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Items: 1 to 20 of 23

1.

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis.

Schauer SN, Carreira PE, Shukla R, Gerhardt DJ, Gerdes P, Sanchez-Luque FJ, Nicoli P, Kindlova M, Ghisletti S, Santos AD, Rapoud D, Samuel D, Faivre J, Ewing AD, Richardson SR, Faulkner GJ.

Genome Res. 2018 May;28(5):639-653. doi: 10.1101/gr.226993.117. Epub 2018 Apr 11.

2.

Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

Sendorek DH, Caloian C, Ellrott K, Bare JC, Yamaguchi TN, Ewing AD, Houlahan KE, Norman TC, Margolin AA, Stuart JM, Boutros PC.

BMC Bioinformatics. 2018 Jan 31;19(1):28. doi: 10.1186/s12859-018-2046-0.

3.

On the role of H3.3 in retroviral silencing.

Wolf G, Rebollo R, Karimi MM, Ewing AD, Kamada R, Wu W, Wu B, Bachu M, Ozato K, Faulkner GJ, Mager DL, Lorincz MC, Macfarlan TS.

Nature. 2017 Aug 2;548(7665):E1-E3. doi: 10.1038/nature23277. No abstract available.

PMID:
28770848
4.

Analysis of LINE-1 Elements in DNA from Postmortem Brains of Individuals with Schizophrenia.

Doyle GA, Crist RC, Karatas ET, Hammond MJ, Ewing AD, Ferraro TN, Hahn CG, Berrettini WH.

Neuropsychopharmacology. 2017 Dec;42(13):2602-2611. doi: 10.1038/npp.2017.115. Epub 2017 Jun 6.

PMID:
28585566
5.

Reading LINEs within the cocaine addicted brain.

Doyle GA, Doucet-O'Hare TT, Hammond MJ, Crist RC, Ewing AD, Ferraro TN, Mash DC, Kazazian HH Jr, Berrettini WH.

Brain Behav. 2017 Apr 6;7(5):e00678. doi: 10.1002/brb3.678. eCollection 2017 May.

6.

Heritable L1 retrotransposition in the mouse primordial germline and early embryo.

Richardson SR, Gerdes P, Gerhardt DJ, Sanchez-Luque FJ, Bodea GO, Muñoz-Lopez M, Jesuadian JS, Kempen MHC, Carreira PE, Jeddeloh JA, Garcia-Perez JL, Kazazian HH Jr, Ewing AD, Faulkner GJ.

Genome Res. 2017 Aug;27(8):1395-1405. doi: 10.1101/gr.219022.116. Epub 2017 May 8.

7.

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.

Carreira PE, Ewing AD, Li G, Schauer SN, Upton KR, Fagg AC, Morell S, Kindlova M, Gerdes P, Richardson SR, Li B, Gerhardt DJ, Wang J, Brennan PM, Faulkner GJ.

Mob DNA. 2016 Nov 11;7:21. doi: 10.1186/s13100-016-0076-6. eCollection 2016.

8.

Transposable element detection from whole genome sequence data.

Ewing AD.

Mob DNA. 2015 Dec 29;6:24. doi: 10.1186/s13100-015-0055-3. eCollection 2015. Review.

9.

Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution.

Ewing AD, Gacita A, Wood LD, Ma F, Xing D, Kim MS, Manda SS, Abril G, Pereira G, Makohon-Moore A, Looijenga LH, Gillis AJ, Hruban RH, Anders RA, Romans KE, Pandey A, Iacobuzio-Donahue CA, Vogelstein B, Kinzler KW, Kazazian HH Jr, Solyom S.

Genome Res. 2015 Oct;25(10):1536-45. doi: 10.1101/gr.196238.115. Epub 2015 Aug 10.

10.

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY; ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC.

Nat Methods. 2015 Jul;12(7):623-30. doi: 10.1038/nmeth.3407. Epub 2015 May 18.

11.

Ubiquitous L1 mosaicism in hippocampal neurons.

Upton KR, Gerhardt DJ, Jesuadian JS, Richardson SR, Sánchez-Luque FJ, Bodea GO, Ewing AD, Salvador-Palomeque C, van der Knaap MS, Brennan PM, Vanderver A, Faulkner GJ.

Cell. 2015 Apr 9;161(2):228-39. doi: 10.1016/j.cell.2015.03.026.

12.

RADIA: RNA and DNA integrated analysis for somatic mutation detection.

Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D.

PLoS One. 2014 Nov 18;9(11):e111516. doi: 10.1371/journal.pone.0111516. eCollection 2014.

13.

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.

Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D.

Nature. 2014 Dec 11;516(7530):242-5. doi: 10.1038/nature13760. Epub 2014 Sep 28.

14.

Global optimization of somatic variant identification in cancer genomes with a global community challenge.

Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM.

Nat Genet. 2014 Apr;46(4):318-319. doi: 10.1038/ng.2932. No abstract available.

15.

Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles.

Mandal PK, Ewing AD, Hancks DC, Kazazian HH Jr.

Hum Mol Genet. 2013 Sep 15;22(18):3730-48. doi: 10.1093/hmg/ddt225. Epub 2013 May 21.

16.

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes.

Ewing AD, Ballinger TJ, Earl D; Broad Institute Genome Sequencing and Analysis Program and Platform, Harris CC, Ding L, Wilson RK, Haussler D.

Genome Biol. 2013 Mar 13;14(3):R22. doi: 10.1186/gb-2013-14-3-r22.

17.

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.

18.

Pathogenic orphan transduction created by a nonreference LINE-1 retrotransposon.

Solyom S, Ewing AD, Hancks DC, Takeshima Y, Awano H, Matsuo M, Kazazian HH Jr.

Hum Mutat. 2012 Feb;33(2):369-71. doi: 10.1002/humu.21663. Epub 2011 Dec 8.

19.

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.

20.

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.

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