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1. Full Text Deblur rapidly resolves single-nucleotide community sequence patterns
by Amir, Amnon and McDonald, Daniel and Navas-Molina, Jose A and Kopylova, Evguenia and Morton, James T and Xu, Zhenjiang Zech and Kightley, Eric P and Thompson, Luke R and Hyde, Embriette R and Gonzalez, Antonio and Knight, Rob
mSystems, ISSN 2379-5077, 03/2017, Volume 2, Issue 2, p. e00191-16
DNA sequencing | Microbiome | Next-generation sequencing
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2. Full Text Subsistence strategies in traditional societies distinguish gut microbiomes
by Obregon-Tito, Alexandra J and Tito, Raul Y and Metcalf, Jessica and Sankaranarayanan, Krithivasan and Clemente, Jose C and Ursell, Luke K and Zech Xu, Zhenjiang and Van Treuren, Will and Knight, Rob and Gaffney, Patrick M and Spicer, Paul and Lawson, Paul and Marin-Reyes, Luis and Trujillo-Villarroel, Omar and Foster, Morris and Guija-Poma, Emilio and Troncoso-Corzo, Luzmila and Warinner, Christina and Ozga, Andrew T and Lewis, Cecil M
Nature communications, ISSN 2041-1723, 2015, Volume 6, Issue 1, pp. 6505 - 6505
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Humans | Middle Aged | Oklahoma | Child, Preschool | Firmicutes - genetics | Infant | Male | Biodiversity | Treponema - genetics | Young Adult | Metagenome - genetics | Actinobacteria - genetics | Classification | Adult | Female | Actinobacteria - isolation & purification | Agriculture | Child | Bacteroidetes - isolation & purification | Firmicutes - isolation & purification | Treponema - isolation & purification | Gastrointestinal Microbiome - genetics | Diet, Paleolithic | Diet | Adolescent | RNA, Ribosomal, 16S - genetics | High-Throughput Nucleotide Sequencing | Industrial Development | Bacteroidetes - genetics | Peru | Index Medicus
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3. Full Text A communal catalogue reveals Earth's multiscale microbial diversity
by Thompson, Luke R and Sanders, Jon G and McDonald, Daniel and Amir, Amnon and Ladau, Joshua and Locey, Kenneth J and Prill, Robert J and Tripathi, Anupriya and Gibbons, Sean M and Ackermann, Gail and Navas-Molina, Jose A and Janssen, Stefan and Kopylova, Evguenia and Vazquez-Baeza, Yoshiki and Gonzalez, Antonio and Morton, James T and Mirarab, Siavash and Xu, Zhenjiang Zech and Jiang, Lingjing and Haroon, Mohamed F and Kanbar, Jad and Zhu, Qiyun and Song, Se Jin and Kosciolek, Tomasz and Bokulich, Nicholas A and Lefler, Joshua and Brislawn, Colin J and Humphrey, Gregory and Owens, Sarah M and Hampton-Marcell, Jarrad and Berg-Lyons, Donna and McKenzie, Valerie and Fierer, Noah and Fuhrman, Jed A and Clauset, Aaron and Stevens, Rick L and Shade, Ashley and Pollard, Katherine S and Goodwin, Kelly D and Jansson, Janet K and Gilbert, Jack A and Knight, Rob and Earth Microbiome Project Consortiu and Earth Microbiome Project Consortium and The Earth Microbiome Project Consortium and Argonne National Lab. (ANL), Argonne, IL (United States) and Pacific Northwest National Lab. (PNNL), Richland, WA (United States) and Naturvetenskapliga fakulteten and Faculty of Sciences and Göteborgs universitet and Gothenburg University and Institutionen för marina vetenskaper and Department of marine sciences
Nature (London), ISSN 0028-0836, 11/2017, Volume 551, Issue 7681, pp. 457 - +
CONSISTENT | ARCHAEAL | EVOLUTION | MARINE BACTERIAL | GLOBAL PATTERNS | BACTERIAL DIVERSITY | OPERON COPY NUMBER | ONTOLOGY | COMMUNITIES | NESTEDNESS | Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Humans | RNA, Ribosomal, 16S - analysis | Geographic Mapping | Plants - microbiology | Gene Dosage | Archaea - isolation & purification | Biodiversity | Bacteria - genetics | Bacteria - isolation & purification | Ecology - methods | Animals | Microbiota - genetics | RNA, Ribosomal, 16S - genetics | Archaea - genetics | Earth, Planet | Environmental aspects | Observations | Microbial colonies | Biological diversity | International marketing | Nucleotide sequencing | Ribosomal RNA | Catalogs | Analysis | DNA sequencing | Microbiological research | Distribution | Genetic aspects | Research | Identification and classification | Analytical methods | Nucleotide sequence | Microbiology | Taxonomy | rRNA | Ecology | Genomes | Ribonucleic acid--RNA | Gene sequencing | Meta-analysis | Earth | Studies | Microorganisms | Phylogenetics | Bacteria | Deoxyribonucleic acid--DNA | Index Medicus | ENVIRONMENTAL SCIENCES | global | BASIC BIOLOGICAL SCIENCES | microbiome | Geosciences, Multidisciplinary | Climate Research | Klimatforskning | Oceanografi, hydrologi, vattenresurser | Oceanography, Hydrology, Water Resources | Annan geovetenskap och miljövetenskap | Multidisciplinär geovetenskap | Ekologi | Other Earth and Related Environmental Sciences | CVI Infection Biology | CVI Infectiebiologie | Food Quality and Design | VLAG | Infectiebiologie | Infection Biology
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4. Full Text Microbial community assembly and metabolic function during mammalian corpse decomposition
by Metcalf, Jessica L and Metcalf, Jessica L and Xu, Zhenjiang Z.ech and Xu, Zhenjiang Zech and Weiss, Sophie and Weiss, Sophie and Lax, Simon and Lax, Simon and Van Treuren, Will and Van Treuren, Will and Hyde, Embriette R and Hyde, Embriette R and Song, Se Jin and Song, Se J.in and Amir, Amnon and Amir, Amnon and Larsen, Peter and Larsen, Peter and Sangwan, Naseer and Sangwan, Naseer and Haarmann, Daniel and Haarmann, Daniel and Humphrey, Greg C and Humphrey, Greg C and Ackermann, Gail and Ackermann, Gail and Thompson, Luke R and Thompson, Luke R and Lauber, Christian and Lauber, Christian and Bibat, Alexander and Bibat, Alexander and Nicholas, Catherine and Nicholas, Catherine and Gebert, Matthew J and Gebert, Matthew J and Petrosino, Joseph F and Petrosino, Joseph F and Reed, Sasha C and Reed, Sasha C and Gilbert, Jack A and Gilbert, Jack A and Lynne, Aaron M and Lynne, Aaron M and Bucheli, Sibyl R and Bucheli, Sibyl R and Carter, David O and Carter, David O and Knight, Rob and Knight, Rob and Argonne National Lab. (ANL), Argonne, IL (United States)
Science (American Association for the Advancement of Science), ISSN 0036-8075, 01/2016, Volume 351, Issue 6269, pp. 158 - 162
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Biodegradation, Environmental | Bacteria - metabolism | Fungi - classification | Soil Microbiology | Fungi - metabolism | Microbial Consortia | Nitrogen Cycle | Soil - classification | Animals | Ecosystem | Soil - chemistry | Bacteria - classification | Mice | Cadaver | Biodegradation | Environmental aspects | Dead | Observations | Properties | Microbial colonies | Microorganisms | Decomposition | Microbiology | Mammals | Metabolism | Index Medicus
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5. Full Text Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota
by Teng, Fei and Yang, Fang and Huang, Shi and Bo, Cunpei and Xu, Zhenjiang Zech and Amir, Amnon and Knight, Rob and Ling, Junqi and Xu, Jian
Cell host & microbe, ISSN 1931-3128, 09/2015, Volume 18, Issue 3, pp. 296 - 306
saliva | microbiota | plaque | early-childhood caries | microbial indicators of caries | Parasitology | Life Sciences & Biomedicine | Microbiology | Science & Technology | Virology | Dental Caries - microbiology | Prognosis | Dental Caries - diagnosis | Humans | Child, Preschool | Molecular Sequence Data | DNA, Bacterial - chemistry | Models, Statistical | DNA, Ribosomal - chemistry | Sequence Analysis, DNA | Dental Plaque - microbiology | Microbiota | DNA, Bacterial - genetics | RNA, Ribosomal, 16S - genetics | Saliva - microbiology | DNA, Ribosomal - genetics | Microbiota (Symbiotic organisms) | Analysis | Indicators (Biology) | Index Medicus
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6. Full Text Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies
by Song, Se Jin and Amir, Amnon and Metcalf, Jessica L and Amato, Katherine R and Xu, Zhenjiang Zech and Humphrey, Greg and Knight, Rob
mSystems, ISSN 2379-5077, 05/2016, Volume 1, Issue 3, p. e00021-16
DNA stability | Sample storage | Fecal microbiome
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7. 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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8. Full Text Toxicant substitutes in immunological assays for mycotoxins detection: A mini review
Food chemistry, 05/2021, Volume 344, pp. 128589 - 128589
Index Medicus
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9. Full Text Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
by Weiss, Sophie and Van Treuren, Will and Lozupone, Catherine and Faust, Karoline and Friedman, Jonathan and Deng, Ye and Xia, Li Charlie and Xu, Zhenjiang Zech and Ursell, Luke and Alm, Eric J and Birmingham, Amanda and Cram, Jacob A and Fuhrman, Jed A and Raes, Jeroen and Sun, Fengzhu and Zhou, Jizhong and Knight, Rob
The ISME Journal, ISSN 1751-7362, 07/2016, Volume 10, Issue 7, pp. 1669 - 1681
Environmental Sciences & Ecology | Ecology | Life Sciences & Biomedicine | Microbiology | Science & Technology | Benchmarking - statistics & numerical data | Microbiota | Humans | Computational Biology | RNA, Ribosomal, 16S - genetics | Statistics as Topic | Models, Statistical | Bacteria - genetics | Microbial Interactions | Index Medicus | Original
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10. 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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