Literature DB >> 22543370

Fast, accurate error-correction of amplicon pyrosequences using Acacia.

Lauren Bragg, Glenn Stone, Michael Imelfort, Philip Hugenholtz, Gene W Tyson.   

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Year:  2012        PMID： 22543370     DOI： 10.1038/nmeth.1990

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  5 in total

1.  Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.

Authors:  Jens Reeder; Rob Knight
Journal:  Nat Methods       Date:  2010-09       Impact factor: 28.547

2.  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

3.  Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim.

Authors:  Susanne Balzer; Ketil Malde; Anders Lanzén; Animesh Sharma; Inge Jonassen
Journal:  Bioinformatics       Date:  2010-09-15       Impact factor: 6.937

4.  Removing noise from pyrosequenced amplicons.

Authors:  Christopher Quince; Anders Lanzen; Russell J Davenport; Peter J Turnbaugh
Journal:  BMC Bioinformatics       Date:  2011-01-28       Impact factor: 3.169

5.  Accuracy and quality of massively parallel DNA pyrosequencing.

Authors:  Susan M Huse; Julie A Huber; Hilary G Morrison; Mitchell L Sogin; David Mark Welch
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583
  5 in total
  147 in total

1.  Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment.

Authors:  Mohammad Bahram; Petr Kohout; Sten Anslan; Helery Harend; Kessy Abarenkov; Leho Tedersoo
Journal:  ISME J       Date:  2015-09-22       Impact factor: 10.302

2.  Microbial community stratification linked to utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest, Minnesota, USA.

Authors:  Xueju Lin; Malak M Tfaily; J Megan Steinweg; Patrick Chanton; Kaitlin Esson; Zamin K Yang; Jeffrey P Chanton; William Cooper; Christopher W Schadt; Joel E Kostka
Journal:  Appl Environ Microbiol       Date:  2014-03-28       Impact factor: 4.792

3.  Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix.

Authors:  Olga Pantos; Pim Bongaerts; Paul G Dennis; Gene W Tyson; Ove Hoegh-Guldberg
Journal:  ISME J       Date:  2015-02-10       Impact factor: 10.302

4.  Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data.

Authors:  Wenjie Deng; Brandon S Maust; Dylan H Westfall; Lennie Chen; Hong Zhao; Brendan B Larsen; Shyamala Iyer; Yi Liu; James I Mullins
Journal:  Bioinformatics       Date:  2013-07-29       Impact factor: 6.937

Review 5.  Analytical tools and databases for metagenomics in the next-generation sequencing era.

Authors:  Mincheol Kim; Ki-Hyun Lee; Seok-Whan Yoon; Bong-Soo Kim; Jongsik Chun; Hana Yi
Journal:  Genomics Inform       Date:  2013-09-30

6.  Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds.

Authors:  Sabine Filker; Anna Gimmler; Micah Dunthorn; Frédéric Mahé; Thorsten Stoeck
Journal:  Extremophiles       Date:  2014-12-04       Impact factor: 2.395

7.  Tree diversity and species identity effects on soil fungi, protists and animals are context dependent.

Authors:  Leho Tedersoo; Mohammad Bahram; Tomáš Cajthaml; Sergei Põlme; Indrek Hiiesalu; Sten Anslan; Helery Harend; Franz Buegger; Karin Pritsch; Julia Koricheva; Kessy Abarenkov
Journal:  ISME J       Date:  2015-07-14       Impact factor: 10.302

8.  Metaproteomics reveals functional differences in intestinal microbiota development of preterm infants.

Authors:  Romy D Zwittink; Diny van Zoeren-Grobben; Rocio Martin; Richard A van Lingen; Liesbeth J Groot Jebbink; Sjef Boeren; Ingrid B Renes; Ruurd M van Elburg; Clara Belzer; Jan Knol
Journal:  Mol Cell Proteomics       Date:  2017-07-06       Impact factor: 5.911

9.  Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands.

Authors:  Jane Oja; Johanna Vahtra; Mohammad Bahram; Petr Kohout; Tiiu Kull; Riinu Rannap; Urmas Kõljalg; Leho Tedersoo
Journal:  Mycorrhiza       Date:  2016-12-30       Impact factor: 3.387

10.  The Impact of Human Immunodeficiency Virus Infection on Gut Microbiota α-Diversity: An Individual-level Meta-analysis.

Authors:  Susan A Tuddenham; Wei Li A Koay; Ni Zhao; James R White; Khalil G Ghanem; Cynthia L Sears
Journal:  Clin Infect Dis       Date:  2020-02-03       Impact factor: 9.079
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