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Items: 1 to 20 of 160

1.

Detecting Alu insertions from high-throughput sequencing data.

David M, Mustafa H, Brudno M.

Nucleic Acids Res. 2013 Sep;41(17):e169. doi: 10.1093/nar/gkt612. Epub 2013 Aug 5.

2.

PAIR: polymorphic Alu insertion recognition.

Sveinbjörnsson JI, Halldórsson BV.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S7. doi: 10.1186/1471-2105-13-S6-S7.

3.

Identification of human-specific AluS elements through comparative genomics.

Lee J, Kim YJ, Mun S, Kim HS, Han K.

Gene. 2015 Jan 25;555(2):208-16. doi: 10.1016/j.gene.2014.11.005. Epub 2014 Nov 7.

PMID:
25447892
4.

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.

5.

Alu repeat discovery and characterization within human genomes.

Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, Yorukoglu D, Dao P, Bakhshi M, Sahinalp SC, Eichler EE.

Genome Res. 2011 Jun;21(6):840-9. doi: 10.1101/gr.115956.110. Epub 2010 Dec 3.

6.

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.

7.

Massively parallel sequencing approaches for characterization of structural variation.

Koboldt DC, Larson DE, Chen K, Ding L, Wilson RK.

Methods Mol Biol. 2012;838:369-84. doi: 10.1007/978-1-61779-507-7_18. Review.

8.

Bellerophon: a hybrid method for detecting interchromosomal rearrangements at base pair resolution using next-generation sequencing data.

Hayes M, Li J.

BMC Bioinformatics. 2013;14 Suppl 5:S6. doi: 10.1186/1471-2105-14-S5-S6. Epub 2013 Apr 10.

9.

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.

Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SR; WGS500 Consortium, Wilkie AO, McVean G, Lunter G.

Nat Genet. 2014 Aug;46(8):912-8. doi: 10.1038/ng.3036. Epub 2014 Jul 13.

PMID:
25017105
10.

Detecting identity by descent and homozygosity mapping in whole-exome sequencing data.

Zhuang Z, Gusev A, Cho J, Pe'er I.

PLoS One. 2012;7(10):e47618. doi: 10.1371/journal.pone.0047618. Epub 2012 Oct 11.

11.

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.

12.

Exome versus transcriptome sequencing in identifying coding region variants.

Ku CS, Wu M, Cooper DN, Naidoo N, Pawitan Y, Pang B, Iacopetta B, Soong R.

Expert Rev Mol Diagn. 2012 Apr;12(3):241-51. doi: 10.1586/erm.12.10. Review.

PMID:
22468815
13.

pIRS: Profile-based Illumina pair-end reads simulator.

Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Y, Mu D, Zhang H, Li N, Yue Z, Bai F, Li H, Fan W.

Bioinformatics. 2012 Jun 1;28(11):1533-5. doi: 10.1093/bioinformatics/bts187. Epub 2012 Apr 15.

14.

Analysis of the human Alu Ye lineage.

Salem AH, Ray DA, Hedges DJ, Jurka J, Batzer MA.

BMC Evol Biol. 2005 Feb 22;5:18.

15.

Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations.

Witherspoon DJ, Zhang Y, Xing J, Watkins WS, Ha H, Batzer MA, Jorde LB.

Genome Res. 2013 Jul;23(7):1170-81. doi: 10.1101/gr.148973.112. Epub 2013 Apr 18.

16.

Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability.

Stenger JE, Lobachev KS, Gordenin D, Darden TA, Jurka J, Resnick MA.

Genome Res. 2001 Jan;11(1):12-27.

17.

AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome.

Mei L, Ding X, Tsang SY, Pun FW, Ng SK, Yang J, Zhao C, Li D, Wan W, Yu CH, Tan TC, Poon WS, Leung GK, Ng HK, Zhang L, Xue H.

BMC Genomics. 2011 Nov 17;12:564. doi: 10.1186/1471-2164-12-564.

18.

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.

19.

High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum.

Samarakoon U, Regier A, Tan A, Desany BA, Collins B, Tan JC, Emrich SJ, Ferdig MT.

BMC Genomics. 2011 Feb 17;12:116. doi: 10.1186/1471-2164-12-116.

20.

VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data.

Gelfand Y, Hernandez Y, Loving J, Benson G.

Nucleic Acids Res. 2014 Aug;42(14):8884-94. doi: 10.1093/nar/gku642. Epub 2014 Jul 23.

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