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Category: Faculty

Arnold, Jonathan

Research Interest
Our lab is interested in the identifying gene regulatory and biochemical networks for fundamental biological processes in fungal systems and validating these biological circuits by fitting them to genomics data. We are interested in reassembling the pieces of DNA from the genome to life. The theme for the genomics and computational biology part of my research is “computing life”, i.e., identifying biological circuits for fundamental processes like carbon metabolism and validating these biological circuits by fitting them to genomics data describing what the cell is doing (i.e., RNA and protein profiling data).


Liu, Liang

Research Interests
My research interests include phylogenetics, modeling biological data, statistical analysis of molecular data, and parallel computing. I am particularly interested in reconstructing species phylogenies from multilocus sequences. My colleagues and I have developed several phylogenetic methods for estimating the evolutionary history of species.


Zhao, Shaying

Research Interest

My lab is using experimental and computational approaches to study  genomic changes occurring during mammalian evolution and disease  development.  The goal is to understand the roles of genomic changes  playing in these normal and abnormal processes, as well as the mechanism  through which these changes have taken place.  The lab has two ongoing  projects currently.  The first one is to identify bona fide colorectal  cancer genes via a novel comparative genomics and oncology strategy – by  searching for genes that are commonly altered in human, dog and mouse  colorectal tumors.  The second project focuses on “the junk DNA” of the  human genome, which has allowed us to discover two giant composite  retrotransposon-like elements DA and Xiao. We are now conducting  experiments to understand the nature of DA/Xiao and to explore their  potential application in medicine and research.


Mrázek, Jan

Research Interest
The long-term goal of our research is to understand the information encoded in the DNA to the extent that we can accurately predict properties of an organism, including its responses to external stimuli, from its genomic sequence. A common approach currently used is to find all genes and open reading frames in a genome, to predict their function from protein sequence comparisons, and, with the predicted complement of all proteins of the organism at hand, to speculate about its metabolic, environmental, cellular, and morphological characteristics.


Our research centers on discovery and analysis of sequence features not directly associated with genes and proteins, and their possible roles in the organism’s physiology and evolution. We are particularly interested in those sequence features that affect DNA structure and/or promote conformational transitions in the DNA molecule.


Kannan, Natarajan


Research Interest
Research in our lab is focused on understanding the evolutionary design principles of cellular signaling proteins, such as protein kinases, which are implicated in many human cancers. We are using a combination of computational and experimental approaches to understand how mutations, and other genomic alterations, in these proteins contribute to human diseases.


Kissinger, Jessica

Research Interest

How do eukaryotic genomes evolve? Our lab is interested in parasite genomics and the biology of genome evolution. The genomes of parasitic eukaryotes are often highly reduced, devoid of recognizable mobile elements and riddled with intracellular and lateral gene transfers. Our approach is to apply molecular, computational and phylogenetic tools to the analysis of dozens of complete parasite genomes. Projects include the development of tools for data mining and data integration including ontology development; comparative genomics and assessment of the phylogenetic distribution of genes. We welcome students interested in working on the bench, at the computer, or both.