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A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing.

Mijušković M, Brown SM, Tang Z, Lindsay CR, Efstathiadis E, Deriano L, Roth DB.

PLoS One. 2012;7(10):e48314. doi: 10.1371/journal.pone.0048314. Epub 2012 Oct 29.


SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.

Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-né P, Nicolas A, Delattre O, Barillot E.

Bioinformatics. 2010 Aug 1;26(15):1895-6. doi: 10.1093/bioinformatics/btq293.


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.


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.


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.


Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score.

Lee H, Schatz MC.

Bioinformatics. 2012 Aug 15;28(16):2097-105. doi: 10.1093/bioinformatics/bts330. Epub 2012 Jun 4.


Reconstructing cancer genomes from paired-end sequencing data.

Oesper L, Ritz A, Aerni SJ, Drebin R, Raphael BJ.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S10. doi: 10.1186/1471-2105-13-S6-S10.


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.


Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.

Barrick JE, Colburn G, Deatherage DE, Traverse CC, Strand MD, Borges JJ, Knoester DB, Reba A, Meyer AG.

BMC Genomics. 2014 Nov 29;15:1039. doi: 10.1186/1471-2164-15-1039.


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.


On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing.

Lucas Lledó JI, Cáceres M.

PLoS One. 2013 Apr 23;8(4):e61292. doi: 10.1371/journal.pone.0061292. Print 2013.


Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts?

Tso KY, Lee SD, Lo KW, Yip KY.

BMC Genomics. 2014 Dec 23;15:1172. doi: 10.1186/1471-2164-15-1172.


Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

Caboche S, Audebert C, Lemoine Y, Hot D.

BMC Genomics. 2014 Apr 5;15:264. doi: 10.1186/1471-2164-15-264.


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.


Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.

Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y.

Genome Res. 2011 May;21(5):665-75. doi: 10.1101/gr.113555.110. Epub 2011 Apr 5.


Comparison of sequencing based CNV discovery methods using monozygotic twin quartets.

Legault MA, Girard S, Lemieux Perreault LP, Rouleau GA, Dubé MP.

PLoS One. 2015 Mar 26;10(3):e0122287. doi: 10.1371/journal.pone.0122287. eCollection 2015.


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.


Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.

McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP.

Genome Res. 2009 Sep;19(9):1527-41. doi: 10.1101/gr.091868.109. Epub 2009 Jun 22.


COPS: a sensitive and accurate tool for detecting somatic Copy Number Alterations using short-read sequence data from paired samples.

Krishnan NM, Gaur P, Chaudhary R, Rao AA, Panda B.

PLoS One. 2012;7(10):e47812. doi: 10.1371/journal.pone.0047812. Epub 2012 Oct 22.


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.


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