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Items: 1 to 20 of 127

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.

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.

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.

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.

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.

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
7.

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
8.

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
9.

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.

10.

svclassify: a method to establish benchmark structural variant calls.

Parikh H, Mohiyuddin M, Lam HY, Iyer H, Chen D, Pratt M, Bartha G, Spies N, Losert W, Zook JM, Salit M.

BMC Genomics. 2016 Jan 16;17:64. doi: 10.1186/s12864-016-2366-2.

11.

Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms.

Bartenhagen C, Dugas M.

Brief Bioinform. 2016 Jan;17(1):51-62. doi: 10.1093/bib/bbv028. Epub 2015 May 20.

PMID:
25998133
12.

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.

13.

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.

Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY.

Bioinformatics. 2015 Aug 15;31(16):2741-4. doi: 10.1093/bioinformatics/btv204. Epub 2015 Apr 10.

14.

Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs.

Zhao P, Li J, Kang H, Wang H, Fan Z, Yin Z, Wang J, Zhang Q, Wang Z, Liu JF.

Sci Rep. 2016 Jan 5;6:18501. doi: 10.1038/srep18501.

15.

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.

16.

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.

17.

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.

18.

Molecular characterization of ring chromosome 18 by low-coverage next generation sequencing.

Ji X, Liang D, Sun R, Liu C, Ma D, Wang Y, Hu P, Xu Z.

BMC Med Genet. 2015 Jul 30;16:57. doi: 10.1186/s12881-015-0206-x.

19.

The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes.

Adams DJ, Doran AG, Lilue J, Keane TM.

Mamm Genome. 2015 Oct;26(9-10):403-12. doi: 10.1007/s00335-015-9579-6. Epub 2015 Jun 30.

PMID:
26123534
20.

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.

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