Manolis Kellis

Manolis Kellis
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  • Position: Professor
  • Office: 32-D524
  • Phone: +1 (617) 253-2419
  • Email: manoli@mit.edu
  • Areas of Study: Disease genomics, epigenomics, comparative genomics, ENCODE, Roadmap, GTEx, genetic variation, human disease, personal genomics
  • Personal Website
  • Last Update: June 27, 2016
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Biography

I am a 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.

Tag Cloud for Manolis Kellis

    Disease genomics, epigenomics, comparative genomics, ENCODE, Roadmap, GTEx, genetic variation, human disease, personal genomics

Publications

PUBLICATIONS

142. HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. (pdf) (scholar) 139. FTO Obesity Variant Circuitry and Adipocyte Browning in Humans (pdf) (scholar) 137. Deep learning for regulatory genomics (pdf) (scholar) 134. Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes (pdf) (scholar) 131. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans (pdf) (scholar)

    GTEx Consortium; Ardlie, Deluca, Segrè, Sullivan, Young, Gelfand, Trowbridge, Maller, Tukiainen, Lek, Ward, Kheradpour, Iriarte, Meng, Palmer, Esko, Winckler, Hirschhorn, Kellis, MacArthur, Getz, Shabalin, Li, Zhou, Nobel, Rusyn, Wright, Lappalainen, Ferreira, Ongen, Rivas, Battle, Mostafavi, Monlong, Sammeth, Melé, Reverter, Goldmann, Koller, Guigó, McCarthy, Dermitzakis, Gamazon, Im, Konkashbaev, Nicolae, Cox, Flutre, Wen, Stephens, Pritchard, Tu, Zhang, Huang, Long, Lin, Yang, Zhu, Liu, Brown, Mestichelli, Tidwell, Lo, Salvatore, Shad, Thomas, Lonsdale, Moser, Gillard, Karasik, Ramsey, Choi, Foster, Syron, Fleming, Magazine, Hasz, Walters, Bridge, Miklos, Sullivan, Barker, Traino, Mosavel, Siminoff, Valley, Rohrer, Jewell, Branton, Sobin, Barcus, Qi, McLean, Hariharan, Um, Wu, Tabor, Shive, Smith, Buia, Undale, Robinson, Roche, Valentino, Britton, Burges, Bradbury, Hambright, Seleski, Korzeniewski, Erickson, Marcus, Tejada, Taherian, Lu, Basile, Mash, Volpi, Struewing, Temple, Boyer, Colantuoni, Little, Koester, Carithers, Moore, Guan, Compton, Sawyer, Demchok, Vaught, Rabiner, Lockhart, Ardlie, Getz, Wright, Kellis, Volpi, Dermitzakis

    Science 348(6235):648-60. May 8, 2015
127. Integrative analysis of 111 reference human epigenomes (pdf) (scholar)

    Roadmap Epigenomics Consortium, Kundaje, Meuleman, Ernst, Bilenky, Yen, Heravi-Moussavi, Kheradpour, Zhang, Wang, Ziller, Amin, Whitaker, Schultz, Ward, Sarkar, Quon, Sandstrom, Eaton, Wu, Pfenning, Wang, Claussnitzer, Liu, Coarfa, Harris, Shoresh, Epstein, Gjoneska, Leung, Xie, Hawkins, Lister, Hong, Gascard, Mungall, Moore, Chuah, Tam, Canfield, Hansen, Kaul, Sabo, Bansal, Carles, Dixon, Farh, Feizi, Karlic, Kim, Kulkarni, Li, Lowdon, Elliott, Mercer, Neph, Onuchic, Polak, Rajagopal, Ray, Sallari, Siebenthall, Sinnott-Armstrong, Stevens, Thurman, Wu, Zhang, Zhou, Beaudet, Boyer, De Jager, Farnham, Fisher, Haussler, Jones, Li, Marra, McManus, Sunyaev, Thomson, Tlsty, Tsai, Wang, Waterland, Zhang, Chadwick, Bernstein, Costello, Ecker, Hirst, Meissner, Milosavljevic, Ren, Stamatoyannopoulos, Wang, Kellis

    Nature 518:317-30. Feb 19, 2015 doi:10.1038/nature14248. PMID 25693563
126. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease (pdf) (scholar) 124. Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues (pdf) (scholar) 117. Comparative analysis of regulatory information and circuits across distant species (pdf) (scholar)

    Boyle, Araya, Brdlik, Cayting, Cheng, Cheng, Gardner, Hillier, Janette, Jiang, Kasper, Kawli, Kheradpour, Kundaje, Li, Ma, Niu, Rehm, Rozowsky, Slattery, Spokony, Terrell, Vafeados, Wang, Weisdepp, Wu, Xie, Yan, Feingold, Good, Pazin, Huang, Bickel, Brenner, Reinke, Waterston, Gerstein, White, Kellis, Snyder

    Nature 512(7515):453-6, Aug 28, 2014
108. Defining functional DNA elements in the human genome (pdf) (scholar)

    Kellis, Wold, Snyder, Bernstein, Kundaje, Marinov, Ward, Birney, Crawford, Dekker, Dunham, Elnitski, Farnham, Feingold, Gerstein, Giddings, Gilbert, Gingeras, Green, Guigo, Hubbard, Kent, Lieb, Myers, Pazin, Ren, Stamatoyannopoulos, Weng, White, Hardison

    PNAS Apr 23, 2014
107. Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals (pdf) (scholar) 104. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments (pdf) (scholar) 101. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo (pdf) (scholar) 100. Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments (pdf) (scholar) 99. Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees (pdf) (scholar) 97. Extensive Variation in Chromatin States Across Humans (pdf) (scholar)

    Kasowski, Kyriazopoulou-Panagiotopoulou, Grubert, Zaugg, Kundaje, Liu, Boyle, Zhang, Zakharia, Spacek, Li, Xie, Olarerin-George, Steinmetz, Hogenesch, Kellis, Batzoglou, Snyder

    Science. Oct 17, 2013
96. Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss (pdf) (scholar) 94. Network deconvolution as a general method to distinguish direct dependencies in networks (pdf) (scholar) 89. Systematic dissection of regulatory motifs in 2,000 predicted human enhancers using a massively parallel reporter assay (pdf) (scholar) 81. Interpreting noncoding genetic variation in complex traits and human disease (pdf) (scholar) 77. Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions (pdf) (scholar) 74. An integrated encyclopedia of DNA elements in the human genome (pdf) (scholar) 61. A high-resolution map of human evolutionary constraint using 29 mammals (pdf) (scholar)

    Lindblad-Toh, Garber, Zuk, Lin, Parker, Washietl, Kheradpour, Ernst, Jordan, Mauceli, Ward, Lowe, Holloway, Clamp, Gnerre, Alfoldi, Beal, Chang, Clawson, Palma, Fitzgerald, Flicek, Guttman, Hubisz, Jaffe, Jungreis, Kostka, Lara, Martins, Massingham, Moltke, Raney, Rasmussen, Stark, Vilella, Wen, Xie, Zody, Worley, Kovar, Muzny, Gibbs, Warren, Mardis, Weinstock, Wilson, Birney, Margulies, Herrero, Green, Haussler, Siepel, Goldman, Pollard, Pedersen, Lander, Kellis

    Nature 478:476-82, Oct 12 2011
49. Mapping and analysis of chromatin state dynamics in nine human cell types (pdf) (scholar) 48. A Cis-Regulatory Map of the Drosophila Genome (pdf) (scholar)

    Negre, Brown, Ma, Bristow, Miller, Kheradpour, Loriaux, Sealfon, Li, Ishii, Spokony, Chen, Hwang, Wagner, Auburn, Domanus, Shah, Morrison, Zieba, Suchy, Senderowicz, Victorsen, Bild, Grundstad, Hanley, Mannervik, Venken, Bellen, White, Russell, Grossman, Ren, Posakony, Kellis, White

    Nature 471:527-531, March 23, 2011.
47. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster (pdf) (scholar) 46. Identification of functional elements and regulatory circuits in Drosophila by large-scale data integration (pdf) (scholar)

    The modENCODE Consortium, Roy, Ernst, Kharchenko, Kheradpour, Negre, Eaton, Landolin, Bristow, Ma, Lin, Washietl, Arshinoff, Ay, Meyer, Robine, Washington, Di Stefano, Berezikov, Brown, Brown, Candeias, Carlson, Carr, Jungreis, Marbach, Sealfon, Tolstorukov, Alekseyenko, Artieri, Boley, Booth, Brooks, Dai, Davis, Duff, Feng, Gorchakov, Gu, Henikoff, Kapranov, Li, Li, MacAlpine, Malone, Minoda, Nordman, Okamura, Perry, Powell, Riddle, Sakai, Samsonova, Sandler, Schwartz, Sher, Spokony, Sturgill, van Baren, Will, Wan, Yang, Yu, Feingold, Good, Guyer, Lowdon, Ahmad, Andrews, Berger, Bickel, Brenner, Brent, Cherbas, Elgin, Gingeras, Grossman, Hoskins, Kaufman, Kent, Kuroda, Orr-Weaver, Perrimon, Pirrotta, Posakony, Ren, Russell, Cherbas, Graveley, Lewis, Micklem, Oliver, Park, Celniker, Henikoff, Karpen, Lai, MacAlpine, Stein, White, Kellis

    Science, Dec 24, 2010.
42. Discovery and characterization of chromatin states for systematic annotation of the human genome (pdf) (scholar) 34. Evolution of pathogenicity and sexual reproduction in eight Candida genomes (pdf) (scholar)

    Butler, Rasmussen, Lin, Santos, Sakthikumar, Munro, Rheinbay, Grabherr, Forche, Reedy, Agrafioti, Arnaud, Bates, Brown, Brunke, Costanzo, Fitzpatrick, de, Harris, Hoyer, Hube, Klis, Kodira, Lennard, Logue, Martin, Neiman, Nikolaou, Quail, Quinn, Santos, Schmitzberger, Sherlock, Shah, Silverstein, Skrzypek, Soll, Staggs, Stansfield, Stumpf, Sudbery, Srikantha, Zeng, Berman, Berriman, Heitman, Gow, Lorenz, Birren, Kellis, Cuomo

    Nature. 2009 Jun 4;459(7247):657-62. PMCID: PMC2834264 PMID: 19465905
33. Histone modifications at human enhancers reflect global cell-type-specific gene expression (pdf) (scholar) 32. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals (pdf) (scholar) 28. Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes (pdf) (scholar) 17. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes (pdf) (scholar) 6. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae (pdf) (scholar) 2. Sequencing and comparison of yeast species to identify genes and regulatory elements (pdf) (scholar) C01. Crust: A new Voronoi-Based Surface Reconstruction Algorithm (pdf) (scholar)

Links

Quick links: Manolis Kellis at MIT - Manolis Kellis Computational Biology Group - Manolis Kellis at MIT EECS - Manolis Kellis at MIT CSAIL - Manolis Kellis on Twitter - Manolis Kellis at TR35 - Manolis Kellis on Google Scholar - Manolis Kellis at CSBi - Manolis Kellis News Stories on Storify - Manolis Kellis Videos on Storify - Manolis Kellis Videos on YouTube - Manolis Kellis Talk at TEDx - Manolis Kellis Video at TEDxCambridge - Manolis Kellis on LinkedIn - Manolis Kellis on Research Gate - Manolis Kellis at MIT Admissions - Manolis Kellis at AIT - Manolis Kellis at IHEC - Manolis Kellis at Broad Institute Interview - Manolis Kellis at Bio IT World - Manolis Kellis at Greek USA Reporter - Manolis Kellis at National Documentation Institute - Manolis Kellis at Epigenomics of Common Diseases 2014 - Manolis Kellis at Broad Midsummer Science Night - Manolis Kellis at CSBi News - Manolis Kellis at Broad Institute search

Awards

  • MIT EECS: Faculty Research Innovation Fellowship (2016)
  • Athens Technology Center for Research and Education (AIT): Niki Award (2011)
  • National Science Foundation: 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)