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Items: 1 to 20 of 98

1.

Development of coupling controlled polymerizations by adapter-ligation in mate-pair sequencing for detection of various genomic variants in one single assay.

Dong Z, Zhao X, Li Q, Yang Z, Xi Y, Alexeev A, Shen H, Wang O, Ruan J, Ren H, Wei H, Qi X, Li J, Zhu X, Zhang Y, Dai P, Kong X, Kirkconnell K, Alferov O, Giles S, Yamtich J, Kermani BG, Dong C, Liu P, Mi Z, Zhang W, Xu X, Drmanac R, Choy KW, Jiang Y.

DNA Res. 2019 Jun 7. pii: dsz011. doi: 10.1093/dnares/dsz011. [Epub ahead of print]

PMID:
31173071
2.

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

Ramos E, Levinson BT, Chasnoff S, Hughes A, Young AL, Thornton K, Li A, Vallania FL, Province M, Druley TE.

BMC Genomics. 2012 Dec 6;13:683. doi: 10.1186/1471-2164-13-683.

3.

SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing (MPseq).

Johnson SH, Smadbeck JB, Smoley SA, Gaitatzes A, Murphy SJ, Harris FR, Drucker TM, Zenka RM, Pitel BA, Rowsey RA, Hoppman NL, Aypar U, Sukov WR, Jenkins RB, Feldman AL, Kearney HM, Vasmatzis G.

Cancer Genet. 2018 Feb;221:1-18. doi: 10.1016/j.cancergen.2017.11.009. Epub 2017 Dec 2.

PMID:
29405991
4.

SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads.

Hampton OA, English AC, Wang M, Salerno WJ, Liu Y, Muzny DM, Han Y, Wheeler DA, Worley KC, Lupski JR, Gibbs RA.

BMC Genomics. 2017 Oct 3;18(Suppl 6):691. doi: 10.1186/s12864-017-4021-y.

5.

BIMA V3: an aligner customized for mate pair library sequencing.

Drucker TM, Johnson SH, Murphy SJ, Cradic KW, Therneau TM, Vasmatzis G.

Bioinformatics. 2014 Jun 1;30(11):1627-9. doi: 10.1093/bioinformatics/btu078. Epub 2014 Feb 12.

PMID:
24526710
6.

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.

Jiang H, Lei R, Ding SW, Zhu S.

BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182.

7.

Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.

Gillet-Markowska A, Richard H, Fischer G, Lafontaine I.

Bioinformatics. 2015 Mar 15;31(6):801-8. doi: 10.1093/bioinformatics/btu730. Epub 2014 Nov 7.

PMID:
25380961
8.

Small RNA-seq: The RNA 5'-end adapter ligation problem and how to circumvent it.

Lama L, Cobo J, Buenaventura D, Ryan K.

J Biol Methods. 2019;6(1). pii: e108. doi: 10.14440/jbm.2019.269. Epub 2019 Feb 20.

9.

Preparing a re-sequencing DNA library of 2 cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions.

Su Y, Lin L, Tian G, Chen C, Liu T, Xu X, Qi X, Zhang X, Yang H.

Sci China C Life Sci. 2009 May;52(5):483-91. doi: 10.1007/s11427-009-0066-8. Epub 2009 May 27.

PMID:
19471873
10.

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.

11.

Mate pair sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations.

Vergult S, Van Binsbergen E, Sante T, Nowak S, Vanakker O, Claes K, Poppe B, Van der Aa N, van Roosmalen MJ, Duran K, Tavakoli-Yaraki M, Swinkels M, van den Boogaard MJ, van Haelst M, Roelens F, Speleman F, Cuppen E, Mortier G, Kloosterman WP, Menten B.

Eur J Hum Genet. 2014 May;22(5):652-9. doi: 10.1038/ejhg.2013.220. Epub 2013 Oct 9.

12.

Balanced Chromosomal Rearrangement Detection by Low-Pass Whole-Genome Sequencing.

Dong Z, Ye L, Yang Z, Chen H, Yuan J, Wang H, Guo X, Li Y, Wang J, Chen F, Cheung SW, Morton CC, Jiang H, Choy KW.

Curr Protoc Hum Genet. 2018 Jan 24;96:8.18.1-8.18.16. doi: 10.1002/cphg.51.

13.

NxTrim: optimized trimming of Illumina mate pair reads.

O'Connell J, Schulz-Trieglaff O, Carlson E, Hims MM, Gormley NA, Cox AJ.

Bioinformatics. 2015 Jun 15;31(12):2035-7. doi: 10.1093/bioinformatics/btv057. Epub 2015 Feb 5.

PMID:
25661542
14.

BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity.

Cantarel BL, Weaver D, McNeill N, Zhang J, Mackey AJ, Reese J.

BMC Bioinformatics. 2014 Apr 12;15:104. doi: 10.1186/1471-2105-15-104.

15.

CleanTag Adapters Improve Small RNA Next-Generation Sequencing Library Preparation by Reducing Adapter Dimers.

Shore S, Henderson JM, McCaffrey AP.

Methods Mol Biol. 2018;1712:145-161. doi: 10.1007/978-1-4939-7514-3_10.

PMID:
29224073
16.

Mate pair sequencing of whole-genome-amplified DNA following laser capture microdissection of prostate cancer.

Murphy SJ, Cheville JC, Zarei S, Johnson SH, Sikkink RA, Kosari F, Feldman AL, Eckloff BW, Karnes RJ, Vasmatzis G.

DNA Res. 2012 Oct;19(5):395-406. doi: 10.1093/dnares/dss021. Epub 2012 Sep 18.

17.

Multiplex single nucleotide polymorphism genotyping by adapter ligation-mediated allele-specific amplification.

Wang WP, Ni KY, Zhou GH.

Anal Biochem. 2006 Aug 15;355(2):240-8. Epub 2006 May 5.

PMID:
16836969
18.

3' Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3'OH ends in DNA or RNA.

Wang L, Xi Y, Zhang W, Wang W, Shen H, Wang X, Zhao X, Alexeev A, Peters BA, Albert A, Xu X, Ren H, Wang O, Kirkconnell K, Perazich H, Clark S, Hurowitz E, Chen A, Xu X, Drmanac R, Jiang Y.

DNA Res. 2019 Feb 1;26(1):45-53. doi: 10.1093/dnares/dsy037.

19.

Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling.

Zhang G, Wang J, Yang J, Li W, Deng Y, Li J, Huang J, Hu S, Zhang B.

BMC Genomics. 2015 Aug 5;16:581. doi: 10.1186/s12864-015-1796-6.

20.

ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation.

Sante T, Vergult S, Volders PJ, Kloosterman WP, Trooskens G, De Preter K, Dheedene A, Speleman F, De Meyer T, Menten B.

PLoS One. 2014 Dec 12;9(12):e113800. doi: 10.1371/journal.pone.0113800. eCollection 2014.

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