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Results: 1 to 20 of 252

1.

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing.

Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE.

Bioinformatics. 2010 Jan 1;26(1):38-45. doi: 10.1093/bioinformatics/btp614. Epub 2009 Oct 27.

PMID:
19861355
[PubMed - indexed for MEDLINE]
Free Article
2.

Optimal spliced alignments of short sequence reads.

De Bona F, Ossowski S, Schneeberger K, R├Ątsch G.

Bioinformatics. 2008 Aug 15;24(16):i174-80. doi: 10.1093/bioinformatics/btn300.

PMID:
18689821
[PubMed - indexed for MEDLINE]
Free Article
3.

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.

Hong C, Clement NL, Clement S, Hammoud SS, Carrell DT, Cairns BR, Snell Q, Clement MJ, Johnson WE.

BMC Bioinformatics. 2013 Nov 21;14:337. doi: 10.1186/1471-2105-14-337.

PMID:
24261665
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Probabilistic base calling of Solexa sequencing data.

Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F.

BMC Bioinformatics. 2008 Oct 13;9:431. doi: 10.1186/1471-2105-9-431.

PMID:
18851737
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets.

Droege M, Hill B.

J Biotechnol. 2008 Aug 31;136(1-2):3-10. doi: 10.1016/j.jbiotec.2008.03.021. Epub 2008 Jun 21. Review.

PMID:
18616967
[PubMed - indexed for MEDLINE]
6.

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

Chen Y, Souaiaia T, Chen T.

Bioinformatics. 2009 Oct 1;25(19):2514-21. doi: 10.1093/bioinformatics/btp486. Epub 2009 Aug 12.

PMID:
19675096
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

De novo sequencing of plant genomes using second-generation technologies.

Imelfort M, Edwards D.

Brief Bioinform. 2009 Nov;10(6):609-18. doi: 10.1093/bib/bbp039. Review.

PMID:
19933209
[PubMed - indexed for MEDLINE]
Free Article
8.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.

Bioinformatics. 2010 Mar 15;26(6):730-6. doi: 10.1093/bioinformatics/btq040. Epub 2010 Feb 3.

PMID:
20130035
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Consensus generation and variant detection by Celera Assembler.

Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Sutton G.

Bioinformatics. 2008 Apr 15;24(8):1035-40. doi: 10.1093/bioinformatics/btn074. Epub 2008 Mar 4.

PMID:
18321888
[PubMed - indexed for MEDLINE]
Free Article
10.

Using quality scores and longer reads improves accuracy of Solexa read mapping.

Smith AD, Xuan Z, Zhang MQ.

BMC Bioinformatics. 2008 Feb 28;9:128. doi: 10.1186/1471-2105-9-128.

PMID:
18307793
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Li H, Ruan J, Durbin R.

Genome Res. 2008 Nov;18(11):1851-8. doi: 10.1101/gr.078212.108. Epub 2008 Aug 19.

PMID:
18714091
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

ZOOM Lite: next-generation sequencing data mapping and visualization software.

Zhang Z, Lin H, Ma B.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W743-8. doi: 10.1093/nar/gkq538. Epub 2010 Jun 8.

PMID:
20530531
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

SHRiMP: accurate mapping of short color-space reads.

Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M.

PLoS Comput Biol. 2009 May;5(5):e1000386. doi: 10.1371/journal.pcbi.1000386. Epub 2009 May 22.

PMID:
19461883
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The fragment assembly string graph.

Myers EW.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii79-85.

PMID:
16204131
[PubMed - indexed for MEDLINE]
Free Article
15.

TagDust--a program to eliminate artifacts from next generation sequencing data.

Lassmann T, Hayashizaki Y, Daub CO.

Bioinformatics. 2009 Nov 1;25(21):2839-40. doi: 10.1093/bioinformatics/btp527. Epub 2009 Sep 7.

PMID:
19737799
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

BING: biomedical informatics pipeline for Next Generation Sequencing.

Kriseman J, Busick C, Szelinger S, Dinu V.

J Biomed Inform. 2010 Jun;43(3):428-34. doi: 10.1016/j.jbi.2009.11.003. Epub 2009 Nov 28.

PMID:
19925883
[PubMed - indexed for MEDLINE]
Free Article
17.

Correction of sequencing errors in a mixed set of reads.

Salmela L.

Bioinformatics. 2010 May 15;26(10):1284-90. doi: 10.1093/bioinformatics/btq151. Epub 2010 Apr 8.

PMID:
20378555
[PubMed - indexed for MEDLINE]
Free Article
18.

PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands.

Srivastava GP, Guo J, Shi H, Xu D.

Bioinformatics. 2008 Sep 1;24(17):1837-42. doi: 10.1093/bioinformatics/btn320. Epub 2008 Jun 25.

PMID:
18579568
[PubMed - indexed for MEDLINE]
Free Article
19.

Assembling genomic DNA sequences with PHRAP.

de la Bastide M, McCombie WR.

Curr Protoc Bioinformatics. 2007 Mar;Chapter 11:Unit11.4. doi: 10.1002/0471250953.bi1104s17.

PMID:
18428783
[PubMed - indexed for MEDLINE]
20.

Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects.

Noto K, Craven M.

Bioinformatics. 2007 Jan 15;23(2):e156-62.

PMID:
17237085
[PubMed - indexed for MEDLINE]
Free Article

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