This talk will describe the data integration efforts of the MIT Computational Biology Group, and their application to both comparative and functional datasets especially in the context of the ENCODE and modENCODE projects (ENCyclopedia of DNA Elements). We have defined evolutionary signatures in the nucleotide alignments of multiple related species, enabling the systematic discovery and characterization of diverse classes of functional elements, including protein-coding genes, RNA structures, microRNAs, developmental enhancers, regulatory motifs, and biological networks. We have also defined distinct chromatin signatures, or combinations of chromatin marks, in genome-wide epigenomic datasets, revealing numerous classes of promoter, enhancer, transcribed, and repressed regions, each with distinct functional properties. These techniques have enabled us to discover many new insights into animal gene regulation, including abundant translational read-through in neuronal proteins, functionality of anti-sense microRNA transcripts, and thousands of novel large intergenic non-coding RNAs. Going forward, we are applying such techniques to understand the logic of global gene regulation during development and differentiation in human and fly, in the context of the ENCODE and modENCODE regions.

Manolis Kellis is an Associate Professor of Computer Science at MIT, a member of the Computer Science and Artificial Intelligence Laboratory and of the Broad Institute of MIT and Harvard, where he directs the MIT Computational Biology Group (compbio.mit.edu). His group has recently been funded to lead the integrative analysis efforts of the modENCODE project for Drosophila melanogaster, and also for integrative analysis of the NIH Epigenome Roadmap Project. He has received the NSF CAREER award, an NIH R01 for work in Computational Genomics, the Alfred P. Sloan Fellowship, the Karl Van Tassel chair in EECS, and the Distinguished Alumnus 1964 chair. He was recognized for his research in genomics as one of the top young innovators under the age of 35 by Technology Review Magazine, one of the principal investigators of the future by Genome Technology magazine, and one of three young scientists representing the next generation in biotechnology by the Boston Museum of Science.He obtained his Ph.D. from MIT, where he received the Sprowls award for the best doctorate thesis in computer science, and the first Paris Kanellakis graduate fellowship.  Prior to computational biology, he worked on artificial intelligence, sketch and image recognition, robotics, and computational geometry, at MIT and at the Xerox Palo Alto Research Center.   He lived in Greece and France before moving to the US.