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Items: 1 to 20 of 130

1.

Analysis and comparison of very large metagenomes with fast clustering and functional annotation.

Li W.

BMC Bioinformatics. 2009 Oct 28;10:359. doi: 10.1186/1471-2105-10-359.

2.

Sense from sequence reads: methods for alignment and assembly.

Flicek P, Birney E.

Nat Methods. 2009 Nov;6(11 Suppl):S6-S12. doi: 10.1038/nmeth.1376. Review.

PMID:
19844229
3.

Next-generation gap.

McPherson JD.

Nat Methods. 2009 Nov;6(11 Suppl):S2-5. doi: 10.1038/nmeth.f.268. Review.

PMID:
19844227
4.

Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F.

PLoS One. 2009 Oct 9;4(10):e7370. doi: 10.1371/journal.pone.0007370.

5.

Photosystem I gene cassettes are present in marine virus genomes.

Sharon I, Alperovitch A, Rohwer F, Haynes M, Glaser F, Atamna-Ismaeel N, Pinter RY, Partensky F, Koonin EV, Wolf YI, Nelson N, Béjà O.

Nature. 2009 Sep 10;461(7261):258-262. doi: 10.1038/nature08284. Epub 2009 Aug 26.

6.

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes.

Kristiansson E, Hugenholtz P, Dalevi D.

Bioinformatics. 2009 Oct 15;25(20):2737-8. doi: 10.1093/bioinformatics/btp508. Epub 2009 Aug 20.

PMID:
19696045
7.

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.

Brady A, Salzberg SL.

Nat Methods. 2009 Sep;6(9):673-6. doi: 10.1038/nmeth.1358. Epub 2009 Aug 2.

8.

Managing and analyzing next-generation sequence data.

Richter BG, Sexton DP.

PLoS Comput Biol. 2009 Jun;5(6):e1000369. doi: 10.1371/journal.pcbi.1000369. Epub 2009 Jun 26. No abstract available.

9.

Visual and statistical comparison of metagenomes.

Mitra S, Klar B, Huson DH.

Bioinformatics. 2009 Aug 1;25(15):1849-55. doi: 10.1093/bioinformatics/btp341. Epub 2009 Jun 10.

PMID:
19515961
10.

An ORFome assembly approach to metagenomics sequences analysis.

Ye Y, Tang H.

J Bioinform Comput Biol. 2009 Jun;7(3):455-71.

11.

Genome assembly reborn: recent computational challenges.

Pop M.

Brief Bioinform. 2009 Jul;10(4):354-66. doi: 10.1093/bib/bbp026. Epub 2009 May 29.

12.

Genome sequence data: management, storage, and visualization.

Batley J, Edwards D.

Biotechniques. 2009 Apr;46(5):333-4, 336. doi: 10.2144/000113134. Review.

13.

A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment.

Tzahor S, Man-Aharonovich D, Kirkup BC, Yogev T, Berman-Frank I, Polz MF, Béjà O, Mandel-Gutfreund Y.

BMC Genomics. 2009 May 16;10:229. doi: 10.1186/1471-2164-10-229.

14.

Statistical methods for detecting differentially abundant features in clinical metagenomic samples.

White JR, Nagarajan N, Pop M.

PLoS Comput Biol. 2009 Apr;5(4):e1000352. doi: 10.1371/journal.pcbi.1000352. Epub 2009 Apr 10.

15.

Continuous base identification for single-molecule nanopore DNA sequencing.

Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H.

Nat Nanotechnol. 2009 Apr;4(4):265-70. doi: 10.1038/nnano.2009.12. Epub 2009 Feb 22.

PMID:
19350039
16.

Evaluation of next generation sequencing platforms for population targeted sequencing studies.

Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA.

Genome Biol. 2009;10(3):R32. doi: 10.1186/gb-2009-10-3-r32. Epub 2009 Mar 27.

17.

Planning the human variome project: the Spain report.

Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS; Contributors to the Human Variome Project Planning Meeting.

Hum Mutat. 2009 Apr;30(4):496-510. doi: 10.1002/humu.20972.

PMID:
19306394
18.

Effects of experimental choices and analysis noise on surveys of the "rare biosphere".

Hamp TJ, Jones WJ, Fodor AA.

Appl Environ Microbiol. 2009 May;75(10):3263-70. doi: 10.1128/AEM.01931-08. Epub 2009 Mar 6.

19.

Methods for comparative metagenomics.

Huson DH, Richter DC, Mitra S, Auch AF, Schuster SC.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S12. doi: 10.1186/1471-2105-10-S1-S12.

20.

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases.

Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA.

Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1948-53. doi: 10.1073/pnas.0806191105. Epub 2009 Jan 30.

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