email mzhang@cshl.edu, phone (516) 367-8393, fax (516) 367-8461

Investigators in our laboratory are developing mathematical and computational methods that can be combined with advanced experimental technologies to identify (1) functional genetic elements within molecular sequences and (2) pathways that control and regulate gene expression.

The question of how genetic information is stored and processed is a central problem in biology. Key features that define genetic elements are the very cis-elements that also control and regulate gene expression. Understanding such elements is particularly important for studying eukaryotes because these genetic elements help control development, morphogenesis and cell differentiation, tissue specificity, hormonal communication, and cellular stress responses.

We have recently developed a series of computational tools (MZEF, Core_Promoter, CpG_Promoter, JTEF, FirstEF, etc.). Based on multivariate statistical pattern-recognition techniques, these tools can be used to identify exons, promoters, and polyadenylation signals in large genomic DNA sequences.

We are also studying alternatively spliced exons and are collaborating with experimental scientists to characterize splicing enhancers and silencers. We are interested in developing computational tools that can identify alternatively spliced exons and detect enhancers/silencers that may play important roles in human disease.

In addition to our studies of structural genomics, we are currently collaborating with bench scientists on functional genomics. Using large-scale gene-expression and localization techniques such as cDNA microarrays and DNA oligo-chips, we can study the global, dynamic expression patterns of co-regulated genes, promoter elements that govern tissue-specific transcriptional controls, and the networks of gene regulation that underlie fundamental cellular processes.

Please visit the Zhang Lab home page.

See the MZEF Exon Finder

Selected Publications