Literature DB >> 20581189

Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray.

Michael C Schatz1, Adam M Phillippy, Pawel Gajer, Todd Z DeSantis, Gary L Andersen, Jacques Ravel.   

Abstract

PhyloTrac is an integrated desktop application for analysis of PhyloChip microarray data. PhyloTrac combined with PhyloChip provides turnkey and comprehensive identification and analysis of bacterial and archaeal communities in complex environmental samples. PhyloTrac is free for noncommercial organizations and is available for all major operating systems at http://www.phylotrac.org/.

Entities:  

Mesh：

Year:  2010        PMID： 20581189      PMCID： PMC2918976          DOI： 10.1128/AEM.00303-10

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  9 in total

1.  Open source clustering software.

Authors:  M J L de Hoon; S Imoto; J Nolan; S Miyano
Journal:  Bioinformatics       Date:  2004-02-10       Impact factor: 6.937

2.  Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray.

Authors:  Todd Z DeSantis; Carol E Stone; Sonya R Murray; Jordan P Moberg; Gary L Andersen
Journal:  FEMS Microbiol Lett       Date:  2005-04-15       Impact factor: 2.742

3.  Urban aerosols harbor diverse and dynamic bacterial populations.

Authors:  Eoin L Brodie; Todd Z DeSantis; Jordan P Moberg Parker; Ingrid X Zubietta; Yvette M Piceno; Gary L Andersen
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-20       Impact factor: 11.205

4.  Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation.

Authors:  Eoin L Brodie; Todd Z Desantis; Dominique C Joyner; Seung M Baek; Joern T Larsen; Gary L Andersen; Terry C Hazen; Paul M Richardson; Donald J Herman; Tetsu K Tokunaga; Jiamin M Wan; Mary K Firestone
Journal:  Appl Environ Microbiol       Date:  2006-09       Impact factor: 4.792

5.  Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa.

Authors:  J L Flanagan; E L Brodie; L Weng; S V Lynch; O Garcia; R Brown; P Hugenholtz; T Z DeSantis; G L Andersen; J P Wiener-Kronish; J Bristow
Journal:  J Clin Microbiol       Date:  2007-04-04       Impact factor: 5.948

6.  Induction of intestinal Th17 cells by segmented filamentous bacteria.

Authors:  Ivaylo I Ivanov; Koji Atarashi; Nicolas Manel; Eoin L Brodie; Tatsuichiro Shima; Ulas Karaoz; Dongguang Wei; Katherine C Goldfarb; Clark A Santee; Susan V Lynch; Takeshi Tanoue; Akemi Imaoka; Kikuji Itoh; Kiyoshi Takeda; Yoshinori Umesaki; Kenya Honda; Dan R Littman
Journal:  Cell       Date:  2009-10-30       Impact factor: 41.582

7.  Bioconductor: open software development for computational biology and bioinformatics.

Authors:  Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Journal:  Genome Biol       Date:  2004-09-15       Impact factor: 13.583

8.  High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment.

Authors:  Todd Z DeSantis; Eoin L Brodie; Jordan P Moberg; Ingrid X Zubieta; Yvette M Piceno; Gary L Andersen
Journal:  Microb Ecol       Date:  2007-03-02       Impact factor: 4.192

9.  Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data.

Authors:  Micah Hamady; Catherine Lozupone; Rob Knight
Journal:  ISME J       Date:  2009-08-27       Impact factor: 10.302
  9 in total
  11 in total

1.  Influence of geogenic factors on microbial communities in metallogenic Australian soils.

Authors:  Frank Reith; Joel Brugger; Carla M Zammit; Adrienne L Gregg; Katherine C Goldfarb; Gary L Andersen; Todd Z DeSantis; Yvette M Piceno; Eoin L Brodie; Zhenmei Lu; Zhili He; Jizhong Zhou; Steven A Wakelin
Journal:  ISME J       Date:  2012-06-07       Impact factor: 10.302

2.  Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits.

Authors:  Frank Reith; Carla M Zammit; Rebecca Pohrib; Adrienne L Gregg; Steven A Wakelin
Journal:  Appl Environ Microbiol       Date:  2015-09-04       Impact factor: 4.792

3.  PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity.

Authors:  T A Nelson; S Holmes; A V Alekseyenko; M Shenoy; T Desantis; C H Wu; G L Andersen; J Winston; J Sonnenburg; P J Pasricha; A Spormann
Journal:  Neurogastroenterol Motil       Date:  2010-12-03       Impact factor: 3.598

Review 4.  Application of phylogenetic microarrays to interrogation of human microbiota.

Authors:  Oleg Paliy; Richard Agans
Journal:  FEMS Microbiol Ecol       Date:  2011-11-09       Impact factor: 4.194

5.  Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks.

Authors:  Andrey Morgun; Amiran Dzutsev; Xiaoxi Dong; Renee L Greer; D Joseph Sexton; Jacques Ravel; Martin Schuster; William Hsiao; Polly Matzinger; Natalia Shulzhenko
Journal:  Gut       Date:  2015-01-22       Impact factor: 23.059

6.  Firmicutes dominate the bacterial taxa within sugar-cane processing plants.

Authors:  Farhana Sharmin; Steve Wakelin; Flavia Huygens; Megan Hargreaves
Journal:  Sci Rep       Date:  2013-11-01       Impact factor: 4.379

7.  Analysis of Gut Microbiome and Diet Modification in Patients with Crohn's Disease.

Authors:  Sumathi Sankaran Walters; Antonio Quiros; Matthew Rolston; Irina Grishina; Jay Li; Anne Fenton; Todd Z DeSantis; Anne Thai; Gary L Andersen; Peggy Papathakis; Raquel Nieves; Thomas Prindiville; Satya Dandekar
Journal:  SOJ Microbiol Infect Dis       Date:  2014-06-27

8.  Chapter 12: Human microbiome analysis.

Authors:  Xochitl C Morgan; Curtis Huttenhower
Journal:  PLoS Comput Biol       Date:  2012-12-27       Impact factor: 4.475

9.  Comparison of the fecal microbiota in feral and domestic goats.

Authors:  Kassandra M De Jesús-Laboy; Filipa Godoy-Vitorino; Yvette M Piceno; Lauren M Tom; Ida G Pantoja-Feliciano; Michelle J Rivera-Rivera; Gary L Andersen; María G Domínguez-Bello
Journal:  Genes (Basel)       Date:  2011-12-21       Impact factor: 4.096

10.  Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray) analysis.

Authors:  Amlan K Patra; Zhongtang Yu
Journal:  Front Microbiol       Date:  2015-04-10       Impact factor: 5.640
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