Literature DB >> 16304596

Metagenomics: DNA sequencing of environmental samples.

Susannah Green Tringe1, Edward M Rubin.   

Abstract

Although genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms represent only a fraction of the living or once-living organisms of interest. Many species are difficult to study in isolation because they fail to grow in laboratory culture, depend on other organisms for critical processes, or have become extinct. Methods that are based on DNA sequencing circumvent these obstacles, as DNA can be isolated directly from living or dead cells in various contexts. Such methods have led to the emergence of a new field, which is referred to as metagenomics.

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Year:  2005        PMID: 16304596     DOI: 10.1038/nrg1709

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  153 in total

1.  Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA.

Authors:  Rachel Marine; Shawn W Polson; Jacques Ravel; Graham Hatfull; Daniel Russell; Matthew Sullivan; Fraz Syed; Michael Dumas; K Eric Wommack
Journal:  Appl Environ Microbiol       Date:  2011-09-23       Impact factor: 4.792

Review 2.  Integration of metabolic reactions and gene regulation.

Authors:  Chen-Hsiang Yeang
Journal:  Mol Biotechnol       Date:  2011-01       Impact factor: 2.695

3.  Prospecting metagenomic enzyme subfamily genes for DNA family shuffling by a novel PCR-based approach.

Authors:  Qiuyan Wang; Huili Wu; Anming Wang; Pengfei Du; Xiaolin Pei; Haifeng Li; Xiaopu Yin; Lifeng Huang; Xiaolong Xiong
Journal:  J Biol Chem       Date:  2010-10-20       Impact factor: 5.157

4.  Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica.

Authors:  Ying-wu Shi; Kai Lou; Chun Li; Lei Wang; Zhen-yong Zhao; Shuai Zhao; Chang-yan Tian
Journal:  J Microbiol       Date:  2015-10-02       Impact factor: 3.422

5.  Unexpected features of the dark proteome.

Authors:  Nelson Perdigão; Julian Heinrich; Christian Stolte; Kenneth S Sabir; Michael J Buckley; Bruce Tabor; Beth Signal; Brian S Gloss; Christopher J Hammang; Burkhard Rost; Andrea Schafferhans; Seán I O'Donoghue
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-17       Impact factor: 11.205

Review 6.  The role of the gut microbiome in systemic inflammatory disease.

Authors:  Jose C Clemente; Julia Manasson; Jose U Scher
Journal:  BMJ       Date:  2018-01-08

7.  Sequencing and analysis of Neanderthal genomic DNA.

Authors:  James P Noonan; Graham Coop; Sridhar Kudaravalli; Doug Smith; Johannes Krause; Joe Alessi; Feng Chen; Darren Platt; Svante Pääbo; Jonathan K Pritchard; Edward M Rubin
Journal:  Science       Date:  2006-11-17       Impact factor: 47.728

Review 8.  Ten years of bacterial genome sequencing: comparative-genomics-based discoveries.

Authors:  Tim T Binnewies; Yair Motro; Peter F Hallin; Ole Lund; David Dunn; Tom La; David J Hampson; Matthew Bellgard; Trudy M Wassenaar; David W Ussery
Journal:  Funct Integr Genomics       Date:  2006-05-12       Impact factor: 3.410

9.  New avenues in protein function prediction.

Authors:  Iddo Friedberg; Martin Jambon; Adam Godzik
Journal:  Protein Sci       Date:  2006-06       Impact factor: 6.725

10.  Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH).

Authors:  Peng Liu; Robert J Meagher; Yooli K Light; Suzan Yilmaz; Romy Chakraborty; Adam P Arkin; Terry C Hazen; Anup K Singh
Journal:  Lab Chip       Date:  2011-07-14       Impact factor: 6.799

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