Combinatorial, additive and dose-dependent drug-microbiome associations

Autor: Forslund, SK, Chakaroun, R, Zimmermann-Kogadeeva, M, Markó, L, Aron-Wisnewsky, J, Nielsen, T, Moitinho-Silva, L, Schmidt, TSB, Falony, G, Vieira-Silva, S, Adriouch, S, Alves, RJ, Assmann, K, Bastard, J-P, Birkner, T, Caesar, R, Chilloux, J, Coelho, LP, Fezeu, L, Galleron, N, Helft, G, Isnard, R, Ji, B, Kuhn, M, Le Chatelier, E, Myridakis, A, Olsson, L, Pons, N, Prifti, E, Quinquis, B, Roume, H, Salem, J-E, Sokolovska, N, Tremaroli, V, Valles-Colomer, M, Lewinter, C, Søndertoft, NB, Pedersen, HK, Hansen, TH, Amouyal, C, Andersson Galijatovic, EA, Andreelli, F, Barthelemy, O, Batisse, J-P, Belda, E, Berland, M, Bittar, R, Blottière, H, Bosquet, F, Boubrit, R, Bourron, O, Camus, M, Cassuto, D, Ciangura, C, Collet, J-P, Dao, M-C, Djebbar, M, Doré, A, Engelbrechtsen, L, Fellahi, S, Fromentin, S, Galan, P, Gauguier, D, Giral, P, Hartemann, A, Hartmann, B, Holst, JJ, Hornbak, M, Hoyles, L, Hulot, J-S, Jaqueminet, S, Jørgensen, NR, Julienne, H, Justesen, J, Kammer, J, Krarup, N, Kerneis, M, Khemis, J, Kozlowski, R, Lejard, V, Levenez, F, Lucas-Martini, L, Massey, R, Martinez-Gili, L, Maziers, N, Medina-Stamminger, J, Montalescot, G, Moute, S, Neves, AL, Olanipekun, M, Le Pavin, LP, Poitou, C, Pousset, F, Pouzoulet, L, Rodriguez-Martinez, A, Rouault, C, Silvain, J, Svendstrup, M, Swartz, T, Vanduyvenboden, T, Vatier, C, Walther, S, Gøtze, JP, Køber, L, Vestergaard, H, Hansen, T, Zucker, J-D, Hercberg, S, Oppert, J-M, Letunic, I, Nielsen, J, Bäckhed, F, Ehrlich, SD, Dumas, M-E, Raes, J, Pedersen, O, Clément, K, Stumvoll, M, Bork, P, The MetaCardis Consortium (Hoyles, L.)

Publikováno v: Nature
Nature, 2021, 600 (7889), pp.500-505. ⟨10.1038/s41586-021-04177-9⟩

During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery1-5. Here, through integrated mu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d63d45a4e7d6e8c270f49c7d2bf0ce1
http://edoc.mdc-berlin.de/21160/1/21160oa.pdf

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

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Publikováno v: Brown, P & Zhou, Y 2019, ' Large expert-curated database for benchmarking document similarity detection in biomedical literature search ', Database . https://doi.org/10.1093/database/baz085
BASE-Bielefeld Academic Search Engine
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
Database-The Journal of Biological Databases and Curation
r-FISABIO: Repositorio Institucional de Producción Científica
Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)
Database, 2019:baz085. Oxford University Press
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search ', Database: The Journal of Biological Databases and Curation, vol. 2019, baz085 . https://doi.org/10.1093/database/baz085
Repositorio EdocUR-U. Rosario
Universidad del Rosario
instacron:Universidad del Rosario
Brown, P, RELISH Consortium & Zhou, Y 2019, ' Large expert-curated database for benchmarking document similarity detection in biomedical literature search ', Database: The Journal of Biological Databases and Curation, vol. 2019, baz085 . https://doi.org/10.1093/database/baz085
Brown, P, RELISH Consortium & Zhou, Y 2019, ' Large expert-curated database for benchmarking document similarity detection in biomedical literature search ', Database, vol. 2019, 085, pp. 1-67 . https://doi.org/10.1093/database/baz085
r-FISABIO. Repositorio Institucional de Producción Científica
instname
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Database
Database (Oxford)
Database: The Journal of Biological Databases and Curation
Web of Science
Repositório Institucional da UNESP
Universidade Estadual Paulista (UNESP)
instacron:UNESP
Database-the Journal Of Biological Databases And Curation (1758-0463) (Oxford Univ Press), 2019-10, Vol. 2019, P. baz085 (66p.)

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http://hdl.handle.net/11573/1331892

A catalog of small proteins from the global microbiome.

Autor: Duan Y; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China., Santos-Júnior CD; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.; Laboratory of Microbial Processes & Biodiversity - LMPB; Department of Hydrobiology, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo, Brazil., Schmidt TS; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.; APC Microbiome and School of Medicine, University College Cork, Cork, Ireland., Fullam A; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany., de Almeida BLS; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China., Zhu C; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China., Kuhn M; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany., Zhao XM; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.; Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.; Lingang Laboratory, Shanghai, 200031, China. xmzhao@fudan.edu.cn.; State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn., Bork P; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.; Max Delbrück Centre for Molecular Medicine, Berlin, Germany.; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany., Coelho LP; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China. luispedro@big-data-biology.org.; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD, Australia. luispedro@big-data-biology.org.; Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia. luispedro@big-data-biology.org.

Publikováno v: Nature communications [Nat Commun] 2024 Aug 31; Vol. 15 (1), pp. 7563. Date of Electronic Publication: 2024 Aug 31.

Discovery of antimicrobial peptides in the global microbiome with machine learning.

Autor: Santos-Júnior CD; Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Laboratory of Microbial Processes & Biodiversity - LMPB, Department of Hydrobiology, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo 13565-905, Brazil., Torres MDT; Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA., Duan Y; Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China., Rodríguez Del Río Á; Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223 Madrid, Spain., Schmidt TSB; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; APC Microbiome & School of Medicine, University College Cork, Cork, Ireland., Chong H; Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China., Fullam A; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany., Kuhn M; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany., Zhu C; Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China., Houseman A; Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China., Somborski J; Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China., Vines A; Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China., Zhao XM; Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China; State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China., Bork P; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Max Delbrück Centre for Molecular Medicine, Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany., Huerta-Cepas J; Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223 Madrid, Spain., de la Fuente-Nunez C; Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA. Electronic address: cfuente@upenn.edu., Coelho LP; Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD, Australia. Electronic address: luispedro@big-data-biology.org.

Publikováno v: Cell [Cell] 2024 Jul 11; Vol. 187 (14), pp. 3761-3778.e16. Date of Electronic Publication: 2024 Jun 05.

A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer.

Autor: Dmitrijeva M; Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Zurich, Switzerland.; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland., Tackmann J; Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Zurich, Switzerland., Matias Rodrigues JF; Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Zurich, Switzerland., Huerta-Cepas J; Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Madrid, Spain., Coelho LP; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China. luispedro@big-data-biology.org.; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia. luispedro@big-data-biology.org., von Mering C; Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Zurich, Switzerland. mering@mls.uzh.ch.

Publikováno v: Nature ecology & evolution [Nat Ecol Evol] 2024 May; Vol. 8 (5), pp. 986-998. Date of Electronic Publication: 2024 Mar 05.