Tal Pupko - researchr alias

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Viewing Publication 1 - 36 from 36

2024

Effect of tokenization on transformers for biological sequencesEdo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov. bioinformatics, 40(4), 2024. [doi]

Statistical framework to determine indel-length distributionElya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose, Tal Pupko. bioinformatics, 40(2), February 2024. [doi]

2023

2022

Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectorsNaama Wagner, Oren Avram, Dafna Gold-Binshtok, Ben Zerah, Doron Teper, Tal Pupko. bioinformatics, 38(8):2341-2343, 2022. [doi]

2021

PASA: Proteomic analysis of serum antibodies web serverOren Avram, Aya Kigel, Anna Vaisman-Mentesh, Sharon Kligsberg, Shai Rosenstein, Yael Dror, Tal Pupko, Yariv Wine. ploscb, 17(1), 2021. [doi]

2019

M1CR0B1AL1Z3R - a user-friendly web server for the analysis of large-scale microbial genomics dataOren Avram, Dana Rapoport, Shir Portugez, Tal Pupko. nar, 47(Webserver-Issue), 2019. [doi]

Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matricesAsher Moshe, Tal Pupko. bioinformatics, 35(15):2562-2568, 2019. [doi]

2017

SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithmHaim Ashkenazy, Eli Levy Karin, Zach Mertens, Reed A. Cartwright, Tal Pupko. nar, 45(Webserver-Issue), 2017. [doi]

TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sitesEli Levy Karin, Haim Ashkenazy, Susann Wicke, Tal Pupko, Itay Mayrose. nar, 45(Webserver-Issue), 2017. [doi]

2016

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromoleculesHaim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. nar, 44(Webserver-Issue), 2016. [doi]

2015

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parametersItamar Sela, Haim Ashkenazy, Kazutaka Katoh, Tal Pupko. nar, 43(Webserver-Issue), 2015. [doi]

2013

CoPAP: Coevolution of Presence-Absence PatternsOfir Cohen, Haim Ashkenazy, Eli Levy Karin, David Burstein, Tal Pupko. nar, 41(Webserver-Issue):232-237, 2013. [doi]

2012

FastML: a web server for probabilistic reconstruction of ancestral sequencesHaim Ashkenazy, Osnat Penn, Adi Doron-Faigenboim, Ofir Cohen, Gina Cannarozzi, Oren Zomer, Tal Pupko. nar, 40(Web-Server-Issue):580-584, 2012. [doi]

Uncovering the co-evolutionary network among prokaryotic genesOfir Cohen, Haim Ashkenazy, David Burstein, Tal Pupko. bioinformatics, 28(18):389-394, 2012. [doi]

2010

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acidsHaim Ashkenazy, Elana Erez, Eric Martz, Tal Pupko, Nir Ben-Tal. nar, 38(Web-Server-Issue):529-533, 2010. [doi]

GLOOME: gain loss mapping engineOfir Cohen, Haim Ashkenazy, Frida Belinky, Dorothée Huchon, Tal Pupko. bioinformatics, 26(22):2914-2915, 2010. [doi]

GUIDANCE: a web server for assessing alignment confidence scoresOsnat Penn, Eyal Privman, Haim Ashkenazy, Giddy Landan, Dan Graur, Tal Pupko. nar, 38(Web-Server-Issue):23-28, 2010. [doi]

2009

Epitopia: a web-server for predicting B-cell epitopesNimrod D. Rubinstein, Itay Mayrose, Eric Martz, Tal Pupko. bmcbi, 10:287, 2009. [doi]

2008

Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 SubtypesOsnat Penn, Adi Stern, Nimrod D. Rubinstein, Julien Dutheil, Eran Bacharach, Nicolas Galtier, Tal Pupko. ploscb, 4(11), 2008. [doi]

2007

Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous ratesItay Mayrose, Adi Doron-Faigenboim, Eran Bacharach, Tal Pupko. ismb 2007: 319-327 [doi]

Pepitope: epitope mapping from affinity-selected peptidesItay 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. bioinformatics, 23(23):3244-3246, 2007. [doi]

Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary ratesMatan Ninio, Eyal Privman, Tal Pupko, Nir Friedman. bioinformatics, 23(2):136-141, 2007. [doi]

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approachAdi Stern, Adi Doron-Faigenboim, Elana Erez, Eric Martz, Eran Bacharach, Tal Pupko. nar, 35(Web-Server-Issue):506-511, 2007. [doi]

2005

2004

ConSeq: the identification of functionally and structurally important residues in protein sequencesCarine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, Nir Ben-Tal. bioinformatics, 20(8):1322-1324, 2004. [doi]

Incomplete Directed Perfect PhylogenyItsik Pe er, Tal Pupko, Ron Shamir, Roded Sharan. SICOMP, 33(3):590-607, 2004. [doi]

2003

ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic InformationFabian Glaser, Tal Pupko, Inbal Paz, Rachel E. Bell, Dalit Bechor-Shental, Eric Martz, Nir Ben-Tal. bioinformatics, 19(1):163-164, 2003.

2002

2001

A structural EM algorithm for phylogenetic inferenceNir Friedman, Matan Ninio, Itsik Pe er, Tal Pupko. recomb 2001: 132-140 [doi]

A Chemical-Distance-Based Test for Positive Darwinian SelectionTal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur. wabi 2001: 142-155 [doi]

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