Group: Thorne Group
PhD, University of California at Berkeley
Office: 314 Ricks Hall
I am working on a Population Genomic Approach to Modeling Insertion-Deletion Evolution Between Species.
One of the key ways in which genomes differ is that they have segments of DNA that have been inserted or deleted. These are known as indels, and they comprise an important class of variation both within and among species. If species are distantly related their genomes may contain many indels, potentially making the same stretch of DNA unrecognizable. But because the genomes of members of the same species are very similar, indels present are easier to identify. Genomes of many individuals will be compared in the same species to discover indels in the population. Estimates of the strength of natural selection acting on these indels of different sizes and in different parts of the genome will be used to develop a mathematical model of the evolutionary process that accounts for the size and genomic context of indels. This model will help to better understand the important role that indels play in the genomic evolution of different species.
Training objectives include the strengthening of skills in genomic analysis, probabilistic modeling, and computer programming. This project bridges the fields of population genomics and statistics and will foster collaborations between researchers in different areas while directly involving undergraduate students in scientific research.
Nasrallah CA, Mathews DH, Huelsenbeck JP. (2011). Quantifying the Impact of Dependent Evolution Among Sites in Phylogenetic Inference. Systematic Biology. 60(1):60–73.
Fandy TE, Herman JG, Kerns P, Jiemjit A, Sugar EA, Choi S, Yang AS, Aucott T, Dauses T, Odchimar-Reissig R, Licht J, McConnell MJ, Nasrallah CA, Kim MKH, Zhang W, Sun Y, Murgo A, Espinoza-Delgado I, Oteiza K, Owoeye I, Silverman LR, Gore SD, and Carraway H. (2009). Early epigenetic changes and DNA damage do not predict clinical response in an overlapping schedule of 5-azacytidine and entinostat in patients with myeloid malignancies. Blood. 114:2764–2773.
Iancu-Rubin C, Nasrallah CA, Atweh, GF. (2005). Stathmin Prevents the Transition from a Normal to an Endomitotic Cell Cycle during Megakaryocytic Differentiation. Cell Cycle 4:1774–1782.