaches to integrate molecular and physiolo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c16363c42b2c5ae7ada249c7e089c6d2
https://doi.org/10.15252/msb.20198982

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Autor: Santosh Vempala, Jennifer Modamio, Alejandro Maass, Costas D. Maranas, Sylvain Arreckx, Masoud Ahookhosh, Miguel A.P. Oliveira, Stefania Magnusdottir, Nathan E. Lewis, Chiam Yu Ng, Aarash Bordbar, Bernhard O. Palsson, Inna Kuperstein, Lemmer P. El Assal, Lin Wang, Benjamin Cousins, German Preciat, Sarah M. Keating, Egils Stalidzans, Iñigo Apaolaza, Nicolas Sompairac, William A. Bryant, Vanja Vlasov, Phan Tu Vuong, Siu Hung Joshua Chan, Andrejs Kostromins, Laurent Heirendt, Yuekai Sun, Sebastián N. Mendoza, Ronan M. T. Fleming, Francisco J. Aragón Artacho, Michael Hucka, Hulda S. Haraldsdóttir, Jacek Wachowiak, Susan Ghaderi, Marouen Ben Guebila, Almut Heinken, Ines Thiele, Hoai M. Le, Thomas Sauter, James T. Yurkovich, Alise Žagare, Diana C. El Assal, Maike K. Aurich, H. Scott Hinton, Alberto Noronha, Catherine M. Clancy, Thomas Pfau, Andrei Zinovyev, Michael A. Saunders, Luis Vitores Valcárcel, John T. Sauls, Anne Richelle, Ding Ma, Francisco J. Planes

Publikováno v: Nature Protocols
Nature Protocols, Nature Publishing Group, 2019, 14 (3), pp.639-702. ⟨10.1038/s41596-018-0098-2⟩
Nature Protocols, 14(3), 639-702. Nature Publishing Group
RUA. Repositorio Institucional de la Universidad de Alicante
Universidad de Alicante (UA)
Nature protocols, vol 14, iss 3
Heirendt, L, Arreckx, S, Pfau, T, Mendoza, S N, Richelle, A, Heinken, A, Haraldsdóttir, H S, Wachowiak, J, Keating, S M, Vlasov, V, Magnusdóttir, S, Ng, C Y, Preciat, G, Žagare, A, Chan, S H J, Aurich, M K, Clancy, C M, Modamio, J, Sauls, J T, Noronha, A, Bordbar, A, Cousins, B, El Assal, D C, Valcarcel, L V, Apaolaza, I, Ghaderi, S, Ahookhosh, M, Ben Guebila, M, Kostromins, A, Sompairac, N, Le, H M, Ma, D, Sun, Y, Wang, L, Yurkovich, J T, Oliveira, M A P, Vuong, P T, El Assal, L P, Kuperstein, I, Zinovyev, A, Hinton, H S, Bryant, W A, Aragón Artacho, F J, Planes, F J, Stalidzans, E, Maass, A, Vempala, S, Hucka, M, Saunders, M A, Maranas, C D, Lewis, N E, Sauter, T, Palsson, B, Thiele, I & Fleming, R M T 2019, ' Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 ', Nature Protocols, vol. 14, no. 3, pp. 639-702 . https://doi.org/10.1038/s41596-018-0098-2
Heirendt, L, Arreckx, S, Pfau, T, Mendoza, S N, Richelle, A, Heinken, A, 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, Noronha, A, Bordbar, A, Cousins, B, El Assal, D C, Valcarcel, L V, Apaolaza, I, Ghaderi, S, Ahookhosh, M, Ben Guebila, M, Kostromins, A, Sompairac, N, Le, H M, Ma, D, Sun, Y, Wang, L, Yurkovich, J T, Oliveira, M A P, Vuong, P T, El Assal, L P, Kuperstein, I, Zinovyev, A, Hinton, H S, Bryant, W A, Aragon Artacho, F J, Planes, F J, Stalidzans, E, Maass, 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 2019, ' Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 ', Nature Protocols, vol. 14, no. 3, pp. 639-702 . https://doi.org/10.1038/s41596-018-0098-2

Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenot

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b74785501fe1d16bceba71588b87c863
https://hal.archives-ouvertes.fr/hal-03211136

Recon3D enables a three-dimensional view of gene variation in human metabolism

Autor: Daniel C. Zielinski, Maike K. Aurich, Ali Altunkaya, German Andres Preciat Gonzalez, Bernhard O. Palsson, Stephen K. Burley, Alberto Noronha, Francesco Gatto, Jens Nielsen, Peter W. Rose, Almut Heinken, Anna Dröfn Daníelsdóttir, Andreas Dräger, Ines Thiele, Andreas Prlić, Swagatika Sahoo, Elizabeth Brunk, Anand V. Sastry, Ronan M. T. Fleming, Nathan Mih, Avlant Nilsson

Publikováno v: Brunk, E, Sahoo, S, Zielinski, D C, Altunkaya, A, Dräger, A, Mih, N, Gatto, F, Nilsson, A, Preciat Gonzalez, G A, 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 2018, ' Recon3D enables a three-dimensional view of gene variation in human metabolism ', Nature Biotechnology, vol. 36, no. 3, pp. 272-281 . https://doi.org/10.1038/nbt.4072
Nature Biotechnology
Nature biotechnology, vol 36, iss 3

Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6d047f71d10401e1033fbefa70ae82d1
https://orbit.dtu.dk/en/publications/ff31b1fb-e412-4280-9737-c3673a9ee05e

Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine

Autor: Ines Thiele, Maike K. Aurich

Publikováno v: Methods in Molecular Biology ISBN: 9781493932825

Modern high-throughput techniques offer immense opportunities to investigate whole-systems behavior, such as those underlying human diseases. However, the complexity of the data presents challenges in interpretation, and new avenues are needed to add

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::6412633ee728b0924f6e9dc07bb3d37b
https://doi.org/10.1007/978-1-4939-3283-2_12