Rosa Karlić

Postdoctoral fellow 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

1. Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller, Viren Amin, John W Whitaker, Matthew D Schultz, Lucas D Ward, Abhishek Sarkar, Gerald Quon, Richard S Sandstrom, Matthew L Eaton, Yi-Chieh Wu, Andreas R Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R Alan Harris, Noam Shoresh, Charles B Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J Mungall, Richard Moore, Eric Chuah, Angela Tam, Theresa K Canfield, R Scott Hansen, Rajinder Kaul, Peter J Sabo, Mukul S Bansal, Annaick Carles, Jesse R Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell Elliott, Tim R Mercer, Shane J Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C Sallari, Kyle T Siebenthall, Nicholas A Sinnott-Armstrong, Michael Stevens, Robert E Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E Beaudet, Laurie A Boyer, Philip L De Jager, Peggy J Farnham, Susan J Fisher, David Haussler, Steven J M Jones, Wei Li, Marco A Marra, Michael T McManus, Shamil Sunyaev, James A Thomson, Thea D Tlsty, Li-Huei Tsai, Wei Wang, Robert A Waterland, Michael Q Zhang, Lisa H Chadwick, Bradley E Bernstein, Joseph F Costello, Joseph R Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A Stamatoyannopoulos, Ting Wang, Manolis Kellis, and Roadmap Epigenomics Consortium. 2015. “Integrative Analysis of 111 Reference Human Epigenomes.” Nature 518(7539): 317–30. link

2. Polak, Paz, Rosa Karlić, Amnon Koren, Robert Thurman, Richard Sandstrom, Michael S Lawrence, Alex Reynolds, Eric Rynes, Kristian Vlahoviček, John A Stamatoyannopoulos, and Shamil R Sunyaev. 2015. “Cell-of-Origin Chromatin Organization Shapes the Mutational Landscape of Cancer.” Nature 518(7539): 360–64. link

3. Koren, Amnon, Robert E Handsaker, Nolan Kamitaki, Rosa Karlić, Sulagna Ghosh, Paz Polak, Kevin Eggan, and Steven A McCarroll. 2014. “Genetic Variation in Human DNA Replication Timing.” Cell 159(5): 1015–26. link

4. Karlić, Rosa, Ho-Ryun Chung, Julia Lasserre, Kristian Vlahoviček, and Martin Vingron. 2010. “Histone Modification Levels Are Predictive for Gene Expression.” Proceedings of the National Academy of Sciences of the United States of America 107(7): 2926–31. (October 19, 2014). link