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Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans.

Ewing AD, Kazazian HH Jr.

Genome Res. 2011 Jun;21(6):985-90. doi: 10.1101/gr.114777.110. Epub 2010 Oct 27.


High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes.

Ewing AD, Kazazian HH Jr.

Genome Res. 2010 Sep;20(9):1262-70. doi: 10.1101/gr.106419.110. Epub 2010 May 20.


Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis.

Paterson AL, Weaver JM, Eldridge MD, Tavaré S, Fitzgerald RC, Edwards PA; OCCAMs Consortium..

BMC Genomics. 2015 Jul 10;16:473. doi: 10.1186/s12864-015-1685-z.


Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies.

Konkel MK, Wang J, Liang P, Batzer MA.

Gene. 2007 Apr 1;390(1-2):28-38. Epub 2006 Aug 30.


SNP detection for massively parallel whole-genome resequencing.

Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J.

Genome Res. 2009 Jun;19(6):1124-32. doi: 10.1101/gr.088013.108. Epub 2009 May 6.


LINE-1 preTa elements in the human genome.

Salem AH, Myers JS, Otieno AC, Watkins WS, Jorde LB, Batzer MA.

J Mol Biol. 2003 Feb 28;326(4):1127-46.


Following the LINEs: an analysis of primate genomic variation at human-specific LINE-1 insertion sites.

Vincent BJ, Myers JS, Ho HJ, Kilroy GE, Walker JA, Watkins WS, Jorde LB, Batzer MA.

Mol Biol Evol. 2003 Aug;20(8):1338-48. Epub 2003 May 30.


Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals.

Streva VA, Jordan VE, Linker S, Hedges DJ, Batzer MA, Deininger PL.

BMC Genomics. 2015 Mar 21;16:220. doi: 10.1186/s12864-015-1374-y.


Identity by descent and DNA sequence variation of human SINE and LINE elements.

Salem AH, Ray DA, Batzer MA.

Cytogenet Genome Res. 2005;108(1-3):63-72.


Extensive somatic L1 retrotransposition in colorectal tumors.

Solyom S, Ewing AD, Rahrmann EP, Doucet T, Nelson HH, Burns MB, Harris RS, Sigmon DF, Casella A, Erlanger B, Wheelan S, Upton KR, Shukla R, Faulkner GJ, Largaespada DA, Kazazian HH Jr.

Genome Res. 2012 Dec;22(12):2328-38. doi: 10.1101/gr.145235.112. Epub 2012 Sep 11.


HapFABIA: identification of very short segments of identity by descent characterized by rare variants in large sequencing data.

Hochreiter S.

Nucleic Acids Res. 2013 Dec;41(22):e202. doi: 10.1093/nar/gkt1013. Epub 2013 Oct 29.


Fast computation and applications of genome mappability.

Derrien T, Estellé J, Marco Sola S, Knowles DG, Raineri E, Guigó R, Ribeca P.

PLoS One. 2012;7(1):e30377. doi: 10.1371/journal.pone.0030377. Epub 2012 Jan 19.


Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing.

Helman E, Lawrence MS, Stewart C, Sougnez C, Getz G, Meyerson M.

Genome Res. 2014 Jul;24(7):1053-63. doi: 10.1101/gr.163659.113. Epub 2014 May 13.


Genome-wide targeted search for human specific and polymorphic L1 integrations.

Buzdin A, Ustyugova S, Gogvadze E, Lebedev Y, Hunsmann G, Sverdlov E.

Hum Genet. 2003 May;112(5-6):527-33. Epub 2003 Feb 25.


Deep whole-genome sequencing of 100 southeast Asian Malays.

Wong LP, Ong RT, Poh WT, Liu X, Chen P, Li R, Lam KK, Pillai NE, Sim KS, Xu H, Sim NL, Teo SM, Foo JN, Tan LW, Lim Y, Koo SH, Gan LS, Cheng CY, Wee S, Yap EP, Ng PC, Lim WY, Soong R, Wenk MR, Aung T, Wong TY, Khor CC, Little P, Chia KS, Teo YY.

Am J Hum Genet. 2013 Jan 10;92(1):52-66. doi: 10.1016/j.ajhg.2012.12.005. Epub 2013 Jan 3.


The insertional history of an active family of L1 retrotransposons in humans.

Boissinot S, Entezam A, Young L, Munson PJ, Furano AV.

Genome Res. 2004 Jul;14(7):1221-31. Epub 2004 Jun 14.


Long Interspersed Element Sequencing (L1-Seq): A Method to Identify Somatic LINE-1 Insertions in the Human Genome.

Doucet TT, Kazazian HH Jr.

Methods Mol Biol. 2016;1400:79-93. doi: 10.1007/978-1-4939-3372-3_5.


The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.

Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, Park D, Lee YS, Kim S, Reja R, Jho S, Kim CG, Cha JY, Kim KH, Lee B, Bhak J, Kim SJ.

Genome Res. 2009 Sep;19(9):1622-9. doi: 10.1101/gr.092197.109. Epub 2009 May 26.


A probabilistic approach for SNP discovery in high-throughput human resequencing data.

Hoberman R, Dias J, Ge B, Harmsen E, Mayhew M, Verlaan DJ, Kwan T, Dewar K, Blanchette M, Pastinen T.

Genome Res. 2009 Sep;19(9):1542-52. doi: 10.1101/gr.092072.109. Epub 2009 Jul 15.

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