Community-led, integrated, reproducible multi-omics with anvi’o,Nature Microbiology

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Community-led, integrated, reproducible multi-omics with anvi’o
Nature Microbiology ( IF 20.5 ) Pub Date : 2020-12-21 , DOI: 10.1038/s41564-020-00834-3
A Murat Eren _{1,

2,

3,

4} , Evan Kiefl _{1,

4} , Alon Shaiber _{1,

4} , Iva Veseli _{1,

4} , Samuel E Miller ₁ , Matthew S Schechter _{1,

2} , Isaac Fink ₁ , Jessica N Pan ₁ , Mahmoud Yousef ₁ , Emily C Fogarty _{1,

2} , Florian Trigodet ₁ , Andrea R Watson _{1,

2} , Özcan C Esen ₁ , Ryan M Moore ₅ , Quentin Clayssen ₆ , Michael D Lee _{7,

8} , Veronika Kivenson ₉ , Elaina D Graham ₁₀ , Bryan D Merrill ₁₁ , Antti Karkman ₁₂ , Daniel Blankenberg _{13,

14} , John M Eppley ₁₅ , Andreas Sjödin ₁₆ , Jarrod J Scott ₁₇ , Xabier Vázquez-Campos ₁₈ , Luke J McKay _{19,

20} , Elizabeth A McDaniel ₂₁ , Sarah L R Stevens _{22,

23} , Rika E Anderson ₂₄ , Jessika Fuessel ₁ , Antonio Fernandez-Guerra ₂₅ , Lois Maignien _{3,

26} , Tom O Delmont ₂₇ , Amy D Willis ₂₈

Affiliation

Department of Medicine, University of Chicago, Chicago, IL, USA.
Committee on Microbiology, University of Chicago, Chicago, IL, USA.
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA.
Center for Bioinformatics and Computational Biology, University of Delaware, Delaware, DE, USA.
Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA.
Blue Marble Space Institute of Science, Seattle, WA, USA.
Department of Microbiology, Oregon State University, Corvallis, OR, USA.
Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Microbiology, University of Helsinki, Helsinki, Finland.
Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA.
Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA.
Division of CBRN Security and Defence, Swedish Defence Research Agency - FOI, Umea, Sweden.
Smithsonian Tropical Research Institute, Bocas del Toro, Republic of Panama.
NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia.
Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.
American Family Insurance Data Science Institute, University of Wisconsin-Madison, Madison, WI, USA.
Department of Biology, Carleton College, Northfield, MN, USA.
Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, Copenhagen, Denmark.
Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Univ. Brest, CNRS, IFREMER, Plouzané, France.
Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France.
Department of Biostatistics, University of Washington, Seattle, WA, USA.

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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