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Example files and supporting material for "EMPeror: An interactive analysis and visualization tool for high throughput microbial ecology datasets."
Example files and supporting material for "EMPeror: An interactive analysis and visualization tool for high throughput microbial ecology datasets."
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Example files and supporting material for "EMPeror: An interactive analysis and visualization tool for high throughput microbial ecology datasets."

Vázquez-Baeza, Y ; Pirrung, M ; Gonzalez, A ; Knight, R

GigaScience Database 2013

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2
Meta-analyses of studies of the human microbiota
Meta-analyses of studies of the human microbiota
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Meta-analyses of studies of the human microbiota

Lozupone, Catherine A ; Stombaugh, Jesse ; Gonzalez, Antonio ; Ackermann, Gail ; Wendel, Doug ; Vázquez-Baeza, Yoshiki ; Jansson, Janet K ; Gordon, Jeffrey I ; Knight, Rob

Genome research, 2013-10, Vol.23 (10), p.1704-1714 [Periódico revisado por pares]

United States: Cold Spring Harbor Laboratory Press

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3
Longitudinal analysis of microbial interaction between humans and the indoor environment
Longitudinal analysis of microbial interaction between humans and the indoor environment
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Longitudinal analysis of microbial interaction between humans and the indoor environment

Lax, Simon ; Smith, Daniel P. ; Hampton-Marcell, Jarrad ; Owens, Sarah M. ; Handley, Kim M. ; Scott, Nicole M. ; Gibbons, Sean M. ; Larsen, Peter ; Shogan, Benjamin D. ; Weiss, Sophie ; Metcalf, Jessica L. ; Ursell, Luke K. ; Vázquez-Baeza, Yoshiki ; Van Treuren, Will ; Hasan, Nur A. ; Gibson, Molly K. ; Colwell, Rita ; Dantas, Gautam ; Knight, Rob ; Gilbert, Jack A.

Science (American Association for the Advancement of Science), 2014-08, Vol.345 (6200), p.1048-1052 [Periódico revisado por pares]

United States: American Association for the Advancement of Science

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4
Avoiding Pandemic Fears in the Subway and Conquering the Platypus
Avoiding Pandemic Fears in the Subway and Conquering the Platypus
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Avoiding Pandemic Fears in the Subway and Conquering the Platypus

Gonzalez, A ; Vázquez-Baeza, Y ; Pettengill, J B ; Ottesen, A ; McDonald, D ; Knight, R

mSystems, 2016-05, Vol.1 (3) [Periódico revisado por pares]

United States: American Society for Microbiology

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5
Avoiding Pandemic Fears in the Subway and Conquering the Platypus
Avoiding Pandemic Fears in the Subway and Conquering the Platypus
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Avoiding Pandemic Fears in the Subway and Conquering the Platypus

Gonzalez, A ; Vázquez-Baeza, Y ; Pettengill, JB ; Ottesen, A ; McDonald, D ; Knight, R

mSystems, 2016-06, Vol.1 (3), p.e00050-e00016

eScholarship, University of California

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6
Dynamics of the human gut microbiome in inflammatory bowel disease
Dynamics of the human gut microbiome in inflammatory bowel disease
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Dynamics of the human gut microbiome in inflammatory bowel disease

Halfvarson, Jonas ; Brislawn, Colin J ; Lamendella, Regina ; Vázquez-Baeza, Yoshiki ; Walters, William A ; Bramer, Lisa M ; D'Amato, Mauro ; Bonfiglio, Ferdinando ; McDonald, Daniel ; Gonzalez, Antonio ; McClure, Erin E ; Dunklebarger, Mitchell F ; Knight, Rob ; Jansson, Janet K

Nature microbiology, 2017-02, Vol.2 (5), p.17004-17004, Article 17004 [Periódico revisado por pares]

England: Nature Publishing Group

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7
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R ; Bokulich, Nicholas A ; Abnet, Christian C ; Al-Ghalith, Gabriel A ; Alexander, Harriet ; Alm, Eric J ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J ; Brown, C Titus ; Callahan, Benjamin J ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K ; Diener, Christian ; Dorrestein, Pieter C ; Douglas, Gavin M ; Durall, Daniel M ; Duvallet, Claire ; Edwardson, Christian F ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M ; Gibson, Deanna L ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A ; Janssen, Stefan ; Jarmusch, Alan K ; Jiang, Lingjing ; Kaehler, Benjamin D ; Kang, Kyo Bin ; Keefe, Christopher R ; Keim, Paul ; Kelley, Scott T ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G I ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong-Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D ; McDonald, Daniel ; Melnik, Alexey V ; Morgan, Sydney C ; Morton, Jamie T ; Naimey, Ahmad Turan ; Navas-Molina, Jose A ; Nothias, Louis Felix ; Orchanian, Stephanie B ; Pearson, Talima ; Peoples, Samuel L ; Petras, Daniel ; Preuss, Mary Lai ; Rasmussen, Lasse Buur ; Robeson, 2nd, Michael S ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Song, Se Jin ; Spear, John R ; Swafford, Austin D ; Thompson, Luke R ; Torres, Pedro J ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J ; Ul-Hasan, Sabah ; van der Hooft, Justin J J ; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; von Hippel, Max ; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Weber, Kyle C ; Williamson, Charles H D ; Willis, Amy D ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J Gregory

Nature biotechnology, 2019-08, Vol.37 (8), p.852-857 [Periódico revisado por pares]

United States: Nature Publishing Group

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8
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis
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Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis

Melnik, Alexey V. ; Vázquez-Baeza, Yoshiki ; Aksenov, Alexander A. ; Hyde, Embriette ; McAvoy, Andrew C. ; Wang, Mingxun ; da Silva, Ricardo R. ; Protsyuk, Ivan ; Wu, Jason V. ; Bouslimani, Amina ; Lim, Yan Wei ; Luzzatto-Knaan, Tal ; Comstock, William ; Quinn, Robert A. ; Wong, Richard ; Humphrey, Greg ; Ackermann, Gail ; Spivey, Timothy ; Brouha, Sharon S. ; Bandeira, Nuno ; Lin, Grace Y. ; Rohwer, Forest ; Conrad, Douglas J. ; Alexandrov, Theodore ; Knight, Rob ; Dorrestein, Pieter C. ; Garg, Neha Arumugam, Mani

mSystems, 2019-09, Vol.4 (5) [Periódico revisado por pares]

Washington: American Society for Microbiology

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9
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis
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Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis

Melnik, Alexey V ; Vázquez-Baeza, Yoshiki ; Aksenov, Alexander A ; Hyde, Embriette ; McAvoy, Andrew C ; Wang, Mingxun ; da Silva, Ricardo R ; Protsyuk, Ivan ; Wu, Jason V ; Bouslimani, Amina ; Lim, Yan Wei ; Luzzatto-Knaan, Tal ; Comstock, William ; Quinn, Robert A ; Wong, Richard ; Humphrey, Greg ; Ackermann, Gail ; Spivey, Timothy ; Brouha, Sharon S ; Bandeira, Nuno ; Lin, Grace Y ; Rohwer, Forest ; Conrad, Douglas J ; Alexandrov, Theodore ; Knight, Rob ; Dorrestein, Pieter C ; Garg, Neha

mSystems, 2019-10, Vol.4 (5), p.e00375-e00319

eScholarship, University of California

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10
OP31 Meta–omics reveals microbiome-driven proteolysis as a contributing factor to the severity of ulcerative colitis disease activity
OP31 Meta–omics reveals microbiome-driven proteolysis as a contributing factor to the severity of ulcerative colitis disease activity
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OP31 Meta–omics reveals microbiome-driven proteolysis as a contributing factor to the severity of ulcerative colitis disease activity

Mills, R ; Dulai, P ; Vázquez-Baeza, Y ; Zhu, Q ; Humphrey, G ; DeRight Goldasich, L ; Quinn, R ; Gewirtz, A ; Chassaing, B ; Chu, H ; Sandborn, W ; Dorrestein, P ; Knight, R ; Gonzalez, D

Journal of Crohn's and colitis, 2020-01, Vol.14 (Supplement_1), p.S030-S031 [Periódico revisado por pares]

US: Oxford University Press

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