Literature DB >> 11788827

Identification of foreign gene sequences by transcript filtering against the human genome.

Griffin Weber1, Jay Shendure, David M Tanenbaum, George M Church, Matthew Meyerson.   

Abstract

We have developed a computational subtraction approach to detect microbial causes for putative infectious diseases by filtering a set of human tissue-derived sequences against the human genome. We demonstrate the potential of this method by identifying sequences from known pathogens in established expressed-sequence tag libraries.

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Year:  2002        PMID： 11788827     DOI： 10.1038/ng818

Source DB:  PubMed          Journal:  Nat Genet        ISSN： 1061-4036            Impact factor:   38.330


  36 in total

1.  Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments.

Authors:  Torstein Tengs; Thomas LaFramboise; Robert B Den; David N Hayes; Jianhua Zhang; Saikat DebRoy; Robert C Gentleman; Keith O'Neill; Bruce Birren; Matthew Meyerson
Journal:  Nucleic Acids Res       Date:  2004-08-25       Impact factor: 16.971

2.  Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma.

Authors:  Mauro Castellarin; René L Warren; J Douglas Freeman; Lisa Dreolini; Martin Krzywinski; Jaclyn Strauss; Rebecca Barnes; Peter Watson; Emma Allen-Vercoe; Richard A Moore; Robert A Holt
Journal:  Genome Res       Date:  2011-10-18       Impact factor: 9.043

3.  Impact of the next generation DNA sequencers.

Authors:  Kikuya Kato
Journal:  Int J Clin Exp Med       Date:  2009-07-08

Review 4.  Gut Microbiota, Inflammation, and Colorectal Cancer.

Authors:  Caitlin A Brennan; Wendy S Garrett
Journal:  Annu Rev Microbiol       Date:  2016-09-08       Impact factor: 15.500

Review 5.  Focus on periodontal disease and colorectal carcinoma.

Authors:  D Lauritano; L Sbordone; M Nardone; A Iapichino; L Scapoli; F Carinci
Journal:  Oral Implantol (Rome)       Date:  2017-11-30

6.  PathSeq: software to identify or discover microbes by deep sequencing of human tissue.

Authors:  Aleksandar D Kostic; Akinyemi I Ojesina; Chandra Sekhar Pedamallu; Joonil Jung; Roel G W Verhaak; Gad Getz; Matthew Meyerson
Journal:  Nat Biotechnol       Date:  2011-05       Impact factor: 54.908

Review 7.  Advances in understanding cancer genomes through second-generation sequencing.

Authors:  Matthew Meyerson; Stacey Gabriel; Gad Getz
Journal:  Nat Rev Genet       Date:  2010-10       Impact factor: 53.242

8.  A novel algorithm for computational identification of contaminated EST libraries.

Authors:  Rotem Sorek; Hershel M Safer
Journal:  Nucleic Acids Res       Date:  2003-02-01       Impact factor: 16.971

9.  Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma.

Authors:  Huichen Feng; Jennifer L Taylor; Panayiotis V Benos; Robert Newton; Keith Waddell; Sebastien B Lucas; Yuan Chang; Patrick S Moore
Journal:  J Virol       Date:  2007-08-08       Impact factor: 5.103

10.  Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction.

Authors:  Torstein Tengs; Haibo Zhang; Arne Holst-Jensen; Jon Bohlin; Melinka A Butenko; Anja Bråthen Kristoffersen; Hilde-Gunn Opsahl Sorteberg; Knut G Berdal
Journal:  BMC Biotechnol       Date:  2009-10-08       Impact factor: 2.563
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