Tal Pupko

发表

Selecton: a server for detecting evolutionary forces at a single amino-acid site

Adi Doron-Faigenboim, Adi Stern, Itay Mayrose, 2005, Bioinform..

A Chemical-Distance-Based Test for Positive Darwinian Selection

Roded Sharan, Ron Shamir, Tal Pupko, 2001, WABI.

SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm

Tal Pupko, Haim Ashkenazy, Eli Levy Karin, 2017, Nucleic Acids Res..

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

Itay Mayrose, Tal Pupko, Fabian Glaser, 2005, Nucleic Acids Res..

TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites

Itay Mayrose, Tal Pupko, Haim Ashkenazy, 2017, Nucleic Acids Res..

Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates

Itay Mayrose, Eran Bacharach, Tal Pupko, 2007, ISMB/ECCB.

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues

Itay Mayrose, Tal Pupko, Fabian Glaser, 2002, ISMB.

CoPAP: Coevolution of Presence–Absence Patterns

Tal Pupko, David Burstein, Ofir Cohen, 2013, Nucleic Acids Res..

ConSeq: the identification of functionally and structurally important residues in protein sequences

Piero Fariselli, Tal Pupko, Rita Casadio, 2004, Bioinform..

HENA, heterogeneous network-based data set for Alzheimer’s disease

Hedi Peterson, Henning Hermjakob, Tal Pupko, 2019, Scientific Data.

A gentle Introduction to Probabilistic Evolutionary Models

Itay Mayrose, Tal Pupko, T. Pupko, 2020 .

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

Itay Mayrose, Tal Pupko, Shiran Abadi, 2016, Nucleic Acids Res..

Epitopia: a web-server for predicting B-cell epitopes

Itay Mayrose, Tal Pupko, Eric Martz, 2009, BMC Bioinformatics.

In silico identification of functional regions in proteins

Tal Pupko, Fabian Glaser, Nir Ben-Tal, 2005, ISMB.

M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data

Tal Pupko, Oren Avram, Dana Rapoport, 2020 .

A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families

Tal Pupko, Nir Friedman, Dan Graur, 2002, Bioinform..

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

Tal Pupko, Kazutaka Katoh, Haim Ashkenazy, 2015, Nucleic Acids Res..

GLOOME: gain loss mapping engine

Tal Pupko, Ofir Cohen, Haim Ashkenazy, 2010, Bioinform..

A Structural EM Algorithm for Phylogenetic Inference

Tal Pupko, Nir Friedman, Itsik Pe'er, 2002, J. Comput. Biol..

A structural EM algorithm for phylogenetic inference

Tal Pupko, Nir Friedman, Itsik Pe'er, 2001, J. Comput. Biol..

Incomplete Directed Perfect Phylogeny

Ron Shamir, Tal Pupko, Roded Sharan, 2000, CPM.

Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates

Tal Pupko, Nir Friedman, Matan Ninio, 2007, Bioinform..

A Gamma mixture model better accounts for among site rate heterogeneity

Itay Mayrose, Tal Pupko, Nir Friedman, 2005, ECCB/JBI.

Uncovering the co-evolutionary network among prokaryotic genes

Tal Pupko, David Burstein, Ofir Cohen, 2012, Bioinform..

ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning

Itay Mayrose, Tal Pupko, Saharon Rosset, 2020, bioRxiv.

Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes

Adi Stern, Eran Bacharach, Tal Pupko, 2008, PLoS Comput. Biol..

A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions

Itay Mayrose, Tal Pupko, Reed A. Cartwright, 2020, bioRxiv.

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

Tal Pupko, Nir Ben-Tal, Haim Ashkenazy, 2010, Nucleic Acids Res..

Model selection may not be a mandatory step for phylogeny reconstruction

Itay Mayrose, Tal Pupko, Shiran Abadi, 2019, Nature Communications.

Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices

Tal Pupko, Asher Moshe, T. Pupko, 2019, Bioinform..

Structural Genomics

Tal Pupko, Inbal Paz, Fabian Glaser, 2005 .

GUIDANCE: a web server for assessing alignment confidence scores

Tal Pupko, Dan Graur, Giddy Landan, 2010, Nucleic Acids Res..

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach

Adi Doron-Faigenboim, Adi Stern, Eran Bacharach, 2007, Nucleic Acids Res..

Pepitope: epitope mapping from affinity-selected peptides

Roded Sharan, Eytan Ruppin, Itay Mayrose, 2007, Bioinformatics.

Evolution of Microsatellites in the Yeast Saccharomyces cerevisiae: Role of Length and Number of Repeated Units

Tal Pupko, Dan Graur, T. Pupko, 1999, Journal of Molecular Evolution.

A Simulation‐Based Approach to Statistical Alignment

Tal Pupko, Jotun Hein, Haim Ashkenazy, 2018, Systematic biology.

Indel Reliability in Indel-Based Phylogenetic Inference

Tal Pupko, Ofir Cohen, Haim Ashkenazy, 2014, Genome biology and evolution.

Stepwise prediction of conformational discontinuous B‐cell epitopes using the Mapitope algorithm

Itay Mayrose, Tal Pupko, Nimrod D. Rubinstein, 2007, Proteins.

Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal

Tal Pupko, D. Burstein, T. Pupko, 2013, Proceedings of the National Academy of Sciences.

Genome-Scale Identification of Legionella pneumophila Effectors Using a Machine Learning Approach

Tal Pupko, D. Burstein, T. Pupko, 2009, PLoS pathogens.

Inferring Indel Parameters using a Simulation-based Approach

Tal Pupko, Haim Ashkenazy, Reed A. Cartwright, 2015, Genome biology and evolution.

State-of the art methodologies dictate new standards for phylogenetic analysis

Tal Pupko, Hervé Philippe, David A Liberles, 2012, BMC Evolutionary Biology.

Identification of novel Xanthomonas euvesicatoria type III effector proteins by a machine-learning approach.

Tal Pupko, Dor Salomon, D. Burstein, 2016, Molecular plant pathology.

An alignment confidence score capturing robustness to guide tree uncertainty.

Tal Pupko, Dan Graur, Giddy Landan, 2010, Molecular biology and evolution.

Fast computation of maximum likelihood trees by numerical approximation of amino acid replacement probabilities

Tal Pupko, Dan Graur, 2002 .

Probabilistic Methods and Rate Heterogeneity

Itay Mayrose, Tal Pupko, T. Pupko, 2010 .

Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection.

Adi Doron-Faigenboim, Itay Mayrose, Tal Pupko, 2011, Molecular biology and evolution.

ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

Itay Mayrose, Tal Pupko, Fabian Glaser, 2013 .

FastML: a web server for probabilistic reconstruction of ancestral sequences

Adi Doron-Faigenboim, Tal Pupko, Ofir Cohen, 2012, Nucleic Acids Res..

The Conserved Carboxy Terminus of the Capsid Domain of Human Immunodeficiency Virus Type 1 Gag Protein Is Important for Virion Assembly and Release

Eran Bacharach, Tal Pupko, Fabian Glaser, 2004, Journal of Virology.

The “Alternative” Choice of Constitutive Exons throughout Evolution

Adi Doron-Faigenboim, Tal Pupko, Gil Ast, 2007, PLoS genetics.

Improving the performance of positive selection inference by filtering unreliable alignment regions.

Tal Pupko, Osnat Penn, Osnat Penn, 2012, Molecular biology and evolution.

Native homing endonucleases can target conserved genes in humans and in animal models

Tal Pupko, Martin Kupiec, Uri Gophna, 2011, Nucleic acids research.

Inference of Gain and Loss Events from Phyletic Patterns Using Stochastic Mapping and Maximum Parsimony—A Simulation Study

Tal Pupko, Ofir Cohen, T. Pupko, 2011, Genome biology and evolution.

Differential GC content between exons and introns establishes distinct strategies of splice-site recognition.

Schraga Schwartz, Tal Pupko, Gil Ast, 2012, Cell reports.

Alignment errors strongly impact likelihood-based tests for comparing topologies.

Tal Pupko, Edward Susko, T. Pupko, 2014, Molecular biology and evolution.

Detection and analysis of conservation at synonymous sites

Tal Pupko, Nimrod D. Rubinstein, T. Pupko, 2012 .

An evolutionary space-time model with varying among-site dependencies.

Adi Stern, Tal Pupko, T. Pupko, 2006, Molecular biology and evolution.

A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes

Tal Pupko, Nicolas Galtier, T. Pupko, 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

A likelihood framework to analyse phyletic patterns

Adi Stern, Tal Pupko, Ofir Cohen, 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

Assessing the prediction fidelity of ancestral reconstruction by a library approach.

Adi Stern, Tal Pupko, Dan S. Tawfik, 2015, Protein engineering, design & selection : PEDS.

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

Tal Pupko, Dorothée Huchon, Osnat Penn, 2009, BMC Evolutionary Biology.

M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data

Tal Pupko, Oren Avram, Dana Rapoport, 2019, Nucleic Acids Res..

Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation

Tal Pupko, Haim Ashkenazy, Reed A. Cartwright, 2017, Genome biology and evolution.

Deep Panning: Steps towards Probing the IgOme

Tal Pupko, Haim Ashkenazy, Jonathan M. Gershoni, 2012, PloS one.

Inference and Characterization of Horizontally Transferred Gene Families Using Stochastic Mapping

Tal Pupko, Ofir Cohen, T. Pupko, 2009, Molecular biology and evolution.

Combining multiple data sets in a likelihood analysis: which models are the best?

Tal Pupko, Masami Hasegawa, Dorothée Huchon, 2002, Molecular biology and evolution.

An Integrated Model of Phenotypic Trait Changes and Site‐Specific Sequence Evolution

Itay Mayrose, Tal Pupko, Eli Levy Karin, 2017, Systematic biology.

Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction

Tal Pupko, Giddy Landan, Haim Ashkenazy, 2018, Systematic biology.

Maximum likelihood reconstruction of ancestral amino-acid sequences

Tal Pupko, Itsik Pe'er, George S. Wise, 2001 .

Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires

Tal Pupko, Ofir Cohen, Jack A Gilbert, 2016, Nature Genetics.

Combining Multiple Datasets in a Likelihood Analysis : Which Models are Best ?

Tal Pupko, Masami Hasegawa, Dorothée Huchon, 2002 .