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ArticlesPeer ReviewedFull Text
RESCRIPt: Reproducible sequence taxonomy reference database management
Author / Creator:Robeson, Michael S. ; O’Rourke, Devon R. ; Kaehler, Benjamin D. ; Ziemski, Michal ; Dillon, Matthew R. ; Foster, Jeffrey T. ; Bokulich, Nicholas A.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2021-11, Vol.17 (11), p.e1009581
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Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate
Author / Creator:Bokulich, Nicholas A. ; Thorngate, John H. ; Richardson, Paul M. ; Mills, David A.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2014-01, Vol.111 (1), p.E139-E148
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ArticlesPeer ReviewedFull Text
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
Author / Creator:Bokulich, Nicholas A. ; Kaehler, Benjamin D. ; Rideout, Jai Ram ; Dillon, Matthew ; Bolyen, Evan ; Knight, Rob ; Huttley, Gavin A. ; Gregory Caporaso, J.
Publisher:England: BioMed Central Ltd
Journal title:Microbiome, 2018-05, Vol.6 (1), p.90-17, Article 90
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ArticlesPeer ReviewedFull Text
Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment
Author / Creator:Bokulich, Nicholas A. ; Łaniewski, Paweł ; Adamov, Anja ; Chase, Dana M. ; Caporaso, J. Gregory ; Herbst-Kralovetz, Melissa M.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2022-02, Vol.18 (2), p.e1009876
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Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer
Author / Creator:Dominguez-Bello, Maria G ; De Jesus-Laboy, Kassandra M ; Shen, Nan ; Cox, Laura M ; Amir, Amnon ; Gonzalez, Antonio ; Bokulich, Nicholas A ; Song, Se Jin ; Hoashi, Marina ; Rivera-Vinas, Juana I ; Mendez, Keimari ; Knight, Rob ; Clemente, Jose C
Publisher:New York: Nature Publishing Group US
Journal title:Nature medicine, 2016-03, Vol.22 (3), p.250-253
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ArticlesPeer ReviewedFull Text
Species abundance information improves sequence taxonomy classification accuracy
Author / Creator:Kaehler, Benjamin D. ; Bokulich, Nicholas A. ; McDonald, Daniel ; Knight, Rob ; Caporaso, J. Gregory ; Huttley, Gavin A.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2019-10, Vol.10 (1), p.4643-10, Article 4643
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Integrating sequence composition information into microbial diversity analyses with k-mer frequency counting
Author / Creator:Bokulich, Nicholas A.
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2025-03, Vol.10 (3), p.e0155024
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Learning representations of microbe–metabolite interactions
Author / Creator:Morton, James T. ; Aksenov, Alexander A. ; Nothias, Louis Felix ; Foulds, James R. ; Quinn, Robert A. ; Badri, Michelle H. ; Swenson, Tami L. ; Van Goethem, Marc W. ; Northen, Trent R. ; Vazquez-Baeza, Yoshiki ; Wang, Mingxun ; Bokulich, Nicholas A. ; Watters, Aaron ; Song, Se Jin ; Bonneau, Richard ; Dorrestein, Pieter C. ; Knight, Rob
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2019-12, Vol.16 (12), p.1306-1314
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Monitoring Seasonal Changes in Winery-Resident Microbiota
Author / Creator:Bokulich, Nicholas A. ; Ohta, Moe ; Richardson, Paul M. ; Mills, David A.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2013-06, Vol.8 (6), p.e66437
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Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment
Author / Creator:Nobel, Yael R. ; Cox, Laura M. ; Kirigin, Francis F. ; Bokulich, Nicholas A. ; Yamanishi, Shingo ; Teitler, Isabel ; Chung, Jennifer ; Sohn, Jiho ; Barber, Cecily M. ; Goldfarb, David S. ; Raju, Kartik ; Abubucker, Sahar ; Zhou, Yanjiao ; Ruiz, Victoria E. ; Li, Huilin ; Mitreva, Makedonka ; Alekseyenko, Alexander V. ; Weinstock, George M. ; Sodergren, Erica ; Blaser, Martin J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2015-06, Vol.6 (1), p.7486, Article 7486
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ArticlesPeer ReviewedFull Text
q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
Author / Creator:Bokulich, Nicholas A. ; Dillon, Matthew R. ; Zhang, Yilong ; Rideout, Jai Ram ; Bolyen, Evan ; Li, Huilin ; Albert, Paul S. ; Caporaso, J. Gregory
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2018-11, Vol.3 (6)
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ArticlesPeer ReviewedFull Text
Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale
Author / Creator:Bokulich, Nicholas A. ; Bamforth, Charles W. ; Mills, David A.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2012-04, Vol.7 (4), p.e35507
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Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine
Author / Creator:Bokulich, Nicholas A. ; Joseph, C. M. Lucy ; Allen, Greg ; Benson, Andrew K. ; Mills, David A.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2012-05, Vol.7 (5), p.e36357
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NapBiome trial: Targeting gut microbiota to improve sleep rhythm and developmental and behavioural outcomes in early childhood in a birth cohort in Switzerland – a study protocol
Author / Creator:Zimmermann, Petra ; Kurth, Salome ; Giannoukos, Stamatios ; Stocker, Martin ; Bokulich, Nicholas A
Publisher:England: British Medical Journal Publishing Group
Journal title:BMJ open, 2025-03, Vol.15 (3), p.e092938
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Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance
Author / Creator:Bokulich, Nicholas A ; Bergsveinson, Jordyn ; Ziola, Barry ; Mills, David A
Publisher:England: eLife Sciences Publications Ltd
Journal title:eLife, 2015-03, Vol.4
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Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women
Author / Creator:Alemán, José O. ; Bokulich, Nicholas A. ; Swann, Jonathan R. ; Walker, Jeanne M. ; De Rosa, Joel Correa ; Battaglia, Thomas ; Costabile, Adele ; Pechlivanis, Alexandros ; Liang, Yupu ; Breslow, Jan L. ; Blaser, Martin J. ; Holt, Peter R.
Publisher:England: BioMed Central Ltd
Journal title:Journal of translational medicine, 2018-09, Vol.16 (1), p.244-17, Article 244
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A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses
Author / Creator:O'Rourke, Devon R. ; Bokulich, Nicholas A. ; Jusino, Michelle A. ; MacManes, Matthew D. ; Foster, Jeffrey T.
Publisher:England: John Wiley & Sons, Inc
Journal title:Ecology and evolution, 2020-09, Vol.10 (18), p.9721-9739
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The microbiota vault initiative: safeguarding Earth’s microbial heritage for future generations
Author / Creator:Dominguez-Bello, Maria G. ; Steiger, Dominik ; Fankhauser, Manuel ; Egli, Adrian ; Vonaesch, Pascale ; Bokulich, Nicholas A. ; Lavrinienko, Anton ; Hoffmann, Christian ; Zimmermann, Petra ; Muhummed, Abdifatah ; Sayasone, Somphou ; Larbi, Amma ; Padonou, Segla Wilfrid ; Zinsstag, Jakob ; Tschopp, Rea ; Santivarangkna, Chalat ; Albertos Torres, Diana ; Li, Yuen Yi ; Benvenga, Vanni ; Teo, Youzheng ; Houngbédji, Marcel ; Kwarteng, Alex ; Knight, Rob ; Gilbert, Jack A. ; Blaser, Martin J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2025-06, Vol.16 (1), p.5373-6, Article 5373
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Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders
Author / Creator:Zimmermann, Petra ; Kurth, Salome ; Pugin, Benoit ; Bokulich, Nicholas A
Publisher:London: Nature Publishing Group
Journal title:NPJ biofilms and microbiomes, 2024-11, Vol.10 (1), p.139
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Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development
Author / Creator:Pearson, Talima ; Caporaso, J. Gregory ; Yellowhair, Monica ; Bokulich, Nicholas A. ; Padi, Megha ; Roe, Denise J. ; Wertheim, Betsy C. ; Linhart, Mark ; Martinez, Jessica A. ; Bilagody, Cherae ; Hornstra, Heidie ; Alberts, David S. ; Lance, Peter ; Thompson, Patricia A.
Publisher:United States: John Wiley & Sons, Inc
Journal title:Cancer medicine (Malden, MA), 2019-02, Vol.8 (2), p.617-628
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Showing 1 to 20 of 66 results

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RESCRIPt: Reproducible sequence taxonomy reference database management

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Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

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Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

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Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment

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Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer

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Species abundance information improves sequence taxonomy classification accuracy

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Integrating sequence composition information into microbial diversity analyses with k-mer frequency counting

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Learning representations of microbe–metabolite interactions

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Monitoring Seasonal Changes in Winery-Resident Microbiota

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Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

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q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

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Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale

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Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine

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NapBiome trial: Targeting gut microbiota to improve sleep rhythm and developmental and behavioural outcomes in early childhood in a birth cohort in Switzerland – a study protocol

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Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

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Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women

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A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses

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The microbiota vault initiative: safeguarding Earth’s microbial heritage for future generations

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Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders

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Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development

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