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)

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)

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)

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 (ICLR, 2023)