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Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.
Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. Ando M, et al. Among authors: Califano JA. Nat Commun. 2019 May 16;10(1):2188. doi: 10.1038/s41467-019-09937-w. Nat Commun. 2019. PMID: 31097695 Free PMC article.
The NOTCH Pathway in Head and Neck Squamous Cell Carcinoma.
Fukusumi T, Califano JA. Fukusumi T, et al. Among authors: Califano JA. J Dent Res. 2018 Jun;97(6):645-653. doi: 10.1177/0022034518760297. Epub 2018 Feb 28. J Dent Res. 2018. PMID: 29489439 Free PMC article. Review.
Frequency of homozygous deletion at p16/CDKN2 in primary human tumours.
Cairns P, Polascik TJ, Eby Y, Tokino K, Califano J, Merlo A, Mao L, Herath J, Jenkins R, Westra W, Rutter JL, Buckler A, Gabrielson E, Tockman M, Cho KR, Hedrick L, Bova GS, Isaacs W, Koch W, Schwab D, Sidransky D, et al. Cairns P, et al. Among authors: Califano J. Nat Genet. 1995 Oct;11(2):210-2. doi: 10.1038/ng1095-210. Nat Genet. 1995. PMID: 7550353
The major 8p22 tumor suppressor DLC1 is frequently silenced by methylation in both endemic and sporadic nasopharyngeal, esophageal, and cervical carcinomas, and inhibits tumor cell colony formation.
Seng TJ, Low JS, Li H, Cui Y, Goh HK, Wong ML, Srivastava G, Sidransky D, Califano J, Steenbergen RD, Rha SY, Tan J, Hsieh WS, Ambinder RF, Lin X, Chan AT, Tao Q. Seng TJ, et al. Among authors: Califano J. Oncogene. 2007 Feb 8;26(6):934-44. doi: 10.1038/sj.onc.1209839. Epub 2006 Jul 24. Oncogene. 2007. PMID: 16862168
NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva.
Guerrero-Preston R, Soudry E, Acero J, Orera M, Moreno-López L, Macía-Colón G, Jaffe A, Berdasco M, Ili-Gangas C, Brebi-Mieville P, Fu Y, Engstrom C, Irizarry RA, Esteller M, Westra W, Koch W, Califano J, Sidransky D. Guerrero-Preston R, et al. Among authors: Califano J. Cancer Prev Res (Phila). 2011 Jul;4(7):1061-72. doi: 10.1158/1940-6207.CAPR-11-0006. Epub 2011 May 10. Cancer Prev Res (Phila). 2011. PMID: 21558411 Free PMC article.
Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.
Stein-O'Brien G, Kagohara LT, Li S, Thakar M, Ranaweera R, Ozawa H, Cheng H, Considine M, Schmitz S, Favorov AV, Danilova LV, Califano JA, Izumchenko E, Gaykalova DA, Chung CH, Fertig EJ. Stein-O'Brien G, et al. Among authors: Califano JA. Genome Med. 2018 May 23;10(1):37. doi: 10.1186/s13073-018-0545-2. Genome Med. 2018. PMID: 29792227 Free PMC article.
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.
Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Zambo KD, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ. Afsari B, et al. Among authors: Califano JA. Bioinformatics. 2018 Jun 1;34(11):1859-1867. doi: 10.1093/bioinformatics/bty004. Bioinformatics. 2018. PMID: 29342249 Free PMC article.
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