Literature DB >> 22717882

Describing microbial communities and performing global comparisons in the 'omic era.

Tom O Delmont1, Pascal Simonet, Timothy M Vogel.   

Abstract

Mesh：

Year:  2012        PMID： 22717882      PMCID： PMC3425746          DOI： 10.1038/ismej.2012.55

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


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  12 in total

1.  Community structure and metabolism through reconstruction of microbial genomes from the environment.

Authors:  Gene W Tyson; Jarrod Chapman; Philip Hugenholtz; Eric E Allen; Rachna J Ram; Paul M Richardson; Victor V Solovyev; Edward M Rubin; Daniel S Rokhsar; Jillian F Banfield
Journal:  Nature       Date:  2004-02-01       Impact factor: 49.962

2.  Comparative metagenomics of microbial communities.

Authors:  Susannah Green Tringe; Christian von Mering; Arthur Kobayashi; Asaf A Salamov; Kevin Chen; Hwai W Chang; Mircea Podar; Jay M Short; Eric J Mathur; John C Detter; Peer Bork; Philip Hugenholtz; Edward M Rubin
Journal:  Science       Date:  2005-04-22       Impact factor: 47.728

3.  Functional metagenomic profiling of nine biomes.

Authors:  Elizabeth A Dinsdale; Robert A Edwards; Dana Hall; Florent Angly; Mya Breitbart; Jennifer M Brulc; Mike Furlan; Christelle Desnues; Matthew Haynes; Linlin Li; Lauren McDaniel; Mary Ann Moran; Karen E Nelson; Christina Nilsson; Robert Olson; John Paul; Beltran Rodriguez Brito; Yijun Ruan; Brandon K Swan; Rick Stevens; David L Valentine; Rebecca Vega Thurber; Linda Wegley; Bryan A White; Forest Rohwer
Journal:  Nature       Date:  2008-03-12       Impact factor: 49.962

4.  Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products.

Authors:  J Handelsman; M R Rondon; S F Brady; J Clardy; R M Goodman
Journal:  Chem Biol       Date:  1998-10

5.  Metagenomic mining for microbiologists.

Authors:  Tom O Delmont; Cedric Malandain; Emmanuel Prestat; Catherine Larose; Jean-Michel Monier; Pascal Simonet; Timothy M Vogel
Journal:  ISME J       Date:  2011-05-19       Impact factor: 10.302

6.  Identifying biologically relevant differences between metagenomic communities.

Authors:  Donovan H Parks; Robert G Beiko
Journal:  Bioinformatics       Date:  2010-02-03       Impact factor: 6.937

7.  Environmental genome shotgun sequencing of the Sargasso Sea.

Authors:  J Craig Venter; Karin Remington; John F Heidelberg; Aaron L Halpern; Doug Rusch; Jonathan A Eisen; Dongying Wu; Ian Paulsen; Karen E Nelson; William Nelson; Derrick E Fouts; Samuel Levy; Anthony H Knap; Michael W Lomas; Ken Nealson; Owen White; Jeremy Peterson; Jeff Hoffman; Rachel Parsons; Holly Baden-Tillson; Cynthia Pfannkoch; Yu-Hui Rogers; Hamilton O Smith
Journal:  Science       Date:  2004-03-04       Impact factor: 47.728

8.  Structure, fluctuation and magnitude of a natural grassland soil metagenome.

Authors:  Tom O Delmont; Emmanuel Prestat; Kevin P Keegan; Michael Faubladier; Patrick Robe; Ian M Clark; Eric Pelletier; Penny R Hirsch; Folker Meyer; Jack A Gilbert; Denis Le Paslier; Pascal Simonet; Timothy M Vogel
Journal:  ISME J       Date:  2012-02-02       Impact factor: 10.302

9.  The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.

Authors:  F Meyer; D Paarmann; M D'Souza; R Olson; E M Glass; M Kubal; T Paczian; A Rodriguez; R Stevens; A Wilke; J Wilkening; R A Edwards
Journal:  BMC Bioinformatics       Date:  2008-09-19       Impact factor: 3.169

10.  IMG/M: a data management and analysis system for metagenomes.

Authors:  Victor M Markowitz; Natalia N Ivanova; Ernest Szeto; Krishna Palaniappan; Ken Chu; Daniel Dalevi; I-Min A Chen; Yuri Grechkin; Inna Dubchak; Iain Anderson; Athanasios Lykidis; Konstantinos Mavromatis; Philip Hugenholtz; Nikos C Kyrpides
Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971
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  13 in total

1.  Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils.

Authors:  Aman S Gill; Angela Lee; Krista L McGuire
Journal:  Appl Environ Microbiol       Date:  2017-08-01       Impact factor: 4.792

2.  Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications.

Authors:  Natasha DeLeon-Rodriguez; Terry L Lathem; Luis M Rodriguez-R; James M Barazesh; Bruce E Anderson; Andreas J Beyersdorf; Luke D Ziemba; Michael Bergin; Athanasios Nenes; Konstantinos T Konstantinidis
Journal:  Proc Natl Acad Sci U S A       Date:  2013-01-28       Impact factor: 11.205

Review 3.  Metagenomic applications in environmental monitoring and bioremediation.

Authors:  Stephen M Techtmann; Terry C Hazen
Journal:  J Ind Microbiol Biotechnol       Date:  2016-08-24       Impact factor: 3.346

4.  Bacterial communities in the small intestine respond differently to those in the caecum and colon in mice fed low- and high-fat diets.

Authors:  Janet C Onishi; Sara Campbell; Michael Moreau; Falshruti Patel; Andrew I Brooks; Yin Xiu Zhou; Max M Häggblom; Judith Storch
Journal:  Microbiology       Date:  2017-07-26       Impact factor: 2.777

5.  Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil.

Authors:  Matthew J Meier; E Suzanne Paterson; Iain B Lambert
Journal:  Appl Environ Microbiol       Date:  2015-11-20       Impact factor: 4.792

6.  Random whole metagenomic sequencing for forensic discrimination of soils.

Authors:  Anastasia S Khodakova; Renee J Smith; Leigh Burgoyne; Damien Abarno; Adrian Linacre
Journal:  PLoS One       Date:  2014-08-11       Impact factor: 3.240

7.  Analysis of run-to-run variation of bar-coded pyrosequencing for evaluating bacterial community shifts and individual taxa dynamics.

Authors:  Yuan Ge; Joshua P Schimel; Patricia A Holden
Journal:  PLoS One       Date:  2014-06-09       Impact factor: 3.240

8.  Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods.

Authors:  Santosh Keisam; Wahengbam Romi; Giasuddin Ahmed; Kumaraswamy Jeyaram
Journal:  Sci Rep       Date:  2016-09-27       Impact factor: 4.379

9.  Anvi'o: an advanced analysis and visualization platform for 'omics data.

Authors:  A Murat Eren; Özcan C Esen; Christopher Quince; Joseph H Vineis; Hilary G Morrison; Mitchell L Sogin; Tom O Delmont
Journal:  PeerJ       Date:  2015-10-08       Impact factor: 2.984

10.  Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter.

Authors:  Marc Garcia-Garcera; Marie Touchon; Sylvain Brisse; Eduardo P C Rocha
Journal:  Environ Microbiol       Date:  2017-12-01       Impact factor: 5.491
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