Literature DB >> 21552235

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

Aleksandar D Kostic, Akinyemi I Ojesina, Chandra Sekhar Pedamallu, Joonil Jung, Roel G W Verhaak, Gad Getz, Matthew Meyerson.   

Abstract

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Year:  2011        PMID： 21552235      PMCID： PMC3523678          DOI： 10.1038/nbt.1868

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  22 in total

1.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

2.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Authors:  Daniel R Zerbino; Ewan Birney
Journal:  Genome Res       Date:  2008-03-18       Impact factor: 9.043

Review 3.  Next-generation DNA sequencing methods.

Authors:  Elaine R Mardis
Journal:  Annu Rev Genomics Hum Genet       Date:  2008       Impact factor: 8.929

4.  The complete genome of an individual by massively parallel DNA sequencing.

Authors:  David A Wheeler; Maithreyan Srinivasan; Michael Egholm; Yufeng Shen; Lei Chen; Amy McGuire; Wen He; Yi-Ju Chen; Vinod Makhijani; G Thomas Roth; Xavier Gomes; Karrie Tartaro; Faheem Niazi; Cynthia L Turcotte; Gerard P Irzyk; James R Lupski; Craig Chinault; Xing-zhi Song; Yue Liu; Ye Yuan; Lynne Nazareth; Xiang Qin; Donna M Muzny; Marcel Margulies; George M Weinstock; Richard A Gibbs; Jonathan M Rothberg
Journal:  Nature       Date:  2008-04-17       Impact factor: 49.962

5.  Adding pathogens by genomic subtraction.

Authors:  Laura MacConaill; Matthew Meyerson
Journal:  Nat Genet       Date:  2008-04       Impact factor: 38.330

6.  Papillomavirus sequences integrate near cellular oncogenes in some cervical carcinomas.

Authors:  M Dürst; C M Croce; L Gissmann; E Schwarz; K Huebner
Journal:  Proc Natl Acad Sci U S A       Date:  1987-02       Impact factor: 11.205

7.  Clonal integration of a polyomavirus in human Merkel cell carcinoma.

Authors:  Huichen Feng; Masahiro Shuda; Yuan Chang; Patrick S Moore
Journal:  Science       Date:  2008-01-17       Impact factor: 47.728

8.  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

9.  A new arenavirus in a cluster of fatal transplant-associated diseases.

Authors:  Gustavo Palacios; Julian Druce; Lei Du; Thomas Tran; Chris Birch; Thomas Briese; Sean Conlan; Phenix-Lan Quan; Jeffrey Hui; John Marshall; Jan Fredrik Simons; Michael Egholm; Christopher D Paddock; Wun-Ju Shieh; Cynthia S Goldsmith; Sherif R Zaki; Mike Catton; W Ian Lipkin
Journal:  N Engl J Med       Date:  2008-02-06       Impact factor: 91.245

10.  Pathogen discovery.

Authors:  W Ian Lipkin
Journal:  PLoS Pathog       Date:  2008-04-25       Impact factor: 6.823
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  134 in total

1.  Rapid identification of non-human sequences in high-throughput sequencing datasets.

Authors:  Aparna Bhaduri; Kun Qu; Carolyn S Lee; Alexander Ungewickell; Paul A Khavari
Journal:  Bioinformatics       Date:  2012-02-28       Impact factor: 6.937

2.  Detection of a possible bioterrorism agent, Francisella sp., in a clinical specimen by use of next-generation direct DNA sequencing.

Authors:  Makoto Kuroda; Tsuyoshi Sekizuka; Fumiaki Shinya; Fumihiko Takeuchi; Takayuki Kanno; Tetsutaro Sata; Shigeyuki Asano
Journal:  J Clin Microbiol       Date:  2012-02-15       Impact factor: 5.948

Review 3.  Cancer and the microbiota.

Authors:  Wendy S Garrett
Journal:  Science       Date:  2015-04-03       Impact factor: 47.728

4.  Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.

Authors:  Aleksandar D Kostic; Dirk Gevers; Chandra Sekhar Pedamallu; Monia Michaud; Fujiko Duke; Ashlee M Earl; Akinyemi I Ojesina; Joonil Jung; Adam J Bass; Josep Tabernero; José Baselga; Chen Liu; Ramesh A Shivdasani; Shuji Ogino; Bruce W Birren; Curtis Huttenhower; Wendy S Garrett; Matthew Meyerson
Journal:  Genome Res       Date:  2011-10-18       Impact factor: 9.043

5.  Viral metagenomics: a tool for virus discovery and diversity in aquaculture.

Authors:  S V Alavandi; M Poornima
Journal:  Indian J Virol       Date:  2012-08-14

6.  Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome.

Authors:  Ami S Bhatt; Samuel S Freeman; Alex F Herrera; Chandra Sekhar Pedamallu; Dirk Gevers; Fujiko Duke; Joonil Jung; Monia Michaud; Bruce J Walker; Sarah Young; Ashlee M Earl; Aleksander D Kostic; Akinyemi I Ojesina; Robert Hasserjian; Karen K Ballen; Yi-Bin Chen; Gabriela Hobbs; Joseph H Antin; Robert J Soiffer; Lindsey R Baden; Wendy S Garrett; Jason L Hornick; Francisco M Marty; Matthew Meyerson
Journal:  N Engl J Med       Date:  2013-08-08       Impact factor: 91.245

7.  Challenges in benchmarking metagenomic profilers.

Authors:  Zheng Sun; Shi Huang; Meng Zhang; Qiyun Zhu; Niina Haiminen; Anna Paola Carrieri; Yoshiki Vázquez-Baeza; Laxmi Parida; Ho-Cheol Kim; Rob Knight; Yang-Yu Liu
Journal:  Nat Methods       Date:  2021-05-13       Impact factor: 28.547

8.  Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas.

Authors:  Yang Liu; Nilay S Sethi; Toshinori Hinoue; Barbara G Schneider; Andrew D Cherniack; Francisco Sanchez-Vega; Jose A Seoane; Farshad Farshidfar; Reanne Bowlby; Mirazul Islam; Jaegil Kim; Walid Chatila; Rehan Akbani; Rupa S Kanchi; Charles S Rabkin; Joseph E Willis; Kenneth K Wang; Shannon J McCall; Lopa Mishra; Akinyemi I Ojesina; Susan Bullman; Chandra Sekhar Pedamallu; Alexander J Lazar; Ryo Sakai; Vésteinn Thorsson; Adam J Bass; Peter W Laird
Journal:  Cancer Cell       Date:  2018-04-02       Impact factor: 31.743

9.  Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing.

Authors:  Michael J Strong; Tina O'Grady; Zhen Lin; Guorong Xu; Melody Baddoo; Chris Parsons; Kun Zhang; Christopher M Taylor; Erik K Flemington
Journal:  J Virol       Date:  2013-09-18       Impact factor: 5.103

Review 10.  MSMB variation and prostate cancer risk: clues towards a possible fungal etiology.

Authors:  Siobhan Sutcliffe; Angelo M De Marzo; Karen S Sfanos; Martin Laurence
Journal:  Prostate       Date:  2014-01-24       Impact factor: 4.104
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