Detecting Excess Radical Replacements in Phylogenetic Trees (2003)
Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur
There are a few instances in which positive Darwinian selection has been convincingly demonstrated at the molecular level. In this study, we present a novel test for detecting excess of radical...
Inferring Site-Specific Evolutionary Rates: Bayesian Methods are Superior (2003)
Itay Mayrose, Dan Graur, Tal Pupko
Introduction Not all sites in protein sequences evolve at the same rate during the course of evolution. The working hypothesis assumes that evolutionary conserved sites in a protein sequence point to...
Tal Pupko, Dan Graur, Nir Friedman
Motivation: We developed an algorithm to reconstruct ancestral sequences, taking into account the rate variation among sites of the protein sequences. Our algorithm maximizes the joint probability of...
Positive selection 1 A test for positive Darwinian selection (2002)
Tal Pupko, Roded Sharan, Ron Shamir, Dan Graur
Introduction. The neutral theory of molecular evolution maintains that most sequence variation among genomes has no direct relevance to adaptation [1]. The rapidly-growing amount of genomic data...
Tal Pupko, Masami Hasegawa, Dan Graur, Nir Friedman
Motivation: We developed an algorithm to reconstruct ancestral sequences, taking into account the rate variation among sites of the protein sequences. Our algorithm maximizes the joint probability of...
The observed and expected frequencies of occurrence of microsatellites in the yeast Saccharomyces cerevisiae were investigated. In all cases, the observed frequencies exceeded the expected ones. In...
Constructing Phylogenies from Quartets: Elucidation of Eutherian Superordinal Relationships (2001)
Amir Ben-dor, Benny Chor, Dan Graur, Ron Ophir, Dan Pelleg
In this work we present two new approaches for constructing phylogenetic trees. The input is a list of weighted quartets over n taxa. Each quartet is a subtree on four taxa, and its weight represents...
Constructing Phylogenies from Quartets: Elucidation of Eutherian Superordinal Relationships (1999)
Amir Ben-dor, Benny Chor, Dan Graur, Ron Ophir, Dan Pelleg
In this work we present two new approaches for constructing phylogenetic trees. The input is a list of weighted quartets over n taxa. Each quartet is a subtree on four taxa, and its weight represents...
From four-taxon trees to phylogenies: The case of mammalian evolution (1998)
Amir Ben-dor, Benny Chor, Dan Graur, Ron Ophir, Dan Pelleg
In this work we present two new approaches for constructing phylogenetic trees. The input is a list of weighted quartets over n taxa. Each quartet is a subtree on four taxa, and its weight represents...
Theoretical and empirical studies were conducted on the pattern of nucleotide and amino acid substitution in evolution, taking into account the effects of mutation at the nucleotide level and...
Studies on the patterns of nucleotide and amino acid substitutions / (1985)
Thesis (Ph. D.)--University of Texas. Health Science Center at Houston. Graduate School of Biomedical Sciences, 1985.
Alu-Containing Exons are Alternatively Spliced
Sorek, Rotem, Ast, Gil, Graur, Dan
Alu repetitive elements are found in ∼1.4 million copies in the human genome, comprising more than one-tenth of it. Numerous studies describe exonizations of Alu elements, that is,...
AluGene: a database of Alu elements incorporated within protein-coding genes
Dagan, Tal, Sorek, Rotem, Sharon, Eilon, Ast, Gil, Graur, Dan
Alu elements are short interspersed elements (SINEs) ∼300 nucleotides in length. More than 1 million Alus are found in the human genome. Despite their being genetically functionless, recent...
Alu-Containing Exons are Alternatively Spliced
Sorek, Rotem, Ast, Gil, Graur, Dan
Alu repetitive elements are found in ∼1.4 million copies in the human genome, comprising more than one-tenth of it. Numerous studies describe exonizations of Alu elements, that is,...
AluGene: a database of Alu elements incorporated within protein-coding genes
Dagan, Tal, Sorek, Rotem, Sharon, Eilon, Ast, Gil, Graur, Dan
Alu elements are short interspersed elements (SINEs) ∼300 nucleotides in length. More than 1 million Alus are found in the human genome. Despite their being genetically functionless, recent...