List of works - Tal Pupko

A Chemical-Distance-Based Test for Positive Darwinian Selection

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

scientific article published in August 2002

A combined empirical and mechanistic codon model

scientific article published on 16 November 2006

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

scientific article (publication date: 7 July 2002)

A fast algorithm for joint reconstruction of ancestral amino acid sequences

scientific article (publication date: June 2000)

A gamma mixture model better accounts for among site rate heterogeneity

scientific article published in September 2005

A likelihood framework to analyse phyletic patterns

scientific article published on December 2008

A machine learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis

scientific article published on 2 December 2011

A machine-learning approach for predicting B-cell epitopes.

scientific article

A model-based approach for detecting coevolving positions in a molecule

scientific article published on 8 June 2005

A structural EM algorithm for phylogenetic inference

scientific article published in January 2002

Alignment errors strongly impact likelihood-based tests for comparing topologies

scientific article published in August 2014

An Evolutionary Space-Time Model with Varying Among-Site Dependencies

article

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

scientific article

An alignment confidence score capturing robustness to guide tree uncertainty

scientific article

An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes

scientific article

Assessing the prediction fidelity of ancestral reconstruction by a library approach

scientific article published on 13 August 2015

COVID-19 pandemic-related lockdown: response time is more important than its strictness

scientific article published on 19 October 2020

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons

scientific article

CoPAP: Coevolution of presence-absence patterns

scientific article published on 8 June 2013

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

scientific article

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

scientific article

Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers

scientific article (publication date: 23 June 2006)

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior

scientific article published on 16 June 2004

Computational characterization of B-cell epitopes

scientific article published on 26 November 2007

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

scientific article published on 4 February 2013

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

scientific article published on 10 February 2004

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

scientific article

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

scientific article (publication date: July 2010)

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

scientific article

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

article by Gershon Celniker et al published April 2013 in Israel Journal of Chemistry

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

scientific article (publication date: 2003)

DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array

scientific article published on 12 August 2013

Deep Panning: steps towards probing the IgOme

scientific article

Detecting excess radical replacements in phylogenetic trees

scientific article published on 01 November 2003

Detection and analysis of conservation at synonymous sites

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

Emergence of an HIV-1 cluster harbouring the major protease L90M mutation among treatment-naïve patients in Tel Aviv, Israel

scientific article published on 3 November 2011

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm

scientific article

Evolution after gene duplication

article

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

scientific article published on 01 March 1999

Evolution of the metazoan protein phosphatase 2C superfamily

scientific article

Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes

scientific article

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

scientific article published on 20 June 2011

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

article by Tal Pupko & D Graur published August 2002 in Computational Statistics & Data Analysis

FastML: a web server for probabilistic reconstruction of ancestral sequences

scientific article

GLOOME: gain loss mapping engine

scientific article published on 27 September 2010

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

scientific article published on 16 April 2015

GUIDANCE: a web server for assessing alignment confidence scores.

scientific article

Genome-scale identification of Legionella pneumophila effectors using a machine learning approach

scientific article

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

scientific article published on 11 January 2016

Harnessing Machine Learning To Unravel Protein Degradation in Escherichia coli

scientific article published in 2021

Identification of novel Coxiella burnetii Icm/Dot effectors and genetic analysis of their involvement in modulating a mitogen-activated protein kinase pathway

scientific article

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

scientific article published on 23 June 2015

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

scientific article

In silico identification of functional regions in proteins

scientific article published in June 2005

Incomplete Directed Perfect Phylogeny

scholarly article by Itsik Pe'er et al published January 2004 in SIAM Journal on Computing

Indel reliability in indel-based phylogenetic inference

scientific article

Inference and characterization of horizontally transferred gene families using stochastic mapping

scientific article

Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony--a simulation study

scientific article published on 4 October 2011

Inferring Indel Parameters using a Simulation-based Approach

scientific article

Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits.

scientific article published on 6 April 2016

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes

scientific article

Machine-learning of complex evolutionary signals improves classification of SNVs

scientific article published on 07 April 2022

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

scientific article

Novel type III effectors in Pseudomonas aeruginosa

scientific article published on 17 March 2015

Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms

scientific article

Pepitope: epitope mapping from affinity-selected peptides

scientific article

Phosphatidylserine increases IKBKAP levels in familial dysautonomia cells

scientific article

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

scientific article published in January 2007

Probabilistic Methods and Rate Heterogeneity

Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences

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

scientific article published in January 2002

Regulation of alternative splicing at the single-cell level

scientific article published on 28 December 2015

Revealing bacterial targets of growth inhibitors encoded by bacteriophage T7.

scientific article

Revealing the inventory of type III effectors in Pantoea agglomerans gall-forming pathovars by using draft genome sequences and a machine-learning approach.

scientific article published on 26 December 2016

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

scientific article published in 2009

SMARCA2 and other genome-wide supported schizophrenia-associated genes: regulation by REST/NRSF, network organization and primate-specific evolution

scientific article

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

scientific article published on 22 June 2007

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

scientific article

Site-Specific Evolutionary Rate Inference: Taking Phylogenetic Uncertainty into Account

scientific article published on 01 March 2005

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

scientific article

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

scientific article

Synonymous site conservation in the HIV-1 genome

scientific article

The "alternative" choice of constitutive exons throughout evolution

scientific article

The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer

article

The Complexity Hypothesis and Other Connectivity Barriers to Lateral Gene Transfer

article

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.

scientific article

The Cytoskeleton of Parabasalian Parasites Comprises Proteins that Share Properties Common to Intermediate Filament Proteins

scientific article published on 16 September 2016

The Permian Bacterium that Isn't

scientific article published in 2001

The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release

scientific article published on September 2004

The interface of protein structure, protein biophysics, and molecular evolution

scientific article

The operonic location of auto-transcriptional repressors is highly conserved in bacteria.

scientific article

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

article

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans

scientific article published on 8 October 2008

Transfer of noncoding DNA drives regulatory rewiring in bacteria

scientific article

Uncovering the co-evolutionary network among prokaryotic genes

scientific article published on September 2012

List of works by Tal Pupko

A Chemical-Distance-Based Test for Positive Darwinian Selection

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

A combined empirical and mechanistic codon model

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

A fast algorithm for joint reconstruction of ancestral amino acid sequences

A gamma mixture model better accounts for among site rate heterogeneity

A likelihood framework to analyse phyletic patterns

A machine learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis

A machine-learning approach for predicting B-cell epitopes.

A model-based approach for detecting coevolving positions in a molecule

A structural EM algorithm for phylogenetic inference

Alignment errors strongly impact likelihood-based tests for comparing topologies

An Evolutionary Space-Time Model with Varying Among-Site Dependencies

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

An alignment confidence score capturing robustness to guide tree uncertainty

An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes

Assessing the prediction fidelity of ancestral reconstruction by a library approach

COVID-19 pandemic-related lockdown: response time is more important than its strictness

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons

CoPAP: Coevolution of presence-absence patterns

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

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

Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior

Computational characterization of B-cell epitopes

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

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

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

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

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

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

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array

Deep Panning: steps towards probing the IgOme

Detecting excess radical replacements in phylogenetic trees

Detection and analysis of conservation at synonymous sites

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

Emergence of an HIV-1 cluster harbouring the major protease L90M mutation among treatment-naïve patients in Tel Aviv, Israel

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm

Evolution after gene duplication

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

Evolution of the metazoan protein phosphatase 2C superfamily

Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes

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

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

FastML: a web server for probabilistic reconstruction of ancestral sequences

GLOOME: gain loss mapping engine

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

GUIDANCE: a web server for assessing alignment confidence scores.

Genome-scale identification of Legionella pneumophila effectors using a machine learning approach

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

Harnessing Machine Learning To Unravel Protein Degradation in Escherichia coli

Identification of novel Coxiella burnetii Icm/Dot effectors and genetic analysis of their involvement in modulating a mitogen-activated protein kinase pathway

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

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

In silico identification of functional regions in proteins

Incomplete Directed Perfect Phylogeny

Indel reliability in indel-based phylogenetic inference

Inference and characterization of horizontally transferred gene families using stochastic mapping

Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony--a simulation study

Inferring Indel Parameters using a Simulation-based Approach

Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits.

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes

Machine-learning of complex evolutionary signals improves classification of SNVs

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

Novel type III effectors in Pseudomonas aeruginosa

Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms

Pepitope: epitope mapping from affinity-selected peptides

Phosphatidylserine increases IKBKAP levels in familial dysautonomia cells

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

Probabilistic Methods and Rate Heterogeneity

Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences

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

Regulation of alternative splicing at the single-cell level

Revealing bacterial targets of growth inhibitors encoded by bacteriophage T7.

Revealing the inventory of type III effectors in Pantoea agglomerans gall-forming pathovars by using draft genome sequences and a machine-learning approach.

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

SMARCA2 and other genome-wide supported schizophrenia-associated genes: regulation by REST/NRSF, network organization and primate-specific evolution

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