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Genome Research|January 25, 2012
Unified modeling of gene duplication, loss, and coalescence using a locus treeMatthew D Rasmussen, Manolis KellisMolecular Biology and Evolution|July 28, 2010
A Bayesian approach for fast and accurate gene tree reconstructionMatthew D Rasmussen, Manolis KellisGenome Research|November 9, 2007
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomesMatthew D Rasmussen, Manolis KellisMolecular Biology and Evolution|September 9, 2011
Evolution at the subgene level: domain rearrangements in the Drosophila phylogenyYi-Chieh Wu, Matthew D Rasmussen, Manolis KellisGenome Research|December 7, 2013
Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent treesYi-Chieh Wu, Matthew D Rasmussen, Mukul S Bansal, et al.Plos Computational Biology|April 19, 2008
Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomesMichael F Lin, Ameya N Deoras, Matthew D Rasmussen, et al.Systematic Biology|September 6, 2012
TreeFix: statistically informed gene tree error correction using species treesYi-Chieh Wu, Matthew D Rasmussen, Mukul S Bansal, et al.Nucleic Acids Research|December 17, 2013
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experimentsPouya Kheradpour, Manolis KellisNature Biotechnology|February 19, 2015
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissuesJason Ernst, Manolis KellisPageof 34