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Results: 1 to 20 of 112

1.

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
2.

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
3.

Sequence-based characterization of structural variation in the mouse genome.

Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, Nellåker C, Goodstadt L, Nicod J, Bhomra A, Hernandez-Pliego P, Whitley H, Cleak J, Dutton R, Janowitz D, Mott R, Adams DJ, Flint J.

Nature. 2011 Sep 14;477(7364):326-9. doi: 10.1038/nature10432.

PMID:
21921916
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
5.

Mapping copy number variation by population-scale genome sequencing.

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project.

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.

PMID:
21293372
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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]
7.

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
8.

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
9.

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
10.

Identification of structural variation in mouse genomes.

Keane TM, Wong K, Adams DJ, Flint J, Reymond A, Yalcin B.

Front Genet. 2014 Jul 2;5:192. doi: 10.3389/fgene.2014.00192. eCollection 2014. Review.

PMID:
25071822
[PubMed]
Free PMC 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.

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB.

Nat Biotechnol. 2010 Jan;28(1):47-55. doi: 10.1038/nbt.1600. Epub 2009 Dec 27.

PMID:
20037582
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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
14.

Mapping and sequencing of structural variation from eight human genomes.

Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tüzün E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR, Eichler EE.

Nature. 2008 May 1;453(7191):56-64. doi: 10.1038/nature06862.

PMID:
18451855
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.

Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC.

Bioinformatics. 2010 May 15;26(10):1277-83. doi: 10.1093/bioinformatics/btq152. Epub 2010 Apr 12.

PMID:
20385726
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Towards a comprehensive structural variation map of an individual human genome.

Pang AW, MacDonald JR, Pinto D, Wei J, Rafiq MA, Conrad DF, Park H, Hurles ME, Lee C, Venter JC, Kirkness EF, Levy S, Feuk L, Scherer SW.

Genome Biol. 2010;11(5):R52. doi: 10.1186/gb-2010-11-5-r52. Epub 2010 May 19.

PMID:
20482838
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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]
18.

Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing.

Suzuki T, Tsurusaki Y, Nakashima M, Miyake N, Saitsu H, Takeda S, Matsumoto N.

J Hum Genet. 2014 Dec;59(12):649-54. doi: 10.1038/jhg.2014.88. Epub 2014 Oct 9.

PMID:
25296578
[PubMed - in process]
19.

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
20.

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

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