Literature DB >> 22170427

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

Jeffrey J Werner1, Dennis Zhou, J Gregory Caporaso, Rob Knight, Largus T Angenent.   

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Year:  2011        PMID: 22170427      PMCID: PMC3379627          DOI: 10.1038/ismej.2011.186

Source DB:  PubMed          Journal:  ISME J        ISSN: 1751-7362            Impact factor:   10.302


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  13 in total

1.  Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Authors:  J Gregory Caporaso; Christian L Lauber; William A Walters; Donna Berg-Lyons; Catherine A Lozupone; Peter J Turnbaugh; Noah Fierer; Rob Knight
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-03       Impact factor: 11.205

2.  Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

Authors:  T Z DeSantis; P Hugenholtz; N Larsen; M Rojas; E L Brodie; K Keller; T Huber; D Dalevi; P Hu; G L Andersen
Journal:  Appl Environ Microbiol       Date:  2006-07       Impact factor: 4.792

3.  Bacterial community structures are unique and resilient in full-scale bioenergy systems.

Authors:  Jeffrey J Werner; Dan Knights; Marcelo L Garcia; Nicholas B Scalfone; Samual Smith; Kevin Yarasheski; Theresa A Cummings; Allen R Beers; Rob Knight; Largus T Angenent
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-22       Impact factor: 11.205

4.  FastTree 2--approximately maximum-likelihood trees for large alignments.

Authors:  Morgan N Price; Paramvir S Dehal; Adam P Arkin
Journal:  PLoS One       Date:  2010-03-10       Impact factor: 3.240

5.  BIPES, a cost-effective high-throughput method for assessing microbial diversity.

Authors:  Hong-Wei Zhou; Dong-Fang Li; Nora Fung-Yee Tam; Xiao-Tao Jiang; Hai Zhang; Hua-Fang Sheng; Jin Qin; Xiao Liu; Fei Zou
Journal:  ISME J       Date:  2010-10-21       Impact factor: 10.302

6.  PyNAST: a flexible tool for aligning sequences to a template alignment.

Authors:  J Gregory Caporaso; Kyle Bittinger; Frederic D Bushman; Todd Z DeSantis; Gary L Andersen; Rob Knight
Journal:  Bioinformatics       Date:  2009-11-13       Impact factor: 6.937

7.  Bacterial community variation in human body habitats across space and time.

Authors:  Elizabeth K Costello; Christian L Lauber; Micah Hamady; Noah Fierer; Jeffrey I Gordon; Rob Knight
Journal:  Science       Date:  2009-11-05       Impact factor: 47.728

8.  QIIME allows analysis of high-throughput community sequencing data.

Authors:  J Gregory Caporaso; Justin Kuczynski; Jesse Stombaugh; Kyle Bittinger; Frederic D Bushman; Elizabeth K Costello; Noah Fierer; Antonio Gonzalez Peña; Julia K Goodrich; Jeffrey I Gordon; Gavin A Huttley; Scott T Kelley; Dan Knights; Jeremy E Koenig; Ruth E Ley; Catherine A Lozupone; Daniel McDonald; Brian D Muegge; Meg Pirrung; Jens Reeder; Joel R Sevinsky; Peter J Turnbaugh; William A Walters; Jeremy Widmann; Tanya Yatsunenko; Jesse Zaneveld; Rob Knight
Journal:  Nat Methods       Date:  2010-04-11       Impact factor: 28.547

9.  UniFrac: a new phylogenetic method for comparing microbial communities.

Authors:  Catherine Lozupone; Rob Knight
Journal:  Appl Environ Microbiol       Date:  2005-12       Impact factor: 4.792

10.  Evolution of mammals and their gut microbes.

Authors:  Ruth E Ley; Micah Hamady; Catherine Lozupone; Peter J Turnbaugh; Rob Roy Ramey; J Stephen Bircher; Michael L Schlegel; Tammy A Tucker; Mark D Schrenzel; Rob Knight; Jeffrey I Gordon
Journal:  Science       Date:  2008-05-22       Impact factor: 47.728

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  43 in total

1.  Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

Authors:  James J Kozich; Sarah L Westcott; Nielson T Baxter; Sarah K Highlander; Patrick D Schloss
Journal:  Appl Environ Microbiol       Date:  2013-06-21       Impact factor: 4.792

2.  Two-stage microbial community experimental design.

Authors:  Timothy L Tickle; Nicola Segata; Levi Waldron; Uri Weingart; Curtis Huttenhower
Journal:  ISME J       Date:  2013-08-15       Impact factor: 10.302

3.  Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform.

Authors:  Yoon-Seong Jeon; Sang-Cheol Park; Jeongmin Lim; Jongsik Chun; Bong-Soo Kim
Journal:  J Microbiol       Date:  2015-01-04       Impact factor: 3.422

Review 4.  Lung microbiome for clinicians. New discoveries about bugs in healthy and diseased lungs.

Authors:  Leopoldo N Segal; William N Rom; Michael D Weiden
Journal:  Ann Am Thorac Soc       Date:  2014-01

5.  Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum.

Authors:  Andrea Hahn; Amit Sanyal; Geovanny F Perez; Anamaris M Colberg-Poley; Joseph Campos; Mary C Rose; Marcos Pérez-Losada
Journal:  J Microbiol Methods       Date:  2016-09-05       Impact factor: 2.363

6.  Daily Changes in Composition and Diversity of the Intestinal Microbiota in Patients with Anorexia Nervosa: A Series of Three Cases.

Authors:  Susan C Kleiman; Elaine M Glenny; Emily C Bulik-Sullivan; Eun Young Huh; Matthew C B Tsilimigras; Anthony A Fodor; Cynthia M Bulik; Ian M Carroll
Journal:  Eur Eat Disord Rev       Date:  2017-06-06

7.  Microbial community composition and diversity in Caspian Sea sediments.

Authors:  Nagissa Mahmoudi; Michael S Robeson; Hector F Castro; Julian L Fortney; Stephen M Techtmann; Dominique C Joyner; Charles J Paradis; Susan M Pfiffner; Terry C Hazen
Journal:  FEMS Microbiol Ecol       Date:  2014-12-05       Impact factor: 4.194

8.  Illumina sequencing-based analyses of bacterial communities during short-chain fatty-acid production from food waste and sewage sludge fermentation at different pH values.

Authors:  Weixiao Cheng; Hong Chen; ShuHai Yan; Jianqiang Su
Journal:  World J Microbiol Biotechnol       Date:  2014-06-04       Impact factor: 3.312

9.  Conducting a microbiome study.

Authors:  Julia K Goodrich; Sara C Di Rienzi; Angela C Poole; Omry Koren; William A Walters; J Gregory Caporaso; Rob Knight; Ruth E Ley
Journal:  Cell       Date:  2014-07-17       Impact factor: 41.582

10.  Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments.

Authors:  Christopher S Miller; Kim M Handley; Kelly C Wrighton; Kyle R Frischkorn; Brian C Thomas; Jillian F Banfield
Journal:  PLoS One       Date:  2013-02-06       Impact factor: 3.240

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