| 2023 | ICLR | 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 |
| 2007 | ISMB | Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. | Itay Mayrose, Adi Doron-Faigenboim, Eran Bacharach, Tal Pupko |
| 2005 | ECCB | A Gamma mixture model better accounts for among site rate heterogeneity. | Itay Mayrose, Nir Friedman, Tal Pupko |
| 2005 | ISMB | Untitled record | Guy Nimrod, Fabian Glaser, David Steinberg, Nir Ben-Tal, Tal Pupko |
| 2002 | ISMB | 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 |
| 2001 | RECOMB | A structural EM algorithm for phylogenetic inference. | Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko |
| 2001 | WABI | A Chemical-Distance-Based Test for Positive Darwinian Selection. | Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur |