AluGene: a database of Alu elements incorporated within protein-coding genes. - Tal Dagan; Rotem Sorek; Eilon Sharon; Gil Ast; Dan Graur (Nucleic Acids Res., 2004)

Accurate identification of alternatively spliced exons using support vector machine. - Gideon Dror; Rotem Sorek; Ron Shamir (Bioinform., 2005)

Comparative transcriptomics across the prokaryotic tree of life. - Ofir Cohen; Shany Doron; Omri Wurtzel; Daniel Dar; Sarit Edelheit; Iris Karunker; Eran Mick; Rotem Sorek (Nucleic Acids Res., 2016)