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Results: 1 to 20 of 114

1.

SOAPindel: efficient identification of indels from short paired reads.

Li S, Li R, Li H, Lu J, Li Y, Bolund L, Schierup MH, Wang J.

Genome Res. 2013 Jan;23(1):195-200. doi: 10.1101/gr.132480.111. Epub 2012 Sep 12.

PMID:
22972939
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.

Marschall T, Hajirasouliha I, Schönhuth A.

Bioinformatics. 2013 Dec 15;29(24):3143-50. doi: 10.1093/bioinformatics/btt556. Epub 2013 Sep 25.

PMID:
24072733
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Dindel: accurate indel calls from short-read data.

Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R.

Genome Res. 2011 Jun;21(6):961-73. doi: 10.1101/gr.112326.110. Epub 2010 Oct 27.

PMID:
20980555
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly.

Li H.

Bioinformatics. 2012 Jul 15;28(14):1838-44. doi: 10.1093/bioinformatics/bts280. Epub 2012 May 7.

PMID:
22569178
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A universal algorithm for de novo decrypting of heterozygous indel sequences: a tool for personalized medicine.

Lam CW.

Clin Chim Acta. 2008 Mar;389(1-2):7-13. Epub 2007 Nov 23.

PMID:
18078814
[PubMed - indexed for MEDLINE]
6.

A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.

Bansal V, Libiger O.

Bioinformatics. 2011 Aug 1;27(15):2047-53. doi: 10.1093/bioinformatics/btr344. Epub 2011 Jun 7.

PMID:
21653520
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Accurate indel prediction using paired-end short reads.

Grimm D, Hagmann J, Koenig D, Weigel D, Borgwardt K.

BMC Genomics. 2013 Feb 27;14:132. doi: 10.1186/1471-2164-14-132.

PMID:
23442375
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer.

Yeo ZX, Chan M, Yap YS, Ang P, Rozen S, Lee AS.

PLoS One. 2012;7(9):e45798. doi: 10.1371/journal.pone.0045798. Epub 2012 Sep 19.

PMID:
23029247
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Computational techniques for human genome resequencing using mated gapped reads.

Carnevali P, Baccash J, Halpern AL, Nazarenko I, Nilsen GB, Pant KP, Ebert JC, Brownley A, Morenzoni M, Karpinchyk V, Martin B, Ballinger DG, Drmanac R.

J Comput Biol. 2012 Mar;19(3):279-92. doi: 10.1089/cmb.2011.0201. Epub 2011 Dec 16.

PMID:
22175250
[PubMed - indexed for MEDLINE]
10.

ABRA: improved coding indel detection via assembly-based realignment.

Mose LE, Wilkerson MD, Hayes DN, Perou CM, Parker JS.

Bioinformatics. 2014 Oct;30(19):2813-5. doi: 10.1093/bioinformatics/btu376. Epub 2014 Jun 6.

PMID:
24907369
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

GapFiller: a de novo assembly approach to fill the gap within paired reads.

Nadalin F, Vezzi F, Policriti A.

BMC Bioinformatics. 2012;13 Suppl 14:S8. doi: 10.1186/1471-2105-13-S14-S8. Epub 2012 Sep 7.

PMID:
23095524
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.

Bioinformatics. 2009 Nov 1;25(21):2865-71. doi: 10.1093/bioinformatics/btp394. Epub 2009 Jun 26.

PMID:
19561018
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Microindel detection in short-read sequence data.

Krawitz P, Rödelsperger C, Jäger M, Jostins L, Bauer S, Robinson PN.

Bioinformatics. 2010 Mar 15;26(6):722-9. doi: 10.1093/bioinformatics/btq027. Epub 2010 Feb 9.

PMID:
20144947
[PubMed - indexed for MEDLINE]
Free Article
14.

PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data.

Zeng F, Jiang R, Chen T.

Bioinformatics. 2013 Nov 15;29(22):2859-68. doi: 10.1093/bioinformatics/btt512. Epub 2013 Aug 31.

PMID:
23995392
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Automating resequencing-based detection of insertion-deletion polymorphisms.

Bhangale TR, Stephens M, Nickerson DA.

Nat Genet. 2006 Dec;38(12):1457-62. Epub 2006 Nov 19.

PMID:
17115056
[PubMed - indexed for MEDLINE]
16.

Genome assembly quality: assessment and improvement using the neutral indel model.

Meader S, Hillier LW, Locke D, Ponting CP, Lunter G.

Genome Res. 2010 May;20(5):675-84. doi: 10.1101/gr.096966.109. Epub 2010 Mar 19.

PMID:
20305016
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data.

Zhang J, Wu Y.

Bioinformatics. 2011 Dec 1;27(23):3228-34. doi: 10.1093/bioinformatics/btr563. Epub 2011 Oct 12.

PMID:
21994222
[PubMed - indexed for MEDLINE]
Free Article
18.

Sequencing and annotated analysis of the Holstein cow genome.

Kõks S, Lilleoja R, Reimann E, Salumets A, Reemann P, Jaakma Ü.

Mamm Genome. 2013 Aug;24(7-8):309-21. doi: 10.1007/s00335-013-9464-0. Epub 2013 Jul 27.

PMID:
23893136
[PubMed - indexed for MEDLINE]
19.

Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22.

Volfovsky N, Oleksyk TK, Cruz KC, Truelove AL, Stephens RM, Smith MW.

BMC Genomics. 2009 Jan 26;10:51. doi: 10.1186/1471-2164-10-51.

PMID:
19171065
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Short clones or long clones? A simulation study on the use of paired reads in metagenomics.

Mitra S, Schubach M, Huson DH.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S12. doi: 10.1186/1471-2105-11-S1-S12.

PMID:
20122183
[PubMed - indexed for MEDLINE]
Free PMC Article
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