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Results: 1 to 20 of 29

References for PMC Articles for PubMed (Select 22962453)

1.

How to apply de Bruijn graphs to genome assembly.

Compeau PE, Pevzner PA, Tesler G.

Nat Biotechnol. 2011 Nov 8;29(11):987-91. doi: 10.1038/nbt.2023. No abstract available.

PMID:
22068540
2.

Taxonomic classification of metagenomic shotgun sequences with CARMA3.

Gerlach W, Stoye J.

Nucleic Acids Res. 2011 Aug;39(14):e91. doi: 10.1093/nar/gkr225. Epub 2011 May 17.

3.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

4.

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.

Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM.

Science. 2011 Jan 28;331(6016):463-7. doi: 10.1126/science.1200387.

5.

FragGeneScan: predicting genes in short and error-prone reads.

Rho M, Tang H, Ye Y.

Nucleic Acids Res. 2010 Nov;38(20):e191. doi: 10.1093/nar/gkq747. Epub 2010 Aug 30.

6.

Metagenomic sequencing of an in vitro-simulated microbial community.

Morgan JL, Darling AE, Eisen JA.

PLoS One. 2010 Apr 16;5(4):e10209. doi: 10.1371/journal.pone.0010209.

7.

A human gut microbial gene catalogue established by metagenomic sequencing.

Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J.

Nature. 2010 Mar 4;464(7285):59-65. doi: 10.1038/nature08821.

8.

Fast and accurate long-read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2010 Mar 1;26(5):589-95. doi: 10.1093/bioinformatics/btp698. Epub 2010 Jan 15.

9.

De novo assembly of human genomes with massively parallel short read sequencing.

Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J.

Genome Res. 2010 Feb;20(2):265-72. doi: 10.1101/gr.097261.109. Epub 2009 Dec 17.

10.

The effect of sequencing errors on metagenomic gene prediction.

Hoff KJ.

BMC Genomics. 2009 Nov 12;10:520. doi: 10.1186/1471-2164-10-520.

11.

The NIH Human Microbiome Project.

NIH HMP Working Group, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, Little AR, Peavy H, Pontzer C, Portnoy M, Sayre MH, Starke-Reed P, Zakhari S, Read J, Watson B, Guyer M.

Genome Res. 2009 Dec;19(12):2317-23. doi: 10.1101/gr.096651.109. Epub 2009 Oct 9.

12.

An ORFome assembly approach to metagenomics sequences analysis.

Ye Y, Tang H.

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

13.

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.

14.

MetaSim: a sequencing simulator for genomics and metagenomics.

Richter DC, Ott F, Auch AF, Schmid R, Huson DH.

PLoS One. 2008 Oct 8;3(10):e3373. doi: 10.1371/journal.pone.0003373.

15.

Gene-boosted assembly of a novel bacterial genome from very short reads.

Salzberg SL, Sommer DD, Puiu D, Lee VT.

PLoS Comput Biol. 2008 Sep 26;4(9):e1000186. doi: 10.1371/journal.pcbi.1000186.

16.

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R.

Nat Methods. 2008 Mar;5(3):235-7. doi: 10.1038/nmeth.1184. Epub 2008 Feb 10.

17.

Metagenomics: read length matters.

Wommack KE, Bhavsar J, Ravel J.

Appl Environ Microbiol. 2008 Mar;74(5):1453-63. doi: 10.1128/AEM.02181-07. Epub 2008 Jan 11.

18.

Assembly reconciliation.

Zimin AV, Smith DR, Sutton G, Yorke JA.

Bioinformatics. 2008 Jan 1;24(1):42-5. Epub 2007 Dec 5.

19.

An obesity-associated gut microbiome with increased capacity for energy harvest.

Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI.

Nature. 2006 Dec 21;444(7122):1027-31.

PMID:
17183312
20.

Whole-genome re-sequencing.

Bentley DR.

Curr Opin Genet Dev. 2006 Dec;16(6):545-52. Epub 2006 Oct 18. Review.

PMID:
17055251
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