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Results: 1 to 20 of 117

1.

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
2.

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
3.

Paired-end mapping reveals extensive structural variation in the human genome.

Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M.

Science. 2007 Oct 19;318(5849):420-6. Epub 2007 Sep 27.

PMID:
17901297
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
5.

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
6.

Sensitive and accurate detection of copy number variants using read depth of coverage.

Yoon S, Xuan Z, Makarov V, Ye K, Sebat J.

Genome Res. 2009 Sep;19(9):1586-92. doi: 10.1101/gr.092981.109. Epub 2009 Aug 5.

PMID:
19657104
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.

Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC.

Genome Res. 2009 Jul;19(7):1270-8. doi: 10.1101/gr.088633.108. Epub 2009 May 15.

PMID:
19447966
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB.

PLoS Comput Biol. 2009 Jul;5(7):e1000432. doi: 10.1371/journal.pcbi.1000432. Epub 2009 Jul 10.

PMID:
19593373
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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]
11.

A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data.

Hayes M, Pyon YS, Li J.

PLoS One. 2012;7(12):e52881. doi: 10.1371/journal.pone.0052881. Epub 2012 Dec 27.

PMID:
23300804
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER.

Nat Methods. 2009 Sep;6(9):677-81. doi: 10.1038/nmeth.1363. Epub 2009 Aug 9.

PMID:
19668202
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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

Rausch T, Zichner T, Schlattl A, St├╝tz 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
14.

SNVHMM: predicting single nucleotide variants from next generation sequencing.

Bian J, Liu C, Wang H, Xing J, Kachroo P, Zhou X.

BMC Bioinformatics. 2013 Jul 15;14:225. doi: 10.1186/1471-2105-14-225.

PMID:
23855743
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags.

Gong Q, Tao Y, Yang JR, Cai J, Yuan Y, Ruan J, Yang J, Liu H, Li W, Lu X, Zhuang SM, Wang SM, Wu CI.

BMC Genomics. 2013 Jan 24;14:51. doi: 10.1186/1471-2164-14-51.

PMID:
23347462
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Characterizing and interpreting genetic variation from personal genome sequencing.

Johansson AC, Feuk L.

Methods Mol Biol. 2012;838:343-67. doi: 10.1007/978-1-61779-507-7_17.

PMID:
22228021
[PubMed - indexed for MEDLINE]
18.

Sniper: improved SNP discovery by multiply mapping deep sequenced reads.

Simola DF, Kim J.

Genome Biol. 2011 Jun 20;12(6):R55. doi: 10.1186/gb-2011-12-6-r55.

PMID:
21689413
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Detection and interpretation of genomic structural variation in mammals.

Hall IM, Quinlan AR.

Methods Mol Biol. 2012;838:225-48. doi: 10.1007/978-1-61779-507-7_11. Review.

PMID:
22228015
[PubMed - indexed for MEDLINE]
20.

An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome.

Shrestha AM, Frith MC.

Bioinformatics. 2013 Apr 15;29(8):965-72. doi: 10.1093/bioinformatics/btt073. Epub 2013 Feb 14.

PMID:
23413433
[PubMed - indexed for MEDLINE]
Free PMC Article

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