Publications

C. Terranova, M. Tang, E. Orouji, M. Maitituoheti, A. T. Raman, S. Amin, Z. Liu, and K. Rai*.  An Integrated Platform for Genome-wide Mapping of Chromatin States using High-Throughput ChIP-sequencing in Tumor Tissues and Cell Lines. Journal of Visualized Experimentation, Accepted. *Corresponding author.

U. Oleksiewicz, M. Gładych, AT Raman, H. Heyn, E. Mereu, P. Chlebanowska, A. Andrzejewska, B. Sozańska, NS Samant, K. Fąk, P. Auguścik, M. Kosiński, JP Wróblewska, K. Tomczak, K. Kulcenty, R. Płoski, P. Biecek, M. Esteller, PK Shah, ^#K. Rai and  ^#M. Wiznerowicz (2017). TRIM28 and Interacting KRAB-ZNFs Control Self-Renewal of Human Pluripotent Stem Cells through Epigenetic Repression of Pro-differentiation Genes. Stem Cell Reports. Dec 12; 9(6):2065-2080. ^# Co-corresponding author.

^#S. Sarkar, C. A. Bristow, P. Dey, K. Rai, R. Perets, A. Ramirez-Cardenas, S. Malasi, E. Huang-Hobbs, M. Haemmerle, S. Y. Wu, M. McGuire, A. Protopopov, J. Garvey, J. F. Liu, M. S. Hirsch, Q. Chang, A. J. Lazar, A. K. Sood, R. Drapkin, R. DePinho, G. Draetta and ^#L. Chin (2017). PRKCI promotes immune suppression in ovarian cancer. Genes and Development. Jun 1;31(11):1109-1121. ^# Co-corresponding author.

*P. Fiziev, *K.C. Akdemir, J. P. Miller, E. Z. Keung, N.S. Samant, S. Sharma, C. Natale, C.J. Terranova, M. Maitituoheti, SB Amin, E. Martinez-Ledesma, M. Dhamdhere, J. B. Axelrad, A. Shah, C.S. Cheng,  H. Mahadeshwar, S. Seth, M.C. Barton, A. Propopotov, K.Y. Tsai, M.A. Davies, B.A. Garcia, I. Amit, ^#L. Chin, ^#J. Ernst and ^#K. Rai (2017). Systematic Epigenomic Analysis Reveals Chromatin States and Regulators Associated with Melanoma Progression. Cell Reports. 19(4):875-889. *Co-first authors. ^#Co-corresponding Authors.

*K. Rai, K. C. Akdemir, L. Kwong, C. J. Wu, E. Keung, S. Sharma, M. Williams, J. B. Axelrad, N. S. Samant, A. Shah, D.Yang, E. Grimm, M. C. Barton, D. R. Milton, T. P. Heffernan, J. W. Horner, S. Ekmekcioglu, A. Lazar, L. Chin (2015). Dual roles for RNF2 during melanoma progression. Cancer Discovery, 5(12):1314-27.  *Co-corresponding authors

E. Z. Keung and K. Rai* (2016). H3K9me3 Mediated Repression of KLF6: Discovering a Novel Tumor Suppressor in Liposarcoma Using a Systematic Epigenomic Approach. Molecular and Cellular Oncology. Oct 29;3(3):e1093691. * Corresponding author.

E. Z. Keung, K. C. Akdemir, G. C. C. Sannaa, J. Garnett, D. Lev, K. E. Torres, A. J. Lazar, K. Rai and L. Chin* (2015). Increased H3K9me3 drives dedifferentiated phenotype via KLF6 repression in liposarcoma. Journal of Clinical Investigation 10:1172. *Co-corresponding authors.

Rai K*. Genomic Classification of Cutaneous Melanoma (2015). Cell 7(161):1681-96. * TCGA SKCM Analysis working group member

C. Cheng, K. Rai, M. Garber, A. Hollinger, D. Robbins, S. Anderson, A. Rosenthal, A. Tzou, R. Raychowdhury, J. E. Gershenwald, N. Lennon, L. Chin, A. Regev, and I. Amit (2013). Semiconductor based sequencing of histone modification states reveals signatures of cancer progression. Nature Communications. 4: 2462.

*G. Genovese,  *A. Ergun, *S. A. Shukla, B. Campos, J. Hanna,  P. Ghosh,  S. N. Quayle, K. Rai, S. Colla, H. Ying, C.J. Wu, S. Sarkar, Y. Xiao, J. Zhang, H. Zhang, L. Kwong, K. Dunn, W. R. Wiedemeyer, C. Brennan, H. Zheng, D.L. Rimm, J. Collins, L. Chin (2012). microRNA regulatory network inference identifies miR-34a as a novel regulator of TGF signaling in GBM. Cancer Discovery. 2(8):736-49. *Equal contribution.

*K. Rai,  *S. Sarkar, *T. Broadbent, M. Voas, K.F. Grossman,  L. D. Nadauld, S. Dehghanizadeh, F. T. Hagos, Y. Lee, R. K. Toth,  S. Chidester, T. Bahr, E. Johnson, B. Sklow, R. Burt, B. R. Cairns, and D. A. Jones (2010). DNA Demethylase Activity Maintains Zebrafish Intestinal Cells in a Progenitor-like State Following Loss of APC. Cell. 142(6):930-42.* Equal contribution.

K. Rai, S. Chidester, S. R. James, A. R. Karpf, B. R.Cairns and D. A. Jones (2010). Dnmt3 and G9a co-operate to promote zebrafish development. Journal of Biological Chemistry, 285(6):4110-21.

R. A. Phelps, S. Chidester, S. Dehghanizadeh, I. T. Sandoval, J. Phelps, K. Rai, T. Broadbent, S. Sarkar, R. W. Burt and D. A. Jones (2008). A two step model for colon adenomal initiation and progression caused by APC loss. Cell, 137(4):623-34.

K. Rai, I.H. Huggins, S. R. James, A. R. Karpf, D.A. Jones, and B. R. Cairns (2008). DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and Gadd45 (2008). Cell, 135(7):1201-12.

K. Rai, S. Chidester, C. V. Zavala, E. J. Manos, S. R. James, A. R. Karpf, D. A. Jones and B. R. Cairns (2007). Dnmt2 functions in the cytoplasm to promote liver, brain and retina development in zebrafish. Genes and Development, 21(3):261-6.

K. Rai, L. D. Nadauld, S. Chidester, E. J. Manos, S. R. James, A. R. Karpf, B. R.Cairns and D. A. Jones (2006). Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development. Molecular and Cellular Biology. 26(19):7077-85.

L. D. Nadauld, S. Chidester, D. N. Shelton, K. Rai, T. Broadbent, I. T. Sandoval, P. W. Peterson, E. J. Manos, and D. A. Jones (2006).  Dual roles for adenomatous polyposis coli in regulating retinoic acid biosynthesis and Wnt during ocular development. Proceedings of National Academy of Sciences U S A.  5;103(36):13409-14.