Tal Pupko

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 13

Top Topics

Structural Information

Sequence Alignment

Dynamic Content

Top Venues

Nucleic Acids Res.

Publications

Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose, Tal Pupko
Statistical framework to determine indel-length distribution. Bioinform. 40 (2) (2024)
Edo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov
Effect of tokenization on transformers for biological sequences. Bioinform. 40 (4) (2024)
Edo Dotan, Michael Alburquerque, Elya Wygoda, Dorothée Huchon, Tal Pupko
GenomeFLTR: filtering reads made easy. Nucleic Acids Res. 51 (W1) (2023)
Dana Azouri, Oz Granit, Michael Alburquerque, Yishay Mansour, Tal Pupko, Itay Mayrose
The tree reconstruction game: phylogenetic reconstruction using reinforcement learning. CoRR (2023)
Edo Dotan, Yonatan Belinkov, Oren Avram, Elya Wygoda, Noa Ecker, Michael Alburquerque, Omri Keren, Gil Loewenthal, Tal Pupko
Multiple sequence alignment as a sequence-to-sequence learning problem. ICLR (2023)
Naama Wagner, Oren Avram, Dafna Gold-Binshtok, Ben Zerah, Doron Teper, Tal Pupko
Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors. Bioinform. 38 (8) (2022)
Oren Avram, Aya Kigel, Anna Vaisman-Mentesh, Sharon Kligsberg, Shai Rosenstein, Yael Dror, Tal Pupko, Yariv Wine
PASA: Proteomic analysis of serum antibodies web server. PLoS Comput. Biol. 17 (1) (2021)
Asher Moshe, Tal Pupko
Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices. Bioinform. 35 (15) (2019)
Oren Avram, Dana Rapoport, Shir Portugez, Tal Pupko
M1CR0B1AL1Z3R - a user-friendly web server for the analysis of large-scale microbial genomics data. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Eli Levy Karin, Haim Ashkenazy, Susann Wicke, Tal Pupko, Itay Mayrose
TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Haim Ashkenazy, Eli Levy Karin, Zach Mertens, Reed A. Cartwright, Tal Pupko
SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Itamar Sela, Haim Ashkenazy, Kazutaka Katoh, Tal Pupko
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Ofir Cohen, Haim Ashkenazy, Eli Levy Karin, David Burstein, Tal Pupko
CoPAP: Coevolution of Presence-Absence Patterns. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Ofir Cohen, Haim Ashkenazy, David Burstein, Tal Pupko
Uncovering the co-evolutionary network among prokaryotic genes. Bioinform. 28 (18) (2012)
Haim Ashkenazy, Osnat Penn, Adi Doron-Faigenboim, Ofir Cohen, Gina Cannarozzi, Oren Zomer, Tal Pupko
FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Osnat Penn, Eyal Privman, Haim Ashkenazy, Giddy Landan, Dan Graur, Tal Pupko
GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Haim Ashkenazy, Elana Erez, Eric Martz, Tal Pupko, Nir Ben-Tal
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Ofir Cohen, Haim Ashkenazy, Frida Belinky, Dorothée Huchon, Tal Pupko
GLOOME: gain loss mapping engine. Bioinform. 26 (22) (2010)
Nimrod D. Rubinstein, Itay Mayrose, Eric Martz, Tal Pupko
Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinform. 10 (2009)
Osnat Penn, Adi Stern, Nimrod D. Rubinstein, Julien Dutheil, Eran Bacharach, Nicolas Galtier, Tal Pupko
Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes. PLoS Comput. Biol. 4 (11) (2008)
Itay Mayrose, Adi Doron-Faigenboim, Eran Bacharach, Tal Pupko
Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. ISMB/ECCB (Supplement of Bioinformatics) (2007)
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
Pepitope: epitope mapping from affinity-selected peptides. Bioinform. 23 (23) (2007)
Matan Ninio, Eyal Privman, Tal Pupko, Nir Friedman
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates. Bioinform. 23 (2) (2007)
Adi Stern, Adi Doron-Faigenboim, Elana Erez, Eric Martz, Eran Bacharach, Tal Pupko
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Adi Doron-Faigenboim, Adi Stern, Itay Mayrose, Eran Bacharach, Tal Pupko
Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinform. 21 (9) (2005)
Itay Mayrose, Nir Friedman, Tal Pupko
A Gamma mixture model better accounts for among site rate heterogeneity. ECCB/JBI (2005)
Meytal Landau, Itay Mayrose, Yossi Rosenberg, Fabian Glaser, Eric Martz, Tal Pupko, Nir Ben-Tal
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Guy Nimrod, Fabian Glaser, David Steinberg, Nir Ben-Tal, Tal Pupko
identification of functional regions in proteins. ISMB (Supplement of Bioinformatics) (2005)
Itsik Pe'er, Tal Pupko, Ron Shamir, Roded Sharan
Incomplete Directed Perfect Phylogeny. SIAM J. Comput. 33 (3) (2004)
Carine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, Nir Ben-Tal
ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinform. 20 (8) (2004)
Fabian Glaser, Tal Pupko, Inbal Paz, Rachel E. Bell, Dalit Bechor-Shental, Eric Martz, Nir Ben-Tal
ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information. Bioinform. 19 (1) (2003)
Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko
A Structural EM Algorithm for Phylogenetic Inference. J. Comput. Biol. 9 (2) (2002)
Tal Pupko, Rachel E. Bell, Itay Mayrose, Fabian Glaser, Nir Ben-Tal
Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. ISMB (2002)
Tal Pupko, Itsik Pe'er, Masami Hasegawa, Dan Graur, Nir Friedman
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. Bioinform. 18 (8) (2002)
Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko
A structural EM algorithm for phylogenetic inference. RECOMB (2001)
Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur
A Chemical-Distance-Based Test for Positive Darwinian Selection. WABI (2001)