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1. Full Text EMPeror: A tool for visualizing high-throughput microbial community data
by Vázquez-Baeza, Yoshiki and Pirrung, Meg and Gonzalez, Antonio and Knight, Rob
Gigascience, ISSN 2047-217X, 2013, Volume 2, Issue 1, pp. 16 - 16
Microbial ecology | Data visualization | QIIME | Science & Technology - Other Topics | Biology | Multidisciplinary Sciences | Life Sciences & Biomedicine - Other Topics | Life Sciences & Biomedicine | Science & Technology
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2. Full Text Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
by Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian C and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, Titus C and Callahan, Benjamin J and Caraballo-Roíguez, Anés Mauricio and Chase, John and Cope, Emily K and Silva, da, Ricardo and Diener, Christian and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibbons, Sean M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin A and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin D and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan G.I and Lee, Joslynn and Ley, Ruth and Liu, Yong Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan D and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie T and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Peo J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and Hooft, van der, Justin J.J and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and Hippel, von, Max and Walters, William and ...
Nature biotechnology, ISSN 1087-0156, 2019, Volume 37, Issue 8, pp. 852 - 857
Bioinformatics | Bioinformatica | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Data Science | Microbiota | Software | Humans | Computational Biology | Databases, Factual | Physiological aspects | Biotechnology | Microbiota (Symbiotic organisms) | Analysis | Computational biology | Microbiomes | Index Medicus
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3. Full Text Longitudinal analysis of microbial interaction between humans and the indoor environment
by Simon Lax and Daniel P. Smith and Jarrad Hampton-Marcell and Sarah M. Owens and Kim M. Handley and Nicole M. Scott and Sean M. Gibbons and Peter Larsen and Benjamin D. Shogan and Sophie Weiss and Jessica L. Metcalf and Luke K. Ursell and Yoshiki Vázquez-Baeza and Will Van Treuren and Nur A. Hasan and Molly K. Gibson and Rita Colwell and Gautam Dantas and Rob Knight and Jack A. Gilbert and Argonne National Lab. (ANL), Argonne, IL (United States)
Science (American Association for the Advancement of Science), ISSN 0036-8075, 8/2014, Volume 345, Issue 6200, pp. 1048 - 1052
REPORTS | Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Floors and Floorcoverings | Microbiota - physiology | Beds - microbiology | Humans | Bacteria - genetics | Foot - microbiology | Host-Pathogen Interactions | Pets - microbiology | Animals | Microbiota - genetics | Surface Properties | Bacteria - classification | Family | Bacteria - pathogenicity | Hand - microbiology | Nose - microbiology | Metagenome | Household Articles | Host-bacteria relationships | Household ecology | Microbiological research | Research | Families & family life | Microorganisms | Residences | Index Medicus | Communities | Households | Health | Indoor environments | Signatures | Contamination | Inhabitants | Indoor Microbiology | Bacteria | Human Microbiome
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4. Full Text Normalization and microbial differential abundance strategies depend upon data characteristics
by Weiss, Sophie and Xu, Zhenjiang Zech and Peddada, Shyamal and Amir, Amnon and Bittinger, Kyle and Gonzalez, Antonio and Lozupone, Catherine and Zaneveld, Jesse R and Vázquez-Baeza, Yoshiki and Birmingham, Amanda and Hyde, Embriette R and Knight, Rob
Microbiome, ISSN 2049-2618, 2017, Volume 5, Issue 1, pp. 27 - 27
Differential abundance | Normalization | Statistics | Microbiome | Life Sciences & Biomedicine | Microbiology | Science & Technology | DNA, Bacterial - genetics | Gene Library | Base Sequence | Ecosystem | Humans | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Microbial Consortia - genetics | Bacterial Load - statistics & numerical data | Bacteria - genetics | Sequence Analysis, DNA | Microorganisms | Research | Comparative analysis | Ribosomal RNA | Index Medicus
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5. Full Text Suppression of the gut microbiome ameliorates age‐related arterial dysfunction and oxidative stress in mice
by Brunt, Vienna E and Gioscia‐Ryan, Rachel A and Richey, James J and Zigler, Melanie C and Cuevas, Lauren M and Gonzalez, Antonio and Vázquez‐Baeza, Yoshiki and Battson, Micah L and Smithson, Andrew T and Gilley, Andrew D and Ackermann, Gail and Neilson, Andrew P and Weir, Tiffany and Davy, Kevin P and Knight, Rob and Seals, Douglas R
The Journal of physiology, ISSN 0022-3751, 05/2019, Volume 597, Issue 9, pp. 2361 - 2378
arterial stiffness | endothelial function | inflammation | gut dysbiosis | Ageing | Neurosciences | Physiology | Neurosciences & Neurology | Life Sciences & Biomedicine | Science & Technology | Oxidative stress | Medical research | Metabolites | Microbiota (Symbiotic organisms) | Physiological aspects | Medicine, Experimental | Risk factors | Endothelium | Dysbacteriosis | Microbiomes | Antioxidants | Microbiota | Trimethylamine | Antibiotics | Aging | Aorta | Plasma levels | Acetylcholine | Carotid artery | Intestinal microflora | Cardiovascular diseases | Age | Index Medicus | Cardiovascular | Research Paper
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6. Full Text Qiita: rapid, web-enabled microbiome meta-analysis
by Gonzalez, Antonio and Navas-Molina, Jose A and Kosciolek, Tomasz and McDonald, Daniel and Vázquez-Baeza, Yoshiki and Ackermann, Gail and DeReus, Jeff and Janssen, Stefan and Swafford, Austin D and Orchanian, Stephanie B and Sanders, Jon G and Shorenstein, Joshua and Holste, Hannes and Petrus, Semar and Robbins-Pianka, Adam and Brislawn, Colin J and Wang, Mingxun and Rideout, Jai Ram and Bolyen, Evan and Dillon, Matthew and Caporaso, J. Gregory and Dorrestein, Pieter C and Knight, Rob and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Nature methods, ISSN 1548-7091, 10/2018, Volume 15, Issue 10, pp. 796 - 798
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Metagenomics | User-Computer Interface | Computational Biology - methods | Microbiota | Humans | Software | Internet | Usage | Public software | Research | Microbiota (Symbiotic organisms) | Analysis | Meta-analysis | Webs | Microbiomes | Index Medicus | microbiome, bioinformatics software, open source software
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7. Full Text Dynamics of the human gut microbiome in inflammatory bowel disease
by Halfvarson, Jonas and Brislawn, Colin J and Lamendella, Regina and Vázquez-Baeza, Yoshiki and Walters, William A and Bramer, Lisa M and D'Amato, Mauro and Bonfiglio, Ferdinando and McDonald, Daniel and Gonzalez, Antonio and McClure, Erin E and Dunklebarger, Mitchell F and Knight, Rob and Jansson, Janet K and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Nature microbiology, ISSN 2058-5276, 02/2017, Volume 2, Issue 5, pp. 17004 - 17004
Life Sciences & Biomedicine | Microbiology | Science & Technology | Inflammatory bowel diseases | Dysbacteriosis | Immune response | Microbiomes | Crohn's disease | Crohns disease | Inflammatory bowel disease | Intestine | Surgery | Remission | Colon | Intestinal microflora | Ulcerative colitis | Index Medicus | gut, human | inflammatory Bowel | Medicin och hälsovetenskap
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8. Full Text The Treatment-Naive Microbiome in New-Onset Crohn’s Disease
by Gevers, Dirk and Kugathasan, Subra and Denson, Lee A and Vázquez-Baeza, Yoshiki and Van Treuren, Will and Ren, Boyu and Schwager, Emma and Knights, Dan and Song, Se Jin and Yassour, Moran and Morgan, Xochitl C and Kostic, Aleksandar D and Luo, Chengwei and González, Antonio and McDonald, Daniel and Haberman, Yael and Walters, Thomas and Baker, Susan and Rosh, Joel and Stephens, Michael and Heyman, Melvin and Markowitz, James and Baldassano, Robert and Griffiths, Anne and Sylvester, Francisco and Mack, David and Kim, Sandra and Crandall, Wallace and Hyams, Jeffrey and Huttenhower, Curtis and Knight, Rob and Xavier, Ramnik J
Cell host & microbe, ISSN 1931-3128, 03/2014, Volume 15, Issue 3, pp. 382 - 392
Parasitology | Life Sciences & Biomedicine | Microbiology | Science & Technology | Virology | Humans | Child, Preschool | Gastrointestinal Tract - microbiology | Dysbiosis | Crohn Disease - complications | Bacteria - isolation & purification | Microbiota | Adolescent | Bacteria - classification | Crohn Disease - microbiology | Child | Metagenome | Cohort Studies | Gastrointestinal diseases | Analysis | Index Medicus
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9. Full Text Meta-analyses of studies of the human microbiota
by Lozupone, Catherine A and Stombaugh, Jesse and Gonzalez, Antonio and Ackermann, Gail and Wendel, Doug and Vázquez-Baeza, Yoshiki and Jansson, Janet K and Gordon, Jeffrey I and Knight, Rob
Genome research, ISSN 1088-9051, 10/2013, Volume 23, Issue 10, pp. 1704 - 1714
Biochemistry & Molecular Biology | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Crohn Disease - epidemiology | Crohn Disease - genetics | Humans | Metagenomics - methods | Infant | Biodiversity | Bacteria - genetics | Pregnancy Trimester, First | Sequence Analysis, DNA | Pregnancy | Feces - microbiology | Microbiota | DNA, Bacterial - genetics | Aging | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Adult | Crohn Disease - microbiology | Female | Metagenome | Intestines | Genetic aspects | Research | Microbiology | Genetic variation | Index Medicus
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