Rosa Karlić

Assistant professor working on several projects which try to relate chromatin structure and other epigenetic mechanisms to transcriptional regulation, evolution of regulatory elements and the development of complex diseases, especially cancer. Interested in the application of statistical and machine learning methods for the analysis of high-throughput genomic data.Involved in teaching two graduate-level courses: Statistics and machine learning and Computational genomics.

Publications

Kirsten Kübler, Rosa Karlić, Nicholas J. Haradhvala, Kyungsik Ha, Jaegil Kim, Maja Kuzman, Wei Jiao, Sitanshu Gakkhar, Kent W. Mouw, Lior Z. Braunstein, Olivier Elemento, Andrew V. Biankin, Ilse Rooman, Mendy Miller, Wouter R. Karthaus, Christopher D. Nogiec, Edouard Juvenson, Edward Curry, Mari Mino-Kenudson, Leif W. Ellisen, Robert Brown, Alexander Gusev, Cristian Tomasetti, Martijn P. Lolkema, Neeltje Steeghs, Carla van Herpen, Hong-Gee Kim, Hwajin Lee, Kristian Vlahoviček, Bradley E. Bernstein, Charles L. Sawyers, Katherine A. Hoadley, Edwin Cuppen, Amnon Koren, Peter F. Arndt, David N. Louis, Lincoln D. Stein, William D. Foulkes, Paz Polak, Gad Getz Tumor mutational landscape is a record of the pre-malignant state. BioRxiv 517565 (2019)

Consortium, R.E., Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015). Integrative analysis of 111 reference human epigenomes. Nature 518, 317–330.

Franke, V., Ganesh, S., Karlic, R., Malik, R., Pasulka, J., Horvat, F., Kuzman, M., Fulka, H., Cernohorska, M., Urbanova, J., et al. (2017). Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. Genome Res. gr.216150.116.

Karlić, R., Chung, H.-R., Lasserre, J., Vlahoviček, K., and Vingron, M. (2010). Histone modification levels are predictive for gene expression. Proc. Natl. Acad. Sci. 107, 2926–2931.

Karlic, R., Ganesh, S., Franke, V., Svobodova, E., Urbanova, J., Suzuki, Y., Aoki, F., Vlahovicek, K., and Svoboda, P. (2017). Long non-coding RNA exchange during the oocyte-to-embryo transition in mice. DNA Res. Int. J. Rapid Publ. Rep. Genes Genomes.

Koren, A., Handsaker, R.E., Kamitaki, N., Karlić, R., Ghosh, S., Polak, P., Eggan, K., and McCarroll, S.A. (2014). Genetic Variation in Human DNA Replication Timing. Cell 159, 1015–1026.

Maruvka, Y.E., Mouw, K.W., Karlic, R., Parasuraman, P., Kamburov, A., Polak, P., Haradhvala, N.J., Hess, J.M., Rheinbay, E., Brody, Y., et al. (2017). Analysis of somatic microsatellite indels identifies driver events in human tumors. Nat. Biotechnol.

Polak, P., Karlić, R., Koren, A., Thurman, R., Sandstrom, R., Lawrence, M., Reynolds, A., Rynes, E., Vlahoviček, K., Stamatoyannopoulos, J.A., et al. (2015). Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature 518, 360–364.

Polak, P., Kim, J., Braunstein, L.Z., Karlic, R., Haradhavala, N.J., Tiao, G., Rosebrock, D., Livitz, D., Kübler, K., Mouw, K.W., et al. (2017). A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer. Nat. Genet. 49, 1476–1486.

Wardell, C.P., Fujita, M., Yamada, T., Simbolo, M., Fassan, M., Karlic, R., Polak, P., Kim, J., Hatanaka, Y., Maejima, K., et al. (2018). Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations. J. Hepatol. 68, 959–969.