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Results: 1 to 20 of 98

1.

ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs.

Yasuda T, Suzuki S, Nagasaki M, Miyano S.

BMC Bioinformatics. 2012 Oct 30;13:279. doi: 10.1186/1471-2105-13-279.

PMID:
23110596
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.

Zhang J, Wang J, Wu Y.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S6. doi: 10.1186/1471-2105-13-S6-S6.

PMID:
22537045
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information.

Suzuki S, Yasuda T, Shiraishi Y, Miyano S, Nagasaki M.

BMC Bioinformatics. 2011 Dec 14;12 Suppl 14:S7. doi: 10.1186/1471-2105-12-S14-S7.

PMID:
22373054
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Identification of genomic indels and structural variations using split reads.

Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M.

BMC Genomics. 2011 Jul 25;12:375. doi: 10.1186/1471-2164-12-375.

PMID:
21787423
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants.

Jiang Y, Wang Y, Brudno M.

Bioinformatics. 2012 Oct 15;28(20):2576-83. doi: 10.1093/bioinformatics/bts484. Epub 2012 Jul 31.

PMID:
22851530
[PubMed - indexed for MEDLINE]
Free Article
6.

DELLY: structural variant discovery by integrated paired-end and split-read analysis.

Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO.

Bioinformatics. 2012 Sep 15;28(18):i333-i339. doi: 10.1093/bioinformatics/bts378.

PMID:
22962449
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

An integrative probabilistic model for identification of structural variation in sequencing data.

Sindi SS, Onal S, Peng LC, Wu HT, Raphael BJ.

Genome Biol. 2012;13(3):R22. doi: 10.1186/gb-2012-13-3-r22.

PMID:
22452995
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

The fine-scale architecture of structural variants in 17 mouse genomes.

Yalcin B, Wong K, Bhomra A, Goodson M, Keane TM, Adams DJ, Flint J.

Genome Biol. 2012;13(3):R18. doi: 10.1186/gb-2012-13-3-r18.

PMID:
22439878
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Detection of structural variants involving repetitive regions in the reference genome.

Lee H, Popodi E, Foster PL, Tang H.

J Comput Biol. 2014 Mar;21(3):219-33. doi: 10.1089/cmb.2013.0129. Epub 2014 Feb 19.

PMID:
24552580
[PubMed - indexed for MEDLINE]
10.

Statistical challenges associated with detecting copy number variations with next-generation sequencing.

Teo SM, Pawitan Y, Ku CS, Chia KS, Salim A.

Bioinformatics. 2012 Nov 1;28(21):2711-8. doi: 10.1093/bioinformatics/bts535. Epub 2012 Aug 31. Review.

PMID:
22942022
[PubMed - indexed for MEDLINE]
Free Article
11.

iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data.

Mimori T, Nariai N, Kojima K, Takahashi M, Ono A, Sato Y, Yamaguchi-Kabata Y, Nagasaki M.

BMC Syst Biol. 2013;7 Suppl 6:S8. doi: 10.1186/1752-0509-7-S6-S8. Epub 2013 Dec 13.

PMID:
24564972
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
13.

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.

Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM.

Genome Res. 2010 May;20(5):623-35. doi: 10.1101/gr.102970.109. Epub 2010 Mar 22.

PMID:
20308636
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Normal and compound poisson approximations for pattern occurrences in NGS reads.

Zhai Z, Reinert G, Song K, Waterman MS, Luan Y, Sun F.

J Comput Biol. 2012 Jun;19(6):839-54. doi: 10.1089/cmb.2012.0029.

PMID:
22697250
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome.

Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JD, Varshney RK.

Am J Bot. 2012 Feb;99(2):186-92. doi: 10.3732/ajb.1100419. Epub 2012 Feb 1.

PMID:
22301893
[PubMed - indexed for MEDLINE]
Free Article
16.

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly.

Li Y, Zheng H, Luo R, Wu H, Zhu H, Li R, Cao H, Wu B, Huang S, Shao H, Ma H, Zhang F, Feng S, Zhang W, Du H, Tian G, Li J, Zhang X, Li S, Bolund L, Kristiansen K, de Smith AJ, Blakemore AI, Coin LJ, Yang H, Wang J, Wang J.

Nat Biotechnol. 2011 Jul 24;29(8):723-30. doi: 10.1038/nbt.1904.

PMID:
21785424
[PubMed - indexed for MEDLINE]
17.

Incorporating sequence quality data into alignment improves DNA read mapping.

Frith MC, Wan R, Horton P.

Nucleic Acids Res. 2010 Apr;38(7):e100. doi: 10.1093/nar/gkq010. Epub 2010 Jan 27.

PMID:
20110255
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A shot in the genome: how accurately do shotgun 454 sequences represent a genome?

Meglécz E, Pech N, Gilles A, Martin JF, Gardner MG.

BMC Res Notes. 2012 May 28;5:259.

PMID:
22640415
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

Hart SN, Sarangi V, Moore R, Baheti S, Bhavsar JD, Couch FJ, Kocher JP.

PLoS One. 2013 Dec 16;8(12):e83356. doi: 10.1371/journal.pone.0083356. eCollection 2013.

PMID:
24358278
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Structural variation analysis with strobe reads.

Ritz A, Bashir A, Raphael BJ.

Bioinformatics. 2010 May 15;26(10):1291-8. doi: 10.1093/bioinformatics/btq153. Epub 2010 Apr 8.

PMID:
20378554
[PubMed - indexed for MEDLINE]
Free Article

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