Transcriptional Regulation

Dissection of regulatory networks that conrol gene transcription is one of the greatest challenges of functional genomics. The Algorithms Group addressed the problem of modeling generic features of structurally but not textually related DNA motifs. The work divides into several parts: (1) A new approach to the recognition of transcription-factor binding sites, based on the principle that transcription factors divide naturally into families, and that the binding site motifs for transcription factors within the same family have common features. (2) An algorithm and an associated Web-based tool for finding recurrent cis-regulatory modules in the promoter regions of human genes. (3) An algorithm for minimizing the number of gene perturbation pathways whose regulatory structures can be described within the mathematical framework of chain functions. (4) Algorithms for discovering protein complexes and regulatory pathways that are conserved in evolotion, using protein sequence data and protein-protien interaction data for two or more organisms.