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1

Current understanding of the human microbiome

Gilbert, Jack A, Blaser, Martin J, Caporaso, J Gregory, Jansson, Janet K, Lynch, Susan V, Knight, Rob

Journal:

Nature Medicine

Year:

2018

Language:

english

File:

PDF, 655 KB

english, 2018

2

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J Gregory, Kuczynski, Justin, Stombaugh, Jesse, Bittinger, Kyle, Bushman, Frederic D, Costello, Elizabeth K, Fierer, Noah, Peña, Antonio Gonzalez, Goodrich, Julia K, Gordon, Jeffrey I

Journal:

Year:

2010

Language:

english

File:

PDF, 257 KB

english, 2010

3

ORIGINS OF THE GENETIC CODE: The Escaped Triplet Theory

Yarus, Michael, Caporaso, J. Gregory, Knight, Rob

Journal:

Annual Review of Biochemistry

Year:

2005

Language:

english

File:

PDF, 263 KB

english, 2005

4

Soil bacterial and fungal communities across a pH gradient in an arable soil

Rousk, Johannes, Bååth, Erland, Brookes, Philip C, Lauber, Christian L, Lozupone, Catherine, Caporaso, J Gregory, Knight, Rob, Fierer, Noah

Journal:

The ISME Journal

Year:

2010

Language:

english

File:

PDF, 1016 KB

english, 2010

5

Cohabiting family members share microbiota with one another and with their dogs

Song, Se Jin, Lauber, Christian, Costello, Elizabeth K, Lozupone, Catherine A, Humphrey, Gregory, Berg-Lyons, Donna, Caporaso, J Gregory, Knights, Dan, Clemente, Jose C, Nakielny, Sara, Gordon, Jeffre

Journal:

Year:

2013

Language:

english

File:

PDF, 3.46 MB

english, 2013

6

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Bokulich, Nicholas A, Subramanian, Sathish, Faith, Jeremiah J, Gevers, Dirk, Gordon, Jeffrey I, Knight, Rob, Mills, David A, Caporaso, J Gregory

Journal:

Year:

2012

Language:

english

File:

PDF, 413 KB

english, 2012

7

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Langille, Morgan G I, Zaneveld, Jesse, Caporaso, J Gregory, McDonald, Daniel, Knights, Dan, Reyes, Joshua A, Clemente, Jose C, Burkepile, Deron E, Vega Thurber, Rebecca L, Knight, Rob, Beiko, Robert G

Journal:

Nature Biotechnology

Year:

2013

Language:

english

File:

PDF, 1.44 MB

english, 2013

8

Conducting a Microbiome Study

Goodrich, Julia K., Di Rienzi, Sara C., Poole, Angela C., Koren, Omry, Walters, William A., Caporaso, J. Gregory, Knight, Rob, Ley, Ruth E.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.08 MB

english, 2014

9

From Rare to Dominant: A Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

Fuentes, Sebastián, Barra, Bárbara, Caporaso, J Gregory, Seeger, Michael

Journal:

Applied and Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 1.79 MB

english, 2015

10

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome

Neilson, Julia W., Califf, Katy, Cardona, Cesar, Copeland, Audrey, van Treuren, Will, Josephson, Karen L., Knight, Rob, Gilbert, Jack A., Quade, Jay, Caporaso, J. Gregory, Maier, Raina M., Chu, Haiyan

Journal:

Year:

2017

Language:

english

File:

PDF, 1.13 MB

english, 2017

11

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

Gaddy T. Bergmann, Scott T. Bates, Kathryn G. Eilers, Christian L. Lauber, J. Gregory Caporaso, William A. Walters, Rob Knight, Noah Fierer

Journal:

Soil Biology and Biochemistry

Year:

2011

Language:

english

File:

PDF, 416 KB

english, 2011

12

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

Caporaso, J Gregory, Lauber, Christian L, Walters, William A, Berg-Lyons, Donna, Huntley, James, Fierer, Noah, Owens, Sarah M, Betley, Jason, Fraser, Louise, Bauer, Markus, Gormley, Niall, Gilbert, Ja

Journal:

The ISME Journal

Year:

2012

Language:

english

File:

PDF, 230 KB

english, 2012

13

Defining seasonal marine microbial community dynamics

Gilbert, Jack A, Steele, Joshua A, Caporaso, J Gregory, Steinbrück, Lars, Reeder, Jens, Temperton, Ben, Huse, Susan, McHardy, Alice C, Knight, Rob, Joint, Ian, Somerfield, Paul, Fuhrman, Jed A, Field,

Journal:

The ISME Journal

Year:

2012

Language:

english

File:

PDF, 703 KB

english, 2012

14

pH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils

Feng, Youzhi, Grogan, Paul, Caporaso, J. Gregory, Zhang, Huayong, Lin, Xiangui, Knight, Rob, Chu, Haiyan

Journal:

Soil Biology and Biochemistry

Year:

2014

Language:

english

File:

PDF, 1.20 MB

english, 2014

15

Advancing the Microbiome Research Community

Huttenhower, Curtis, Knight, Rob, Brown, C. Titus, Caporaso, J. Gregory, Clemente, Jose C., Gevers, Dirk, Franzosa, Eric A., Kelley, Scott T., Knights, Dan, Ley, Ruth E., Mahurkar, Anup, Ravel, Jacque

Journal:

Year:

2014

Language:

english

File:

PDF, 119 KB

english, 2014

16

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)

Bolnick, Daniel I., Snowberg, Lisa K., Hirsch, Philipp E., Lauber, Christian L., Knight, Rob, Caporaso, J. Gregory, Svanbäck, Richard, Post, David

Journal:

Ecology Letters

Year:

2014

Language:

english

File:

PDF, 1.20 MB

english, 2014

17

Open-Source Sequence Clustering Methods Improve the State Of the Art

Kopylova, Evguenia, Navas-Molina, Jose A., Mercier, Céline, Xu, Zhenjiang Zech, Mahé, Frédéric, He, Yan, Zhou, Hong-Wei, Rognes, Torbjørn, Caporaso, J. Gregory, Knight, Rob, Segata, Nicola

Journal:

Year:

2016

Language:

english

File:

PDF, 5.65 MB

english, 2016

18

Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run

Yeh, Yi-Chun, Needham, David M., Sieradzki, Ella T., Fuhrman, Jed A., Caporaso, J. Gregory

Journal:

Year:

2018

Language:

english

File:

PDF, 1.10 MB

english, 2018

19

Species-level functional profiling of metagenomes and metatranscriptomes

Franzosa, Eric A., McIver, Lauren J., Rahnavard, Gholamali, Thompson, Luke R., Schirmer, Melanie, Weingart, George, Lipson, Karen Schwarzberg, Knight, Rob, Caporaso, J. Gregory, Segata, Nicola, Hutten

Journal:

Year:

2018

Language:

english

File:

PDF, 1.27 MB

english, 2018

20

Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling

Chen, Zigui, Hui, Pak Chun, Hui, Mamie, Yeoh, Yun Kit, Wong, Po Yee, Chan, Martin C. W., Wong, Martin C. S., Ng, Siew C., Chan, Francis K. L., Chan, Paul K. S., Caporaso, J. Gregory

Journal:

Year:

2019

Language:

english

File:

PDF, 5.16 MB

english, 2019

21

Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?

Kaplan, Ian, Bokulich, Nicholas A., Caporaso, J. Gregory, Enders, Laramy S., Ghanem, Wadih, Ingerslew, Kathryn S.

Journal:

Evolutionary Applications

Year:

2020

File:

PDF, 2.23 MB

2020

22

Error Minimization and Coding Triplet/Binding Site Associations Are Independent Features of the Canonical Genetic Code

J. Gregory Caporaso, Michael Yarus, Rob Knight

Journal:

Journal of Molecular Evolution

Year:

2005

Language:

english

File:

PDF, 434 KB

english, 2005

23

Examining the global distribution of dominant archaeal populations in soil

Bates, Scott T, Berg-Lyons, Donna, Caporaso, J Gregory, Walters, William A, Knight, Rob, Fierer, Noah

Journal:

The ISME Journal

Year:

2010

Language:

english

File:

PDF, 611 KB

english, 2010

24

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys

Werner, Jeffrey J, Zhou, Dennis, Caporaso, J Gregory, Knight, Rob, Angenent, Largus T

Journal:

The ISME Journal

Year:

2012

Language:

english

File:

PDF, 284 KB

english, 2012

25

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

J Gregory Caporaso, Sandra Smit, Brett C Easton, Lawrence Hunter, Gavin A Huttley, Rob Knight

Journal:

BMC Evolutionary Biology

Year:

2008

Language:

english

File:

PDF, 2.00 MB

english, 2008

26

Sequencing our way towards understanding global eukaryotic biodiversity

Holly M. Bik, Dorota L. Porazinska, Simon Creer, J. Gregory Caporaso, Rob Knight, W. Kelley Thomas

Journal:

Trends in Ecology & Evolution

Year:

2012

Language:

english

File:

PDF, 1.35 MB

english, 2012

27

Tobacco use and nicotine dependence among HIV-infected and uninfected injection drug users

Mariah M. Marshall, Gregory D. Kirk, Neil E. Caporaso, Meredith C. McCormack, Christian A. Merlo, John C. Hague, Shruti H. Mehta, Eric A. Engels

Journal:

Addictive Behaviors

Year:

2011

Language:

english

File:

PDF, 183 KB

english, 2011

28

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites

Ursell, Luke K., Clemente, Jose C., Rideout, Jai Ram, Gevers, Dirk, Caporaso, J. Gregory, Knight, Rob

Journal:

Journal of Allergy and Clinical Immunology

Year:

2012

Language:

english

File:

PDF, 100 KB

english, 2012

29

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Gregory Caporaso

Journal:

Year:

2012

Language:

english

File:

PDF, 218 KB

english, 2012

30

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

Kirk Harris, J, Gregory Caporaso, J, Walker, Jeffrey J, Spear, John R, Gold, Nicholas J, Robertson, Charles E, Hugenholtz, Philip, Goodrich, Julia, McDonald, Daniel, Knights, Dan, Marshall, Paul, Tufo

Journal:

The ISME Journal

Year:

2013

Language:

english

File:

PDF, 1.02 MB

english, 2013

31

Diversity, distribution and sources of bacteria in residential kitchens

Flores, Gilberto E., Bates, Scott T., Caporaso, J. Gregory, Lauber, Christian L., Leff, Jonathan W., Knight, Rob, Fierer, Noah

Journal:

Environmental Microbiology

Year:

2013

Language:

english

File:

PDF, 2.49 MB

english, 2013

32

Moving pictures of the human microbiome

J Gregory Caporaso, Christian L Lauber, Elizabeth K Costello…

Journal:

Year:

2011

Language:

english

File:

PDF, 2.29 MB

english, 2011

33

Concept recognition for extracting protein interaction relations from biomedical text

William A Baumgartner Jr, Zhiyong Lu, Helen L Johnson, J Gregory Caporaso…

Journal:

Year:

2008

Language:

english

File:

PDF, 738 KB

english, 2008

34

A meta-analysis of changes in bacterial and archaeal communities with time

Shade, Ashley, Gregory Caporaso, J, Handelsman, Jo, Knight, Rob, Fierer, Noah

Journal:

The ISME Journal

Year:

2013

Language:

english

File:

PDF, 713 KB

english, 2013

35

275 The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention

McFadden, Rita-Marie T., Larmonier, Claire B., Midura-Kiela, Monica T., Ramalingam, Rajalakshmy, Harrison, Christy A., Besselsen, David G., Chase, John, Caporaso, Gregory, Ghishan, Fayez K., Kiela, Pa

Journal:

Gastroenterology

Year:

2014

Language:

english

File:

PDF, 58 KB

english, 2014

36

The Western English Channel contains a persistent microbial seed bank

Caporaso, J Gregory, Paszkiewicz, Konrad, Field, Dawn, Knight, Rob, Gilbert, Jack A

Journal:

The ISME Journal

Year:

2012

Language:

english

File:

PDF, 364 KB

english, 2012

37

Individual diet has sex-dependent effects on vertebrate gut microbiota

Bolnick, Daniel I., Snowberg, Lisa K., Hirsch, Philipp E., Lauber, Christian L., Org, Elin, Parks, Brian, Lusis, Aldons J., Knight, Rob, Caporaso, J. Gregory, Svanbäck, Richard

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 2.48 MB

english, 2014

38

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

Bolnick, Daniel I., Snowberg, Lisa K., Caporaso, J. Gregory, Lauber, Chris, Knight, Rob, Stutz, William E.

Journal:

Molecular Ecology

Year:

2014

Language:

english

File:

PDF, 529 KB

english, 2014

39

New Insight into the Diversity of Life's Building Blocks: Evenness, Not Variance

Caporaso, J. Gregory, Knight, Rob

Journal:

Year:

2011

Language:

english

File:

PDF, 46 KB

english, 2011

40

Collaborative cloud-enabled tools allow rapid, reproducible biological insights

Ragan-Kelley, Benjamin, Walters, William Anton, McDonald, Daniel, Riley, Justin, Granger, Brian E, Gonzalez, Antonio, Knight, Rob, Perez, Fernando, Caporaso, J Gregory

Journal:

The ISME Journal

Year:

2013

Language:

english

File:

PDF, 280 KB

english, 2013

41

RAPID PATTERN DEVELOPMENT FOR CONCEPT RECOGNITION SYSTEMS: APPLICATION TO POINT MUTATIONS

CAPORASO, J. GREGORY, BAUMGARTNER, WILLIAM A., RANDOLPH, DAVID A., COHEN, K. BRETONNEL, HUNTER, LAWRENCE

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2007

Language:

english

File:

PDF, 405 KB

english, 2007

42

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

Werner, Jeffrey J, Koren, Omry, Hugenholtz, Philip, DeSantis, Todd Z, Walters, William A, Caporaso, J Gregory, Angenent, Largus T, Knight, Rob, Ley, Ruth E

Journal:

The ISME Journal

Year:

2012

Language:

english

File:

PDF, 705 KB

english, 2012

43

Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone

Kang, Dae-Wook, DiBaise, John K., Ilhan, Zehra Esra, Crowell, Michael D., Rideout, Jai Ram, Caporaso, J. Gregory, Rittmann, Bruce E., Krajmalnik-Brown, Rosa

Journal:

Year:

2015

Language:

english

File:

PDF, 805 KB

english, 2015

44

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

Smith, Chris CR, Snowberg, Lisa K, Gregory Caporaso, J, Knight, Rob, Bolnick, Daniel I

Journal:

The ISME Journal

Year:

2015

Language:

english

File:

PDF, 797 KB

english, 2015

45

Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition

Caporaso, J. Gregory, Knight, Rob, Kelley, Scott T., Gilbert, Jack

Journal:

Year:

2011

Language:

english

File:

PDF, 354 KB

english, 2011

46

Supplement 1: Microbes and Health || Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

J. Gregory Caporaso, Christian L. Lauber, William A. Walters, Donna Berg-Lyons, Catherine A. Lozupone, Peter J. Turnbaugh, Noah Fierer, Rob Knight and Jeffrey I. Gordon

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.56 MB

english, 2011

47

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

Walters, William, Hyde, Embriette R., Berg-Lyons, Donna, Ackermann, Gail, Humphrey, Greg, Parada, Alma, Gilbert, Jack A., Jansson, Janet K., Caporaso, J. Gregory, Fuhrman, Jed A., Apprill, Amy, Knight

Journal:

Year:

2016

Language:

english

File:

PDF, 1.30 MB

english, 2016

48

Phylogenetic organization of bacterial activity

Morrissey, Ember M, Mau, Rebecca L, Schwartz, Egbert, Caporaso, J Gregory, Dijkstra, Paul, van Gestel, Natasja, Koch, Benjamin J, Liu, Cindy M, Hayer, Michaela, McHugh, Theresa A, Marks, Jane C, Price

Journal:

The ISME Journal

Year:

2016

Language:

english

File:

PDF, 510 KB

english, 2016

49

Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

He, Yan, Caporaso, J. Gregory, Jiang, Xiao-Tao, Sheng, Hua-Fang, Huse, Susan M., Rideout, Jai Ram, Edgar, Robert C., Kopylova, Evguenia, Walters, William A., Knight, Rob, Zhou, Hong-Wei

Journal:

Year:

2015

Language:

english

File:

PDF, 330 KB

english, 2015

50

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

He, Yan, Caporaso, J Gregory, Jiang, Xiao-Tao, Sheng, Hua-Fang, Huse, Susan M, Rideout, Jai Ram, Edgar, Robert C, Kopylova, Evguenia, Walters, William A, Knight, Rob, Zhou, Hong-Wei

Journal:

Year:

2015

Language:

english

File:

PDF, 1.12 MB

english, 2015