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Items: 16

1.

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.

Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K.

Cell Rep. 2017 Apr 25;19(4):875-889. doi: 10.1016/j.celrep.2017.03.078.

2.

Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancer.

Genovese G, Carugo A, Tepper J, Robinson FS, Li L, Svelto M, Nezi L, Corti D, Minelli R, Pettazzoni P, Gutschner T, Wu CC, Seth S, Akdemir KC, Leo E, Amin S, Molin MD, Ying H, Kwong LN, Colla S, Takahashi K, Ghosh P, Giuliani V, Muller F, Dey P, Jiang S, Garvey J, Liu CG, Zhang J, Heffernan TP, Toniatti C, Fleming JB, Goggins MG, Wood LD, Sgambato A, Agaimy A, Maitra A, Roberts CW, Wang H, Viale A, DePinho RA, Draetta GF, Chin L.

Nature. 2017 Feb 16;542(7641):362-366. doi: 10.1038/nature21064. Epub 2017 Feb 8.

PMID:
28178232
3.

Systematic analysis of telomere length and somatic alterations in 31 cancer types.

Barthel FP, Wei W, Tang M, Martinez-Ledesma E, Hu X, Amin SB, Akdemir KC, Seth S, Song X, Wang Q, Lichtenberg T, Hu J, Zhang J, Zheng S, Verhaak RG.

Nat Genet. 2017 Mar;49(3):349-357. doi: 10.1038/ng.3781. Epub 2017 Jan 30.

4.

SOX9 chromatin folding domains correlate with its real and putative distant cis-regulatory elements.

Smyk M, Akdemir KC, Stankiewicz P.

Nucleus. 2017 Mar 4;8(2):182-187. doi: 10.1080/19491034.2017.1279776. Epub 2017 Jan 13.

5.

LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56.

Jain AK, Xi Y, McCarthy R, Allton K, Akdemir KC, Patel LR, Aronow B, Lin C, Li W, Yang L, Barton MC.

Mol Cell. 2016 Dec 1;64(5):967-981. doi: 10.1016/j.molcel.2016.10.039.

6.

In Vivo Functional Platform Targeting Patient-Derived Xenografts Identifies WDR5-Myc Association as a Critical Determinant of Pancreatic Cancer.

Carugo A, Genovese G, Seth S, Nezi L, Rose JL, Bossi D, Cicalese A, Shah PK, Viale A, Pettazzoni PF, Akdemir KC, Bristow CA, Robinson FS, Tepper J, Sanchez N, Gupta S, Estecio MR, Giuliani V, Dellino GI, Riva L, Yao W, Di Francesco ME, Green T, D'Alesio C, Corti D, Kang Y, Jones P, Wang H, Fleming JB, Maitra A, Pelicci PG, Chin L, DePinho RA, Lanfrancone L, Heffernan TP, Draetta GF.

Cell Rep. 2016 Jun 28;16(1):133-147. doi: 10.1016/j.celrep.2016.05.063. Epub 2016 Jun 16.

7.

Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins.

Szafranski P, Gambin T, Dharmadhikari AV, Akdemir KC, Jhangiani SN, Schuette J, Godiwala N, Yatsenko SA, Sebastian J, Madan-Khetarpal S, Surti U, Abellar RG, Bateman DA, Wilson AL, Markham MH, Slamon J, Santos-Simarro F, Palomares M, Nevado J, Lapunzina P, Chung BH, Wong WL, Chu YWY, Mok GTK, Kerem E, Reiter J, Ambalavanan N, Anderson SA, Kelly DR, Shieh J, Rosenthal TC, Scheible K, Steiner L, Iqbal MA, McKinnon ML, Hamilton SJ, Schlade-Bartusiak K, English D, Hendson G, Roeder ER, DeNapoli TS, Littlejohn RO, Wolff DJ, Wagner CL, Yeung A, Francis D, Fiorino EK, Edelman M, Fox J, Hayes DA, Janssens S, De Baere E, Menten B, Loccufier A, Vanwalleghem L, Moerman P, Sznajer Y, Lay AS, Kussmann JL, Chawla J, Payton DJ, Phillips GE, Brosens E, Tibboel D, de Klein A, Maystadt I, Fisher R, Sebire N, Male A, Chopra M, Pinner J, Malcolm G, Peters G, Arbuckle S, Lees M, Mead Z, Quarrell O, Sayers R, Owens M, Shaw-Smith C, Lioy J, McKay E, de Leeuw N, Feenstra I, Spruijt L, Elmslie F, Thiruchelvam T, Bacino CA, Langston C, Lupski JR, Sen P, Popek E, Stankiewicz P.

Hum Genet. 2016 May;135(5):569-586. doi: 10.1007/s00439-016-1655-9. Epub 2016 Apr 12.

8.

Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma.

Lissanu Deribe Y, Shi Y, Rai K, Nezi L, Amin SB, Wu CC, Akdemir KC, Mahdavi M, Peng Q, Chang QE, Hornigold K, Arold ST, Welch HC, Garraway LA, Chin L.

Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):E1296-305. doi: 10.1073/pnas.1513801113. Epub 2016 Feb 16.

9.

Dual Roles of RNF2 in Melanoma Progression.

Rai K, Akdemir KC, Kwong LN, Fiziev P, Wu CJ, Keung EZ, Sharma S, Samant NS, Williams M, Axelrad JB, Shah A, Yang D, Grimm EA, Barton MC, Milton DR, Heffernan TP, Horner JW, Ekmekcioglu S, Lazar AJ, Ernst J, Chin L.

Cancer Discov. 2015 Dec;5(12):1314-27. doi: 10.1158/2159-8290.CD-15-0493. Epub 2015 Oct 8.

10.

HiCPlotter integrates genomic data with interaction matrices.

Akdemir KC, Chin L.

Genome Biol. 2015 Sep 21;16:198. doi: 10.1186/s13059-015-0767-1.

11.

Increased H3K9me3 drives dedifferentiated phenotype via KLF6 repression in liposarcoma.

Keung EZ, Akdemir KC, Al Sannaa GA, Garnett J, Lev D, Torres KE, Lazar AJ, Rai K, Chin L.

J Clin Invest. 2015 Aug 3;125(8):2965-78. doi: 10.1172/JCI77976. Epub 2015 Jul 20.

12.

Genome-wide profiling reveals stimulus-specific functions of p53 during differentiation and DNA damage of human embryonic stem cells.

Akdemir KC, Jain AK, Allton K, Aronow B, Xu X, Cooney AJ, Li W, Barton MC.

Nucleic Acids Res. 2014 Jan;42(1):205-23. doi: 10.1093/nar/gkt866. Epub 2013 Sep 27.

13.

The postnatal role of Sox9 in cartilage.

Henry SP, Liang S, Akdemir KC, de Crombrugghe B.

J Bone Miner Res. 2012 Dec;27(12):2511-25. doi: 10.1002/jbmr.1696.

14.

TRIM24 links a non-canonical histone signature to breast cancer.

Tsai WW, Wang Z, Yiu TT, Akdemir KC, Xia W, Winter S, Tsai CY, Shi X, Schwarzer D, Plunkett W, Aronow B, Gozani O, Fischle W, Hung MC, Patel DJ, Barton MC.

Nature. 2010 Dec 16;468(7326):927-32. doi: 10.1038/nature09542.

15.

Direct activation of forkhead box O3 by tumor suppressors p53 and p73 is disrupted during liver regeneration in mice.

Kurinna S, Stratton SA, Tsai WW, Akdemir KC, Gu W, Singh P, Goode T, Darlington GJ, Barton MC.

Hepatology. 2010 Sep;52(3):1023-32. doi: 10.1002/hep.23746.

16.

Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedarius.

Al-Swailem AM, Shehata MM, Abu-Duhier FM, Al-Yamani EJ, Al-Busadah KA, Al-Arawi MS, Al-Khider AY, Al-Muhaimeed AN, Al-Qahtani FH, Manee MM, Al-Shomrani BM, Al-Qhtani SM, Al-Harthi AS, Akdemir KC, Inan MS, Otu HH.

PLoS One. 2010 May 19;5(5):e10720. doi: 10.1371/journal.pone.0010720.

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