Manolis Kellis, Ph.D. Associate Professor of Electrical Engineering and Computer Science (EECS) Principal Investigator, MIT Computer Science and Artificial Intelligence Lab (CSAIL) Associate Member, Broad Institute of MIT and Harvard (Broad) MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) Stata Center, Bldg 32-G564 Cambridge, MA 02139 tel: 617-253-2419 m.a.n.o.l.i @ mit.edu (without the dots)

I am an assistant professor at MIT in the area of Computational Biology, pursuing the computational interpretation of biological signals.

My specific interests are:

(1) in the area of genome interpretation, developing comparative genomics methods to identify genes and regulatory elements in the human genome

(2) in the area of gene regulation, deciphering the combinatorial control of gene expression and cell fate specification, and understanding the dynamic reconfiguration of genetic sub-networks in changing environmental conditions

(3) in the area of evolutionary genomics, understanding the emergence of new functions, reconfiguration of regulatory motifs, and the coordinated evolution of functionally interconnected cellular components.

Grad Students/Postdocs

• Matt Rasmussen
• Mike Lin
• Erez Lieberman
• Aviva Presser
• Xiaohui Xie
• Pouya Kheradpour

Courses

Fall 2001:	18.417	Introduction to Computational Biology
January 2005:	6.092	Bioinformatics and Proteomics: An Engineering-Based Problem Solving Approach
Spring 2005:	6.096	Algorithms for Computational Biology
... more on courses.

Selected Publications

• Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
  
  Xiaohui Xie, Jun Lu, EJ. Kulbokas, Todd Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric Lander, Manolis Kellis
  Nature 2005 Feb 27, doi:10.1038/nature03441 (pdf) (Nature website) (Supplementary Information)
  
  
• Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
  
  Manolis Kellis, Bruce Birren, Eric Lander
  Nature 2004 Apr 8; 428 pp. 617-24 (pdf) (Nature website) (Supplementary Information)
  
  
• Sequencing and comparison of yeast species to identify genes and regulatory motifs
  
  Manolis Kellis, Nick Patterson, Matt Endrizzi, Bruce Birren, Eric Lander
  Nature 2003 May 15; 423 pp. 241-254 (pdf) (Nature website) (Supplementary Information)
  
  
• Transcriptional regulatory code of a eukaryotic genome
  
  Chris Harbison et al.
  Nature 2004 Sep 2; 431 pp. 99-104 (pdf) (Nature website) (Supplementary Information)
  
  
• Genome duplication in the teleost fish Tetraodon nigrovidridis reveals the early vertebrate proto-karyotype
  
  Olivier Jaillon et al.
  Nature 2004 Oct 21; 431 pp. 946-957 (pdf) (Nature website) (Supplementary Information)
  
  
• Methods in comparative genomics: genome correspondence, gene identification, regulatory motif discovery
  
  Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric Lander
  Journal of Computational Biology 2004; 11 pp. 319-55. (pdf).
  
  
  ... more publications.