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1. 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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2. 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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3. 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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4. Full Text Author Correction: 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, C.T 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 9, pp. 1091 - 1091
Bioinformatics | Bioinformatica | Microbiomes | Index Medicus
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5. Full Text Forfeiting the priority effect: turnover defines biofilm community succession
by Brislawn, Colin J and Graham, Emily B and Dana, Karl and Ihardt, Peter and Fansler, Sarah J and Chrisler, William B and Cliff, John B and Stegen, James C and Moran, James J and Bernstein, Hans C
The ISME Journal, ISSN 1751-7362, 07/2019, Volume 13, Issue 7, pp. 1865 - 1877
Environmental Sciences & Ecology | Ecology | Life Sciences & Biomedicine | Microbiology | Science & Technology | Bacteria - classification | Microbiota | Biofilms | Stochastic Processes | Bacteria - genetics | Image resolution | rRNA 16S | Communities | Ecosystems | Stochastic processes | Abundance | Gene sequencing | Ecological effects | Eukaryotes | Succession | Microorganisms | Stable isotopes | Bacteria | Stochasticity | rRNA 18S | Species | Colonization | Tracers | Index Medicus | VDP | Basale biofag: 470 | Generell mikrobiologi: 472 | General microbiology: 472 | Mathematics and natural science: 400 | Matematikk og Naturvitenskap: 400 | Basic biosciences: 470 | Microbial ecology | Environmental microbiology
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6. Full Text Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
by Lloyd-Price, Jason and Arze, Cesar and Ananthakrishnan, Ashwin N and Schirmer, Melanie and Avila-Pacheco, Julian and Poon, Tiffany W and Andrews, Elizabeth and Andrews, Elizabeth and Ajami, Nadim J and Bonham, Kevin S and Brislawn, Colin J and Casero, David and Courtney, Holly and Gonzalez, Antonio and Graeber, Thomas G and Graeber, Thomas G and Hall, A. Brantley and Hall, A Brantley and Lake, Kathleen and Lake, Kathleen and Landers, Carol J and Landers, Carol J and Mallick, Himel and Plichta, Damian R and Prasad, Mahadev and Rahnavard, Gholamali and Sauk, Jenny and Shungin, Dmitry and Shungin, Dmitry and Vázquez-Baeza, Yoshiki and White, Richard A and White, Richard A and Bishai, Jason and Bullock, Kevin and Braun, Jonathan and Denson, Lee A and Deik, Amy and Dennis, Courtney and Jansson, Janet K and Knight, Rob and Kaplan, Jess L and Khalili, Hamed and Kugathasan, Subra and McIver, Lauren J and McGovern, Dermot P B and Petrosino, Joseph F and Moran, Christopher J and Stappenbeck, Thaddeus S and Nguyen, Long and Pierce, Kerry A and Winter, Harland S and Clish, Clary B and Schwager, Randall and Franzosa, Eric A and Sirota-Madi, Alexandra and Vlamakis, Hera and Stevens, Betsy W and Tan, William and Xavier, Ramnik J and Huttenhower, Curtis and ten Hoeve, Johanna J and Weingart, George and Wilson, Robin G and Yajnik, Vijay and Braun, Jonathan and Denson, Lee A and Jansson, Janet K and Knight, Rob and Kugathasan, Subra and McGovern, Dermot P. B and Petrosino, Joseph F and Stappenbeck, Thaddeus S and Winter, Harland S and Clish, Clary B and Franzosa, Eric A and Vlamakis, Hera and Xavier, Ramnik J and Huttenhower, Curtis and IBDMDB Investigators and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Nature (London), ISSN 0028-0836, 05/2019, Volume 569, Issue 7758, pp. 655 - 662
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Viruses - pathogenicity | Species Specificity | Health | Humans | Inflammatory Bowel Diseases - immunology | Transcriptome | Phylogeny | Gastrointestinal Microbiome - genetics | Animals | Inflammatory Bowel Diseases - virology | Fungi - pathogenicity | Inflammatory Bowel Diseases - microbiology | Gastrointestinal Microbiome - immunology | Inflammatory Bowel Diseases - therapy | Inflammatory bowel diseases | Microbiota (Symbiotic organisms) | Genomics | Genetic research | Genetic aspects | Research | Diagnosis | Bile acids | Metabolites | Ecosystems | Analysis | Fatty acids | Ulcerative colitis | Index Medicus | IBD | multiomics | 60 APPLIED LIFE SCIENCES | microbiome
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7. Full Text Genetic and metabolic links between the murine microbiome and memory
by Mao, Jian-Hua and Kim, Young-Mo and Zhou, Yan-Xia and Hu, Dehong and Zhong, Chenhan and Chang, Hang and Brislawn, Colin and Langley, Sasha and Wang, Yunshan and Peisl, B. Y. Loulou and Celniker, Susan E and Threadgill, David W and Wilmes, Paul and Orr, Galya and Metz, Thomas O and Jansson, Janet K and Snijders, Antoine M and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States) and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Microbiome, ISSN 2049-2618, 04/2020, Volume 8, Issue 1, pp. 53 - 53
Life Sciences & Biomedicine | Microbiology | Science & Technology | Metabolomics | Brain | Gnotobiotics | rRNA 16S | Microbiomes | Association analysis | Genomes | Single-nucleotide polymorphism | Gene expression | Metabolism | γ-Aminobutyric acid | Inoculation | Acids | Metabolites | Collaboration | Genetics | Lactic acid | Feces | Intestinal microflora | Short term memory | Index Medicus | BASIC BIOLOGICAL SCIENCES | Collaborative Cross mouse model | Germ-free | Gut–brain axis | Memory | Lactobacillus
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8. Full Text Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture
by Khan, Nymul and Maezato, Yukari and McClure, Ryan S and Brislawn, Colin J and Mobberley, Jennifer M and Isern, Nancy and Chrisler, William B and Markillie, Lye Meng and Barney, Brett M and Song, Hyun-Seob and Nelson, William C and Bernstein, Hans C and Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Scientific reports, ISSN 2045-2322, 12/2018, Volume 8, Issue 1, pp. 297 - 297
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Bacteria - metabolism | Microbiota | Phenotype | Coculture Techniques | Bacteria - classification | Glucose - metabolism | Bacteria - genetics | Microbial Interactions | Xylose | Commensalism | Phenotypes | Metabolites | Heterotrophic bacteria | Nutrient availability | Species | Carbon sources | Environmental conditions | Index Medicus | Environmental Molecular Sciences Laboratory | BASIC BIOLOGICAL SCIENCES
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9. Full Text Alterations in the relative abundance of Faecalibacterium prausnitzii correlate with changes in fecal calprotectin in patients with ileal Crohn's disease: a longitudinal study
by Björkqvist, Olle and Repsilber, Dirk and Seifert, Maike and Brislawn, Colin and Jansson, Janet and Engstrand, Lars and Rangel, Ignacio and Halfvarson, Jonas and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Scandinavian journal of gastroenterology, ISSN 0036-5521, 05/2019, Volume 54, Issue 5, pp. 577 - 585
Faecalibacterium prausnitzii | Crohn's disease | butyrate | calprotectin | dysbiosis | Gastroenterology & Hepatology | Life Sciences & Biomedicine | Science & Technology | Dysbiosis - etiology | Leukocyte L1 Antigen Complex - analysis | Faecalibacterium prausnitzii - isolation & purification | Humans | RNA, Ribosomal, 16S - analysis | Crohn Disease - metabolism | Male | Case-Control Studies | Young Adult | Feces - microbiology | Sweden | Feces - chemistry | Adolescent | Adult | Crohn Disease - microbiology | Female | Ileum - microbiology | Longitudinal Studies | Real-Time Polymerase Chain Reaction | Index Medicus | Calprotectin | 60 APPLIED LIFE SCIENCES | crohn's disease | Medicin och hälsovetenskap
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10. Full Text Impact of dietary resistant starch on the human gut Microbiome, Metaproteome, and Metabolome
by Maier, Tanja V and Lucio, Marianna and Lee, Lang Ho and Verberkmoes, Nathan C and Brislawn, Colin J and Bernhardt, Jörg and Lamendella, Regina and McDermott, Jason E and Bergeron, Nathalie and Heinzmann, Silke S and Morton, James T and González, Antonio and Ackermann, Gail and Knight, Rob and Riedel, Katharina and Krauss, Ronald M and Schmitt-Kopplin, Philippe and Jansson, Janet K and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
mBio, ISSN 2161-2129, 09/2017, Volume 8, Issue 5, p. e01343-17
Human microbiome | Multiomics | Resistant starch | Gut microbiome | Life Sciences & Biomedicine | Microbiology | Science & Technology | Metabolomics | Humans | Bacteria - drug effects | Microbiota - drug effects | Proteome - drug effects | DNA, Bacterial - chemistry | Bacteria - genetics | DNA, Ribosomal - chemistry | Sequence Analysis, DNA | Starch - administration & dosage | Bacteria - growth & development | DNA, Bacterial - genetics | Gastrointestinal Microbiome - drug effects | Metabolome - drug effects | Proteomics | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Diet - methods | DNA, Ribosomal - genetics | Index Medicus | clinical | gut microbiome | proteomics | human microbiome | BASIC BIOLOGICAL SCIENCES | metabolomics | resistant starch | diet | multiomics
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