Metagenomics: DNA sequencing of environmental samples

By Susannah Tringe, Edward M. Rubin. Nature reviews genetics, 2005

604 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0ed00625a01a475030ea6fda1b26f40e4d84a81d

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Citations in the corpus

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes (2012, background): “The value of shotgunmetagenomic analyses is that a far more comprehensive understanding of the traits microbes may use to survive in an individual soil can be identified, traits which are often very difficult to measure using biogeochemical or culturebased approaches (19).”
Using inferred residue contacts to distinguish between correct and incorrect protein models (2008, background): “Recent studies have exploited metagenomic shotgun sequencing to dramatically expand the size of protein sequence space (Tringe and Rubin, 2005).”
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies (2019, positive): “Studies of microbial communities based on microbial isolation and cultivation have been gradually replaced by high throughput, whole genome shotgun sequencing based metagenomics (reviewed in Van Dijk et al., 2014 ; Tringe & Rubin, 2005 ).”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, background): “Environmental shotgun sequencing projects, in which genetic sequences are sampled from communities of microorganisms [10–14], are poised to make a dramatic impact on our understanding of proteins and protein families.”
Gut microbiome-host interactions in health and disease (2011, background): “Recent advances in sequencing technologies have led to the wider use of metagenomic analysis for studying complex ecosystems such as the human gut [34-36], and some key findings from human studies are outlined in Table 1.”
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree (2010, background): “This technology has revolutionized the possibilities for unbiased surveys of environmental microbial diversity, ranging from the human gut to the open ocean [2-8].”
Chlorosomes: Antenna Organelles in Photosynthetic Green Bacteria (2006, background): “It is possible that the recent approach of metagenomics, when applied to DNA isolated from photosynthetic microbial mats, will reveal novel organisms that contain chlorosomes (Tringe and Rubin 2005).”
A human gut microbial gene catalog established by metagenomic sequencing (2010, methodology): “Metagenomic sequencing represents a powerful alternative to rRNA sequencing for analysing complex microbial communities 13–15 .”
A Bioinformatician's Guide to Metagenomics (2008, background): “(134, 135), in which they coined the term environmental gene tags because of the fragmentary nature of the data, akin to expressed sequence tags.”
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products (2013, positive): “Since most bacteria cannot be cultivated in the laboratory (Rappe and Giovannoni, 2003; Tringe and Rubin, 2005) and thus cannot be sequenced, much of the bacterial diversity remains below the radar of NGS projects.”
bold: The Barcode of Life Data System (http://www.barcodinglife.org) (2007, neutral): “2004; Tringe & Rubin 2005).”