Community-led, integrated, reproducible multi-omics with anvi’o
| Type | Article | ||||||||||||
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| Date | 2021-01 | ||||||||||||
| Language | English | ||||||||||||
| Author(s) | Eren A. Murat 1, 2, 3, 4, Kiefl Evan1, 4, Shaiber Alon1, 4, Veseli Iva1, 4, Miller Samuel E.1, Schechter Matthew S.1, 2, Fink Isaac1, Pan Jessica N.1, Yousef Mahmoud1, Fogarty Emily C.1, 2, Trigodet Florian1, Watson Andrea R.1, 2, Esen Özcan C.1, Moore Ryan M.4, Clayssen Quentin5, Lee Michael D.6, 7, Kivenson Veronika8, Graham Elaina D.9, Merrill Bryan D.10, Karkman Antti11, Blankenberg Daniel12, 13, Eppley John M.14, Sjödin Andreas15, Scott Jarrod J.16, Vázquez-Campos Xabier17, McKay Luke J.18, 19, McDaniel Elizabeth A.20, Stevens Sarah L. R.21, 22, Anderson Rika E.23, Fuessel Jessika1, 24, Fernandez-Guerra Antonio25, Maignien Lois2, 26, Delmont Tom O.27, Willis Amy D.28 |
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| Affiliation(s) | 1 : Department of Medicine, University of Chicago, Chicago, IL, USA 2 : Committee on Microbiology, University of Chicago, Chicago, IL, USA 3 : Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA 4 : Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA 5 : Center for Bioinformatics and Computational Biology, University of Delaware, Delaware, DE, USA 6 : Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland 7 : Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA 8 : Blue Marble Space Institute of Science, Seattle, WA, USA 9 : Department of Microbiology, Oregon State University, Corvallis, OR, USA 10 : Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA 11 : Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA 12 : Department of Microbiology, University of Helsinki, Helsinki, Finland 13 : Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA 14 : Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA 15 : Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai’i at Mānoa, Honolulu, HI, USA 16 : Division of CBRN Security and Defence, Swedish Defence Research Agency - FOI, Umea, Sweden 17 : Smithsonian Tropical Research Institute, Bocas del Toro, Republic of Panama 18 : NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia 19 : Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA 20 : Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA 21 : Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, USA 22 : Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, WI, USA 23 : American Family Insurance Data Science Institute, University of Wisconsin–Madison, Madison, WI, USA 24 : Department of Biology, Carleton College, Northfield, MN, USA 25 : Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, Copenhagen, Denmark 26 : Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Univ. Brest, CNRS, IFREMER, Plouzané, France 27 : Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris–Saclay, Evry, France 28 : Department of Biostatistics, University of Washington, Seattle, WA, USA |
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| Source | Nature Microbiology (2058-5276) (Springer Science and Business Media LLC), 2021-01 , Vol. 6 , N. 1 , P. 3-6 | ||||||||||||
| DOI | 10.1038/s41564-020-00834-3 | ||||||||||||
| WOS© Times Cited | 138 | ||||||||||||
| Abstract | Big data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi’o was first published, this community-led multi-omics platform is maturing into an open software ecosystem that reduces constraints in ‘omics data analyses. |
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