Biography
I am an associate professor of Computer Science at MIT in the area of Computational Biology. I am a member of the Computer Science and Artificial Intelligence Laboratory (CSAIL), and of the Broad Institute of MIT and Harvard.
My research interests are in the area of computational biology, genomics, epigenomics, gene regulation, and genome evolution. Specifically:
(1) in the area of genome interpretation, we seek to develop comparative genomics methods to identify genes and regulatory elements systematically in the human genome
(2) in the area of gene regulation, we seek to understand the regulatory motifs involved in cell type specification during development, understand their combinatorial relationships, and how these establish expression domains in the developing embryo.
(3) in the area of epigenomics, we seek to understand the chromatin signatures associated with distinct activity states, the changing chromatin states across different cell types and during differentiation, and the sequencing signals responsible for the establishment and maintenance of chromatin marks.
(4) in the area of evolutionary genomics, understanding the dynamics of gene phylogenies across complete genes, the emergence of new gene functions by duplication and mutation, and the algorithmic principles behind phylogenomics.
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Publications
- Evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network following duplication
Presser, Elowitz, Kellis, Kishony
PNAS Jan 16, 2008, (PNAS) (pdf)
- A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands
Stark, Bushati, Jan, Kheradpour, Hodges, Brennecke, Bartel, Cohen, Kellis
Genes and Development 22:8-13, Jan 1, 2008 (pdf)
- Distinguishing protein-coding and noncoding genes in the human genome
Clamp, Fry, Kamal, Xie, Cuff, Lin, Kellis, Lindblad-Toh, Lander
PNAS 49:19428-19433, Dec 4, 2007 (pdf)
- Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
Stark, Lin, Kheradpour, Pedersen, Parts, Carlson, Crosby, Rasmussen, Roy, Deoras, Ruby, Brennecke, FlyBase curators, Berkeley Drosophila Genome Project, Hodges, Hinrichs, Caspi, Paten, Park, Han, Maeder, Polansky, Robson, Aerts, vanHelden, Hassan, Gilbert, Eastman, Rice, Weir, Hahn, Park, Dewey, Pachter, Kent, Haussler, Lai, Bartel, Hannon, Kaufman, Eisen, Clark, Smith, Celniker, Gelbart, Kellis
Nature, 2007 Nov 8; 450:203-218, 14 pages (pdf) (Nature focus page) (Supplementary Information)
- Evolution of genes and genomes in the Drosophila Phylogeny
Drosophila 12 Genomes Consortium
Nature 450:203-218, Nov 8, 2007 (pdf) (Nature focus page)
- Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
Rasmussen, Kellis
Genome Research, Nov 7, 2007, Early online access (pdf)
- Reliable prediction of regulator targets using 12 Drosophila genomes
Kherapdour, Stark, Roy, Kellis
Genome Research, Nov 7, 2007, Early online access, (pdf)
- Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
Ruby, Stark, Johnston, Kellis, Bartel, Lai
Genome Research, Nov 7, 2007, Early online access (pdf)
- Revisiting the protein-coding gene catalog of Drosophila melanogaster using twelve fly genomes
Lin, Carlson, Crosby, Matthews, Yu, Park, Wan, Schroeder, Gramates, Pierre, Roark, Wiley, Kulathinal, Zhang, Myrick, Antone, Celniker, Gelbart, Kellis
Genome Research, Nov 7, 2007, Early Online Access (pdf)
- Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
Zeitlinger, Zinzen, Stark, Kellis, Zhang, Young, Levine
Genes and Development, 21:385-390, March 2, 2007 (pdf) (paper)
- Distinguishing protein-coding and noncoding genes in the human genome
Clamp, Fry, Kamal, Xie, Cuff, Lin, Kellis, Lindblad-Toh, Lander
PNAS 49:19428-19433, Dec 4, 2007, pdf
- Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
Stark, Kheradpour, Brennecke, Hodges, Hannon, Kellis
Genome Research, Nov 7, 2007, Early online access (pdf)
- Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
Xie, Mikkelsen, Gnirke, Lindblad-Toh, Kellis, Lander
PNAS 104, 7145-7150, April 24, 2007 (pdf)
- Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila
Brennecke, Aravin, Stark, Dus, Kellis, Sachidanandam, Hannon
Cell 128, 1-15, March 23, 2007 (pdf)
- RNA Polymerase Stalling at Developmental Control Genes in the Drosophila Embryo
Zeitlinger, Zinzen, Stark, Kellis, Young, Levine
Nature Genetics, November 11, 2007, early online publication (Nature Genetics)
- 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)
- Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking
Grochow, Kellis
RECOMB 2007, April 22, 2007 (pdf)
- Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
Julia Zeitlinger, Robert Zinzen, Alex Stark, Manolis Kellis, Hailan Zhang, Rick Young, and Mike Levine
Genes and Development, 21:385-390, March 2, 2007 (pdf) (paper)
- 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)
- Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
Xie, Mikkelsen, Gnirke, Lindblad-Toh, Kellis, Lander
PNAS 104, 7145-7150, April 24, 2007 (pdf)
- Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila
Brennecke, Aravin, Stark, Dus, Kellis, Sachidanandam, Hannon
Cell 128, 1-15, March 23, 2007 (pdf)
- Transcriptional regulatory code of a eukaryotic genome
Chris Harbison et al., Ben Gordon, Tony Lee, Nicola Rinaldi, Macisaac, Danford, Hannett, Tagne, Reynolds, Yoo, Jennings, Zeitlinger, Pokholok, Kellis, Rolfe, Takusagawa, Lander, Gifford, Fraenkel, Young.
Nature 2004 Sep 2; 431 pp. 99-104 (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)
Awards- Athens Technology Center for Research and Education (AIT): Niki Award (2011)
- NSF: United States Presidential Early Career Award for Scientists and Engineers (PECASE) (2010)
- MIT: Karl Van Tassel Career Development Professorship (2007)
- National Science Foundation: CAREER award (2007)
- Technology Review: TR35 - Top 35 Innovator Under the Age of 35 (2006)
- Genome Technology: Top Young PIs (2006)
- MIT: Distinguished Alumnus (1964) Career Development Chair (2005)
- MIT EECS: Sprowls Doctoral Dissertation Award (2003)
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