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Results: 1 to 20 of 23

References for PMC Articles for PubMed (Select 22821567)

1.

Meta-IDBA: a de Novo assembler for metagenomic data.

Peng Y, Leung HC, Yiu SM, Chin FY.

Bioinformatics. 2011 Jul 1;27(13):i94-101. doi: 10.1093/bioinformatics/btr216.

2.

A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.

Wu YW, Ye Y.

J Comput Biol. 2011 Mar;18(3):523-34. doi: 10.1089/cmb.2010.0245.

3.

Genovo: de novo assembly for metagenomes.

Laserson J, Jojic V, Koller D.

J Comput Biol. 2011 Mar;18(3):429-43. doi: 10.1089/cmb.2010.0244.

PMID:
21385045
4.

Species abundance distributions and richness estimations in fungal metagenomics--lessons learned from community ecology.

Unterseher M, Jumpponen A, Opik M, Tedersoo L, Moora M, Dormann CF, Schnittler M.

Mol Ecol. 2011 Jan;20(2):275-85. doi: 10.1111/j.1365-294X.2010.04948.x. Epub 2010 Dec 13.

PMID:
21155911
5.

Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers.

Yang B, Peng Y, Leung HC, Yiu SM, Chen JC, Chin FY.

BMC Bioinformatics. 2010 Apr 16;11 Suppl 2:S5. doi: 10.1186/1471-2105-11-S2-S5.

6.

Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data.

Nishito Y, Osana Y, Hachiya T, Popendorf K, Toyoda A, Fujiyama A, Itaya M, Sakakibara Y.

BMC Genomics. 2010 Apr 16;11:243. doi: 10.1186/1471-2164-11-243.

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.

Parallel, tag-directed assembly of locally derived short sequence reads.

Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J.

Nat Methods. 2010 Feb;7(2):119-22. doi: 10.1038/nmeth.1416. Epub 2010 Jan 17.

9.

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.

Zerbino DR, McEwen GK, Margulies EH, Birney E.

PLoS One. 2009 Dec 22;4(12):e8407. doi: 10.1371/journal.pone.0008407.

10.

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.

11.

The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments.

Saeed I, Halgamuge SK.

BMC Genomics. 2009 Dec 3;10 Suppl 3:S10. doi: 10.1186/1471-2164-10-S3-S10.

12.

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.

Maccallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A, Malek J, McKernan K, Ranade S, Shea TP, Williams L, Young S, Nusbaum C, Jaffe DB.

Genome Biol. 2009;10(10):R103. doi: 10.1186/gb-2009-10-10-r103. Epub 2009 Oct 1.

13.

An ORFome assembly approach to metagenomics sequences analysis.

Ye Y, Tang H.

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

14.

ABySS: a parallel assembler for short read sequence data.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.

Genome Res. 2009 Jun;19(6):1117-23. doi: 10.1101/gr.089532.108. Epub 2009 Feb 27.

15.

A bioinformatician's guide to metagenomics.

Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P.

Microbiol Mol Biol Rev. 2008 Dec;72(4):557-78, Table of Contents. doi: 10.1128/MMBR.00009-08. Review.

16.

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

Zerbino DR, Birney E.

Genome Res. 2008 May;18(5):821-9. doi: 10.1101/gr.074492.107. Epub 2008 Mar 18.

17.

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M.

DNA Res. 2007 Aug 31;14(4):169-81. Epub 2007 Oct 3.

18.

MetaGene: prokaryotic gene finding from environmental genome shotgun sequences.

Noguchi H, Park J, Takagi T.

Nucleic Acids Res. 2006;34(19):5623-30. Epub 2006 Oct 5.

19.

Bioinformatics for whole-genome shotgun sequencing of microbial communities.

Chen K, Pachter L.

PLoS Comput Biol. 2005 Jul;1(2):106-12.

20.

Environmental genome shotgun sequencing of the Sargasso Sea.

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO.

Science. 2004 Apr 2;304(5667):66-74. Epub 2004 Mar 4.

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