Tal Pupko

According to our database, Tal Pupko authored at least 36 papers between 2001 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Statistical framework to determine indel-length distribution.

Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose, Tal Pupko

Bioinform., February, 2024

Effect of tokenization on transformers for biological sequences.

Edo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov

Bioinform., 2024

2023

GenomeFLTR: filtering reads made easy.

Edo Dotan, Michael Alburquerque, Elya Wygoda, Dorothée Huchon, Tal Pupko

Nucleic Acids Res., July, 2023

The tree reconstruction game: phylogenetic reconstruction using reinforcement learning.

Dana Azouri, Oz Granit, Michael Alburquerque, Yishay Mansour, Tal Pupko, Itay Mayrose

CoRR, 2023

Multiple sequence alignment as a sequence-to-sequence learning problem.

Edo Dotan, Yonatan Belinkov, Oren Avram, Elya Wygoda, Noa Ecker, Michael Alburquerque, Omri Keren, Gil Loewenthal, Tal Pupko

Proceedings of the Eleventh International Conference on Learning Representations, 2023

2022

Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors.

Naama Wagner, Oren Avram, Dafna Gold-Binshtok, Ben Zerah, Doron Teper, Tal Pupko

Bioinform., 2022

2021

PASA: Proteomic analysis of serum antibodies web server.

Oren Avram, Aya Kigel, Anna Vaisman-Mentesh, Sharon Kligsberg, Shai Rosenstein, Yael Dror, Tal Pupko, Yariv Wine

PLoS Comput. Biol., 2021

2019

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

Oren Avram, Dana Rapoport, Shir Portugez, Tal Pupko

Nucleic Acids Res., 2019

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

Asher Moshe, Tal Pupko

Bioinform., 2019

2017

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

Eli Levy Karin, Haim Ashkenazy, Susann Wicke, Tal Pupko, Itay Mayrose

Nucleic Acids Res., 2017

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

Haim Ashkenazy, Eli Levy Karin, Zach Mertens, Reed A. Cartwright, Tal Pupko

Nucleic Acids Res., 2017

2016

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

Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal

Nucleic Acids Res., 2016

2015

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

Itamar Sela, Haim Ashkenazy, Kazutaka Katoh, Tal Pupko

Nucleic Acids Res., 2015

2013

CoPAP: Coevolution of Presence-Absence Patterns.

Ofir Cohen, Haim Ashkenazy, Eli Levy Karin, David Burstein, Tal Pupko

Nucleic Acids Res., 2013

2012

FastML: a web server for probabilistic reconstruction of ancestral sequences.

Haim Ashkenazy, Osnat Penn, Adi Doron-Faigenboim, Ofir Cohen, Gina Cannarozzi, Oren Zomer, Tal Pupko

Nucleic Acids Res., 2012

Uncovering the co-evolutionary network among prokaryotic genes.

Ofir Cohen, Haim Ashkenazy, David Burstein, Tal Pupko

Bioinform., 2012

2010

GUIDANCE: a web server for assessing alignment confidence scores.

Osnat Penn, Eyal Privman, Haim Ashkenazy, Giddy Landan, Dan Graur, Tal Pupko

Nucleic Acids Res., 2010

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

Haim Ashkenazy, Elana Erez, Eric Martz, Tal Pupko, Nir Ben-Tal

Nucleic Acids Res., 2010

GLOOME: gain loss mapping engine.

Ofir Cohen, Haim Ashkenazy, Frida Belinky, Dorothée Huchon, Tal Pupko

Bioinform., 2010

2009

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

Nimrod D. Rubinstein, Itay Mayrose, Eric Martz, Tal Pupko

BMC Bioinform., 2009

2008

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

Osnat Penn, Adi Stern, Nimrod D. Rubinstein, Julien Dutheil, Eran Bacharach, Nicolas Galtier, Tal Pupko

PLoS Comput. Biol., 2008

2007

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

Adi Stern, Adi Doron-Faigenboim, Elana Erez, Eric Martz, Eran Bacharach, Tal Pupko

Nucleic Acids Res., 2007

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

Matan Ninio, Eyal Privman, Tal Pupko, Nir Friedman

Bioinform., 2007

Pepitope: epitope mapping from affinity-selected peptides.

Itay Mayrose, Osnat Penn, Elana Erez, Nimrod D. Rubinstein, Tomer Shlomi, Natalia Tarnovitski Freund, Erez M. Bublil, Eytan Ruppin, Roded Sharan, Jonathan M. Gershoni, Eric Martz, Tal Pupko

Bioinform., 2007

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

Itay Mayrose, Adi Doron-Faigenboim, Eran Bacharach, Tal Pupko

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2005

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

Meytal Landau, Itay Mayrose, Yossi Rosenberg, Fabian Glaser, Eric Martz, Tal Pupko, Nir Ben-Tal

Nucleic Acids Res., 2005

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

Adi Doron-Faigenboim, Adi Stern, Itay Mayrose, Eran Bacharach, Tal Pupko

Bioinform., 2005

<i>In silico</i> identification of functional regions in proteins.

Guy Nimrod, Fabian Glaser, David Steinberg, Nir Ben-Tal, Tal Pupko

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

A Gamma mixture model better accounts for among site rate heterogeneity.

Itay Mayrose, Nir Friedman, Tal Pupko

Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

2004

Incomplete Directed Perfect Phylogeny.

Itsik Pe'er, Tal Pupko, Ron Shamir, Roded Sharan

SIAM J. Comput., 2004

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

Carine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, Nir Ben-Tal

Bioinform., 2004

2003

ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information.

Fabian Glaser, Tal Pupko, Inbal Paz, Rachel E. Bell, Dalit Bechor-Shental, Eric Martz, Nir Ben-Tal

Bioinform., 2003

2002

A Structural EM Algorithm for Phylogenetic Inference.

Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko

J. Comput. Biol., 2002

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, Itsik Pe'er, Masami Hasegawa, Dan Graur, Nir Friedman

Bioinform., 2002

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

Tal Pupko, Rachel E. Bell, Itay Mayrose, Fabian Glaser, Nir Ben-Tal

Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

2001

A Chemical-Distance-Based Test for Positive Darwinian Selection.

Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur

Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001