Our research focuses on the computational approaches to problems in molecular biology. In particular, we are interested in exploring gene regulatory networks, mostly in metazoan genomes. We approach the subject through an integrated analysis of DNA sequence and gene expression data. We also strive to understand how sequences involved in gene regulation have evolved, and how such evolutionary dynamics may inform the discovery of novel regulatory sequences. Broadly speaking, our work may be said to fall in the areas of comparative and regulatory genomics.

FEATURED RESEARCH

Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse
Miriam R. Kantorovitz, Majid Kazemian, Sarah Kinston, Diego Miranda-Saavedra, Qiyun Zhu, Gene E. Robinson, Berthold Göttgens, Marc S. Halfon, Saurabh Sinha
Developmental Cell, 20 October, 2009. Volume 17, Issue 4. [News coverage]

This paper presents a computational method to discover cis-regulatory sequences (enhancers) in a genome without knowledge of transcription factor motifs. The method is shown to be effective in insect as well as mammalian genomes. It is especially useful for investigation of gene regulatory networks with relatively little prior characterization.

 

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