Matt Rasmussen
MIT CSAIL
32 Vassar Street, 32-G828
Cambridge, MA 02139
rasmus[at]mit[dot]edu

I am a Computer Science MIT graduate student working in CSAIL. My advisor is Manolis Kellis and I am a part of the Compbio lab. My research interest is in comparative genomics, specifically, on phylogenomic algorithms for accurately reconstructing gene trees.

I have a M.S. in Computer Science from MIT, and a B.S. in Math and Computer Science from the University of Minnesota [UofM page].

Publications

• Butler, Rasmussen, Lin, Santos, et al. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 459: 657-662. 2009. [doi]
• Rasmussen, Organ, Baldwin, Kellis, and Edwards. A Phylogenomic Approach to the Evolutionary Dynamics of Gene Duplication in Birds. In Evolution After Gene Duplication (in press). (Eds.) K. Dittmar and D. Liberles. Wiley & Sons.
• Lin, Deoras, Rasmussen, Kellis. Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes. PLoS Comput Biol. 2008 April; 4(4): e1000067 [doi]
• Rasmussen, Kellis. Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Genome Research. 2007 17: 1932-1942. [doi] [website]
• Stark*, Lin*, Kheradpour*, Pederson*, Parts, Carlson, Crosby, Rasmussen, Roy, Deroas, 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. Discovery of functional elements in 12 Drosphila genomes using evolutionary signatures. Nature 450: 219-232. 2007. [doi] [website]
• Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218. 2007. [doi]

Software

I maintain several open source software projects related (some more than others) to my research. My development interests are in phylogenetic software (SPIDIR), scientific visualization (SUMMON), and note-taking for research settings (KeepNote).

SPecies Informed DIstance-based Reconstruction