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Items: 35

1.

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C.

Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z.

2.

Cross-species transcriptional analysis reveals conserved and host-specific neoplastic processes in mammalian glioma.

Connolly NP, Shetty AC, Stokum JA, Hoeschele I, Siegel MB, Miller CR, Kim AJ, Ho CY, Davila E, Simard JM, Devine SE, Rossmeisl JH, Holland EC, Winkles JA, Woodworth GF.

Sci Rep. 2018 Jan 19;8(1):1180. doi: 10.1038/s41598-018-19451-6.

3.

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology.

Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE; 1000 Genomes Project Consortium, Devine SE.

Genome Res. 2017 Nov;27(11):1916-1929. doi: 10.1101/gr.218032.116. Epub 2017 Aug 30.

4.

The Role of Somatic L1 Retrotransposition in Human Cancers.

Scott EC, Devine SE.

Viruses. 2017 May 31;9(6). pii: E131. doi: 10.3390/v9060131. Review.

5.

Corrigendum: Brain feminization requires active repression of masculinization via DNA methylation.

Nugent BM, Wright CL, Shetty AC, Hodes GE, Lenz KM, Mahurkar A, Russo SJ, Devine SE, McCarthy MM.

Nat Neurosci. 2017 May 25;20(6):896. doi: 10.1038/nn0617-896a. No abstract available.

PMID:
28542152
6.

A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer.

Scott EC, Gardner EJ, Masood A, Chuang NT, Vertino PM, Devine SE.

Genome Res. 2016 Jun;26(6):745-55. doi: 10.1101/gr.201814.115. Epub 2016 May 10.

7.

An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

8.

Pulmonary Nontuberculous Mycobacterial Infection. A Multisystem, Multigenic Disease.

Szymanski EP, Leung JM, Fowler CJ, Haney C, Hsu AP, Chen F, Duggal P, Oler AJ, McCormack R, Podack E, Drummond RA, Lionakis MS, Browne SK, Prevots DR, Knowles M, Cutting G, Liu X, Devine SE, Fraser CM, Tettelin H, Olivier KN, Holland SM.

Am J Respir Crit Care Med. 2015 Sep 1;192(5):618-28. doi: 10.1164/rccm.201502-0387OC.

9.

Brain feminization requires active repression of masculinization via DNA methylation.

Nugent BM, Wright CL, Shetty AC, Hodes GE, Lenz KM, Mahurkar A, Russo SJ, Devine SE, McCarthy MM.

Nat Neurosci. 2015 May;18(5):690-7. doi: 10.1038/nn.3988. Epub 2015 Mar 30. Erratum in: Nat Neurosci. 2017 May 25;20(6):896.

10.

Natural genetic variation caused by small insertions and deletions in the human genome.

Mills RE, Pittard WS, Mullaney JM, Farooq U, Creasy TH, Mahurkar AA, Kemeza DM, Strassler DS, Ponting CP, Webber C, Devine SE.

Genome Res. 2011 Jun;21(6):830-9. doi: 10.1101/gr.115907.110. Epub 2011 Apr 1.

11.

Small insertions and deletions (INDELs) in human genomes.

Mullaney JM, Mills RE, Pittard WS, Devine SE.

Hum Mol Genet. 2010 Oct 15;19(R2):R131-6. doi: 10.1093/hmg/ddq400. Epub 2010 Sep 21. Review.

12.

Natural mutagenesis of human genomes by endogenous retrotransposons.

Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE.

Cell. 2010 Jun 25;141(7):1253-61. doi: 10.1016/j.cell.2010.05.020.

13.

Expanding the definition of the classical bipartite nuclear localization signal.

Lange A, McLane LM, Mills RE, Devine SE, Corbett AH.

Traffic. 2010 Mar;11(3):311-23. doi: 10.1111/j.1600-0854.2009.01028.x. Epub 2009 Dec 15.

14.

Active Alu retrotransposons in the human genome.

Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE.

Genome Res. 2008 Dec;18(12):1875-83. doi: 10.1101/gr.081737.108. Epub 2008 Oct 3.

15.

The Ty1 integrase protein can exploit the classical nuclear protein import machinery for entry into the nucleus.

McLane LM, Pulliam KF, Devine SE, Corbett AH.

Nucleic Acids Res. 2008 Aug;36(13):4317-26. doi: 10.1093/nar/gkn383. Epub 2008 Jun 27.

16.

A PY-NLS nuclear targeting signal is required for nuclear localization and function of the Saccharomyces cerevisiae mRNA-binding protein Hrp1.

Lange A, Mills RE, Devine SE, Corbett AH.

J Biol Chem. 2008 May 9;283(19):12926-34. doi: 10.1074/jbc.M800898200. Epub 2008 Mar 14.

17.

Which transposable elements are active in the human genome?

Mills RE, Bennett EA, Iskow RC, Devine SE.

Trends Genet. 2007 Apr;23(4):183-91. Epub 2007 Feb 27. Review.

PMID:
17331616
18.

Classical nuclear localization signals: definition, function, and interaction with importin alpha.

Lange A, Mills RE, Lange CJ, Stewart M, Devine SE, Corbett AH.

J Biol Chem. 2007 Feb 23;282(8):5101-5. Epub 2006 Dec 14. Review.

19.

An initial map of insertion and deletion (INDEL) variation in the human genome.

Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE.

Genome Res. 2006 Sep;16(9):1182-90. Epub 2006 Aug 10.

20.

Recently mobilized transposons in the human and chimpanzee genomes.

Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, Devine SE.

Am J Hum Genet. 2006 Apr;78(4):671-9. Epub 2006 Feb 2.

21.

Natural genetic variation caused by transposable elements in humans.

Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE.

Genetics. 2004 Oct;168(2):933-51.

22.

Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map.

Tsui C, Coleman LE, Griffith JL, Bennett EA, Goodson SG, Scott JD, Pittard WS, Devine SE.

Nucleic Acids Res. 2003 Aug 15;31(16):4910-6.

23.

Functional genomics reveals relationships between the retrovirus-like Ty1 element and its host Saccharomyces cerevisiae.

Griffith JL, Coleman LE, Raymond AS, Goodson SG, Pittard WS, Tsui C, Devine SE.

Genetics. 2003 Jul;164(3):867-79.

24.

Yeast retrotransposons: finding a nice quiet neighborhood.

Boeke JD, Devine SE.

Cell. 1998 Jun 26;93(7):1087-9. Review. No abstract available.

25.
26.

A transposon-based strategy for sequencing repetitive DNA in eukaryotic genomes.

Devine SE, Chissoe SL, Eby Y, Wilson RK, Boeke JD.

Genome Res. 1997 May;7(5):551-63.

27.

Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation.

Nam K, Lee G, Trambley J, Devine SE, Boeke JD.

Mol Cell Biol. 1997 Feb;17(2):809-18.

29.

The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability.

Brachmann CB, Sherman JM, Devine SE, Cameron EE, Pillus L, Boeke JD.

Genes Dev. 1995 Dec 1;9(23):2888-902.

31.

Diversity of multidrug resistance in mammalian cells.

Devine SE, Melera PW.

J Biol Chem. 1994 Feb 25;269(8):6133-9.

32.

Functional studies with a full-length P-glycoprotein cDNA encoded by the hamster pgp1 gene.

Devine SE, Melera PW.

Cancer Chemother Pharmacol. 1994;33(6):465-71.

PMID:
7907953
33.

Amino acid substitutions in the sixth transmembrane domain of P-glycoprotein alter multidrug resistance.

Devine SE, Ling V, Melera PW.

Proc Natl Acad Sci U S A. 1992 May 15;89(10):4564-8.

34.

Full length and alternatively spliced pgp1 transcripts in multidrug-resistant Chinese hamster lung cells.

Devine SE, Hussain A, Davide JP, Melera PW.

J Biol Chem. 1991 Mar 5;266(7):4545-55.

35.

12th codon mutation resulting in c-N-ras activation in acute myelogenous leukemia.

Needleman SW, Devine SE, Kraus MH.

Leukemia. 1988 Feb;2(2):91-3.

PMID:
3278172

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