Population Biology of Infectious Disease

Population and Comparative Genomics

Our lab seeks to understand how transcriptional regulation is encoded in the genome, primarily through the development of data mining and integration methods. We have developed effective approaches for learning characteristic predictive patterns between-species genome comparisons, and current work seeks to extend these methods to incorporate within-species comparisons as well as high-throughput experimental data to learn fundamental features of regulatory elements.

Recent publications:

• Taylor J, Tyekucheva S, King DC, Hardison RC, Miller W, and Chiaromonte F. "ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements". Genome Research. 2006 Dec; 16(12):1596-604.
• King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J, ENCODE groups for Transcriptional Regulation and Multispecies Alignment, Chiaromonte F, Miller W, Hardison RC. "Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data". Genome Research. 2007 Jun; 17(6):775-786.