Publications

• A comparative encyclopedia of DNA elements in the mouse genome.
  Yue, Cheng, Breschi, Vierstra, Wu, Ryba, Sandstrom, Ma, Davis, Pope, Shen,, Djebali, Thurman, Kaul, Rynes, Kirilusha, Marinov, Williams, Trout, Amrhein, Fisher- Aylor, Antoshechkin, DeSalvo, See, Fastuca, Drenkow, Zaleski, Dobin, Prieto, Lagarde, Bussotti, Tanzer, Denas, Li, Bender, Zhang, Byron, Groudine, McCleary, Pham, Ye, Kuan, Edsall, Wu, Rasmussen, Bansal, Kellis, Keller, Morrissey, Mishra, Jain,, Harris, Cayting, Kawli, Boyle, Euskirchen, Kundaje, Lin, Lin, Jansen, Malladi,, Erickson, Kirkup, Learned, Sloan, Rosenbloom, Sousa, Beal, Pignatelli, Flicek, Lian, Kahveci, Lee, Kent, Santos, Herrero, Notredame, Johnson, Vong, Lee, Bates,, Diegel, Canfield, Sabo, Wilken, Reh, Giste, Shafer, Kutyavin, Haugen, Dunn,, Neph, Humbert, Hansen, Bruijn, Selleri, Rudensky, Josefowicz, Samstein, Eichler, Orkin, Levasseur, Papayannopoulou, Chang, Skoultchi, Gosh, Disteche, Treuting, Wang, Weiss, Blobel, Cao, Zhong, Wang, Good, Lowdon, Adams, Zhou, Pazin,, Wold, Taylor, Mortazavi, Weissman, Stamatoyannopoulos, Snyder, Guigo, Gingeras, Gilbert, Hardison, Beer, Ren, and Mouse ENCODE Consortium.
  Nature. 2014.
• Phylogenetic Identification and Functional Characterization of Orthologs and Paralogs across Human, Mouse, Fly, and Worm.
  Wu, Bansal, Rasmussen, Herrero, Kellis.
  bioRxiv. 2014.
• Genome-wide inference of ancestral recombination graphs.
  Rasmussen, Hubisz, Gronau, Siepel.
  PLoS Genetics. 2014. [arXiv] [github] [data] [blog post]
• Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.
  Wu, Rasmussen, Bansal, Kellis.
  Genome Research. 2013. [website]
• TreeFix: statistically informed gene tree error correction using species trees
  Wu, Rasmussen, Bansal, Kellis.
  Systematic Biology. 2012. [website]
• Unified modeling of gene duplication, loss, and coalescence using a locus tree.
  Rasmussen, Kellis.
  Genome Research. 2012. [website]
• Replacing and additive horizontal gene transfer in Streptococcus.
  Choi, Rasmussen, Hubisz, Gronau, Stanhope, Siepel.
  Molecular Biology and Evolution. 2012. [website]
• Roles of major facilitator superfamily transporters in phosphate response in Drosophila
  Bergwitz, Rasmussen, DeRobertis, Wee, Sinha, Chen, Huang, Perrimon.
  PLoS One. 2012.
• Evolution at the Sub-gene Level: Domain Rearrangements in the Drosophila Phylogeny.
  Wu, Rasmussen, Kellis.
  Molecular Biology and Evolution. 2011. [website]
• A high-resolution map of human evolutionary constraint using 29 mammals
  Lindblad-Toh, Garber, Zuk, Lin, Parker, Washietl, Kheradpour, Ernst, Jordan, Mauceli, Ward, Lowe, Holloway, Clamp, Gnerre, Alfoldi, Beal, Chang, Clawson, Cuff, Di Palma, Fitzgerald, Flicek, Guttman, Hubisz, Jaffe, Jungreis, Kent, Kostka, Lara, Martins, Massingham, Moltke, Raney, Rasmussen, Robinson, Stark, Vilella, Wen, Xie, Zody, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Worley, Kovar, Muzny, Gibbs, Baylor College of Medicine Human Genome Sequencing Center, Warren, Mardis, Weinstock, Wilson, Genome Institute at Washington University, Birney, Margulies, Herrero, Green, Haussler, Siepel, Goldman, Pollard, Pedersen, Lander, Kellis.
  Nature. 2011.
• A Bayesian approach for fast and accurate gene tree reconstruction.
  Rasmussen, Kellis.
  Molecular Biology and Evolution. 2010. [website]
• A phylogenomic approach to the evolutionary dynamics of gene duplication in birds.
  Organ*, Rasmussen*, Baldwin, Kellis, and Edwards.
  In Evolution After Gene Duplication. (Eds.) K. Dittmar and D. Liberles. Wiley & Sons. 2010.
• Evolution of pathogenicity and sexual reproduction in eight Candida genomes.
  Butler, Rasmussen, Lin, Santos, Sakthikumar, Munro, Rheinbay, Grabherr, Forche, Reedy, Agrafioti, Arnaud, Bates, Brown, Brunke, Costanzo, Fitzpatrick, de Groot, 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, and Cuomo.
  Nature. 2009. [website]
• Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes.
  Lin, Deoras, Rasmussen, Kellis.
  PLoS Computational Biology. 2008.
• Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes.
  Rasmussen, Kellis
  Genome Research. 2007. [website]
• Discovery of functional elements in 12 Drosphila genomes using evolutionary signatures.
  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.
  Nature. 2007. [website]
• Evolution of genes and genomes on the Drosophila phylogeny.
  Drosophila 12 Genomes Consortium.
  Nature. 2007.