The “Alternative” Choice of Constitutive Exons throughout Evolution (2007)
Galit Lev-Maor, Amir Goren, Noa Sela, Eddo Kim, Hadas Keren, Adi Doron-Faigenboim, ...
Alternative cassette exons are known to originate from two processes—exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced...
Shaul, Shaul, Nussinov, Ruth, Pupko, Tal
Abstract Background While the premise that lateral gene transfer (LGT) is a dominant evolutionary force is still in considerable dispute, the case for widespread LGT in the family of aminoacyl-tRNA...
Incomplete Directed Perfect Phylogeny (2003)
Tal Pupko, Ron Shamir, Roded Sharan
Perfect phylogeny is one of the fundamental models for studying evolution. We investigate the following variant of the model: The input is a species-characters matrix. The characters are binary and...
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...
Understanding species adaptation at the molecular level is a challenge in biological science. Most genomic changes occurring between species are neutral (i.e. do not affect the fitness of...
Combining Multiple Datasets in a Likelihood Analysis: Which Models are Best? (2002)
Tal Pupko, Dorothe Huchon, Ying Cao, Norihiro Okada, Masami Hasegawa
Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on...
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...
Tal Pupko, Itay Mayrose, Fabian Glaser
Motivation: A number of proteins of known threedimensional (3D) structure exist, with yet unknown function. In light of the recent progress in structure determination methodology, this number is...
A Structural EM Algorithm for Phylogenetic Inference (2002)
Nir Friedman, Matan Ninio, Tal Pupko
A central task in the study of evolution is the reconstruction of a phylogenetic tree from sequences of current-day taxa. A well supported approach to tree reconstruction is by maximum likelihood...
Fabian Glaser, Tal Pupko, Dalit Bechor, Eric Martz
Summary: Recently, we developed algorithmic tools for the identification of functionally important regions in a protein of known 3D-structure by estimating the degree of conservation of the...
Branch-and-Bound Reconstrucion 1 Branch-and-Bound Reconstruction of Ancestral Sequences (2002)
Introduction The problem of ancestral sequence reconstruction is the statistical inference of sequences that correspond to internal nodes in a phylgenetic tree [1]. Joint reconstruction is the task...
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...
A Structural EM Algorithm for Phylogenetic Inference (2002)
Nir Friedman, Matan Ninio, Tal Pupko
A central task in the study of molecular evolution is the reconstruction of a phylogenetic tree from sequences of current-day taxa. The most established approach to tree reconstruction is maximum...
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...
A Structural EM Algorithm for Phylogenetic Inference (2002)
Nir Friedman, Matan Ninio, Tal Pupko
A central task in the study of molecular evolution is the reconstruction of a phylogenetic tree from sequences of current-day taxa. The most established approach to tree reconstruction is maximum...
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...
Maximum Likelihood Reconstruction of Ancestral Amino-Acid Sequences (2001)
Introduction Maximum-likelihood methods are used extensively in phylogenetic studies [3]. In particular, aminoacid sequences of ancestral species have been inferred using these methods [7]. Such...
A Structural EM Algorithm for Phylogenetic Inference (2001)
Nir Friedman, Matan Ninio, Tal Pupko
A central task in the study of evolution is the reconstruction of a phylogenetic tree from sequences of current-day taxa. A well supported approach to tree reconstruction performs maximum likelihood...
A Structural EM Algorithm for Phylogenetic Inference (2000)
Nir Friedman, Matan Ninio, Tal Pupko
A central task in the study of evolution is the reconstruction of a phylogenetic tree from sequences of current-day taxa. A well supported approach to tree reconstruction is by maximum likelihood...
Melamed, Daniel, Mark-Danieli, Michal, Kenan-Eichler, Michal, Kraus, Osnat, Castiel, Asher, Laham, Nihay, ...
The retroviral Gag precursor plays an important role in the assembly of virion particles. The capsid (CA) protein of the Gag molecule makes a major contribution to this process. In the crystal...
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
Landau, Meytal, Mayrose, Itay, Rosenberg, Yossi, Glaser, Fabian, Martz, Eric, Pupko, Tal, ...
Key amino acid positions that are important for maintaining the 3D structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, DNA or other proteins, are often under...
Melamed, Daniel, Mark-Danieli, Michal, Kenan-Eichler, Michal, Kraus, Osnat, Castiel, Asher, Laham, Nihay, ...
The retroviral Gag precursor plays an important role in the assembly of virion particles. The capsid (CA) protein of the Gag molecule makes a major contribution to this process. In the crystal...
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
Landau, Meytal, Mayrose, Itay, Rosenberg, Yossi, Glaser, Fabian, Martz, Eric, Pupko, Tal, ...
Key amino acid positions that are important for maintaining the 3D structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, DNA or other proteins, are often under...
Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm
Mayrose, Itay, Shlomi, Tomer, Rubinstein, Nimrod D., Gershoni, Jonathan M., Ruppin, Eytan, Sharan, Roded, ...
A phage-display library of random peptides is a combinatorial experimental technique that can be harnessed for studying antibody–antigen interactions. In this technique, a phage peptide library is...
A new method for detecting site-specific variation of evolutionary rate (the so-called covarion process) from protein sequence data is proposed. It involves comparing the maximum-likelihood estimates...
Stern, Adi, Doron-Faigenboim, Adi, Erez, Elana, Martz, Eric, Bacharach, Eran, Pupko, Tal
Biologically significant sites in a protein may be identified by contrasting the rates of synonymous (Ks) and non-synonymous (Ka) substitutions. This enables the inference of site-specific positive...
The “Alternative” Choice of Constitutive Exons throughout Evolution
Lev-Maor, Galit, Goren, Amir, Sela, Noa, Kim, Eddo, Keren, Hadas, Doron-Faigenboim, Adi, ...
Alternative cassette exons are known to originate from two processes—exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced...
Schwartz, Schraga, Silva, João, Burstein, David, Pupko, Tal, Eyras, Eduardo, Ast, Gil
Introns are among the hallmarks of eukaryotic genes. Splicing of introns is directed by three main splicing signals: the 5′ splice site (5′ss), the branch site (BS), and the polypyrimdine...