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Items: 20


Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates.

Deatherage DE, Leon D, Rodriguez ÁE, Omar SK, Barrick JE.

Nucleic Acids Res. 2018 Sep 28;46(17):9236-9250. doi: 10.1093/nar/gky751.


Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures.

Deatherage DE, Kepner JL, Bennett AF, Lenski RE, Barrick JE.

Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E1904-E1912. doi: 10.1073/pnas.1616132114. Epub 2017 Feb 15.


Tempo and mode of genome evolution in a 50,000-generation experiment.

Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE.

Nature. 2016 Aug 11;536(7615):165-70. Epub 2016 Aug 1.


Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq.

Deatherage DE, Traverse CC, Wolf LN, Barrick JE.

Front Genet. 2015 Jan 21;5:468. doi: 10.3389/fgene.2014.00468. eCollection 2014.


Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.

Barrick JE, Colburn G, Deatherage DE, Traverse CC, Strand MD, Borges JJ, Knoester DB, Reba A, Meyer AG.

BMC Genomics. 2014 Nov 29;15:1039. doi: 10.1186/1471-2164-15-1039.


Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli.

Raeside C, Gaffé J, Deatherage DE, Tenaillon O, Briska AM, Ptashkin RN, Cruveiller S, Médigue C, Lenski RE, Barrick JE, Schneider D.

MBio. 2014 Sep 9;5(5):e01377-14. doi: 10.1128/mBio.01377-14.


Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.

Deatherage DE, Barrick JE.

Methods Mol Biol. 2014;1151:165-88. doi: 10.1007/978-1-4939-0554-6_12.


Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli.

Quandt EM, Deatherage DE, Ellington AD, Georgiou G, Barrick JE.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2217-22. doi: 10.1073/pnas.1314561111. Epub 2013 Dec 30.


ChIP-seq defined genome-wide map of TGFβ/SMAD4 targets: implications with clinical outcome of ovarian cancer.

Kennedy BA, Deatherage DE, Gu F, Tang B, Chan MW, Nephew KP, Huang TH, Jin VX.

PLoS One. 2011;6(7):e22606. doi: 10.1371/journal.pone.0022606. Epub 2011 Jul 25.


Aberrant TGFβ/SMAD4 signaling contributes to epigenetic silencing of a putative tumor suppressor, RunX1T1 in ovarian cancer.

Yeh KT, Chen TH, Yang HW, Chou JL, Chen LY, Yeh CM, Chen YH, Lin RI, Su HY, Chen GC, Deatherage DE, Huang YW, Yan PS, Lin HJ, Nephew KP, Huang TH, Lai HC, Chan MW.

Epigenetics. 2011 Jun;6(6):727-39. Epub 2011 Jun 1.


Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer.

Zuo T, Liu TM, Lan X, Weng YI, Shen R, Gu F, Huang YW, Liyanarachchi S, Deatherage DE, Hsu PY, Taslim C, Ramaswamy B, Shapiro CL, Lin HJ, Cheng AS, Jin VX, Huang TH.

Cancer Res. 2011 Mar 1;71(5):1752-62. doi: 10.1158/0008-5472.CAN-10-3573. Epub 2011 Jan 7.


Epigenetic influences of low-dose bisphenol A in primary human breast epithelial cells.

Weng YI, Hsu PY, Liyanarachchi S, Liu J, Deatherage DE, Huang YW, Zuo T, Rodriguez B, Lin CH, Cheng AL, Huang TH.

Toxicol Appl Pharmacol. 2010 Oct 15;248(2):111-21. doi: 10.1016/j.taap.2010.07.014. Epub 2010 Aug 1.


Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping.

Hsu PY, Hsu HK, Singer GA, Yan PS, Rodriguez BA, Liu JC, Weng YI, Deatherage DE, Chen Z, Pereira JS, Lopez R, Russo J, Wang Q, Lamartiniere CA, Nephew KP, Huang TH.

Genome Res. 2010 Jun;20(6):733-44. doi: 10.1101/gr.101923.109. Epub 2010 May 4.


Promoter hypermethylation of FBXO32, a novel TGF-beta/SMAD4 target gene and tumor suppressor, is associated with poor prognosis in human ovarian cancer.

Chou JL, Su HY, Chen LY, Liao YP, Hartman-Frey C, Lai YH, Yang HW, Deatherage DE, Kuo CT, Huang YW, Yan PS, Hsiao SH, Tai CK, Lin HJ, Davuluri RV, Chao TK, Nephew KP, Huang TH, Lai HC, Chan MW.

Lab Invest. 2010 Mar;90(3):414-25. doi: 10.1038/labinvest.2009.138. Epub 2010 Jan 11.


Epigenetic repression of microRNA-129-2 leads to overexpression of SOX4 oncogene in endometrial cancer.

Huang YW, Liu JC, Deatherage DE, Luo J, Mutch DG, Goodfellow PJ, Miller DS, Huang TH.

Cancer Res. 2009 Dec 1;69(23):9038-46. doi: 10.1158/0008-5472.CAN-09-1499. Epub 2009 Nov 3.


Xenoestrogen-induced epigenetic repression of microRNA-9-3 in breast epithelial cells.

Hsu PY, Deatherage DE, Rodriguez BA, Liyanarachchi S, Weng YI, Zuo T, Liu J, Cheng AS, Huang TH.

Cancer Res. 2009 Jul 15;69(14):5936-45. doi: 10.1158/0008-5472.CAN-08-4914. Epub 2009 Jun 23.


Methylation analysis by microarray.

Deatherage DE, Potter D, Yan PS, Huang TH, Lin S.

Methods Mol Biol. 2009;556:117-39. doi: 10.1007/978-1-60327-192-9_9.


Breast cancer-associated fibroblasts confer AKT1-mediated epigenetic silencing of Cystatin M in epithelial cells.

Lin HJ, Zuo T, Lin CH, Kuo CT, Liyanarachchi S, Sun S, Shen R, Deatherage DE, Potter D, Asamoto L, Lin S, Yan PS, Cheng AL, Ostrowski MC, Huang TH.

Cancer Res. 2008 Dec 15;68(24):10257-66. doi: 10.1158/0008-5472.CAN-08-0288.


Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.

Yan PS, Potter D, Deatherage DE, Huang TH, Lin S.

Methods Mol Biol. 2009;507:89-106. doi: 10.1007/978-1-59745-522-0_8.


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