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 (ISMB, 2002)

A Gamma mixture model better accounts for among site rate heterogeneity. - Itay Mayrose; Nir Friedman; Tal Pupko (ECCB/JBI, 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)

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)

Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. - Itay Mayrose; Adi Doron-Faigenboim; Eran Bacharach; Tal Pupko (ISMB/ECCB (Supplement of Bioinformatics), 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)

Epitopia: a web-server for predicting B-cell epitopes. - Nimrod D. Rubinstein; Itay Mayrose; Eric Martz; Tal Pupko (BMC Bioinform., 2009)

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)

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)

A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action. - Shiran Abadi; Winston X. Yan; David Amar; Itay Mayrose (PLoS Comput. Biol., 2017)

A LASSO-based approach to sample sites for phylogenetic tree search. - Noa Ecker; Dana Azouri; Ben Bettisworth; Alexandros Stamatakis; Yishay Mansour; Itay Mayrose; Tal Pupko (Bioinform., 2022)

The tree reconstruction game: phylogenetic reconstruction using reinforcement learning. - Dana Azouri; Oz Granit; Michael Alburquerque; Yishay Mansour; Tal Pupko; Itay Mayrose (CoRR, 2023)

A machine-learning-based alternative to phylogenetic bootstrap. - Noa Ecker; Dorothée Huchon; Yishay Mansour; Itay Mayrose; Tal Pupko (Bioinform., 2024)

Statistical framework to determine indel-length distribution. - Elya Wygoda; Gil Loewenthal; Asher Moshe; Michael Alburquerque; Itay Mayrose; Tal Pupko (Bioinform., 2024)