INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments. - Stefano de Pretis; Theresia Kress; Marco J. Morelli; Giorgio E. M. Melloni; Laura Riva; Bruno Amati; Mattia Pelizzola (Bioinform., 2015)

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. - Kamal Kishore; Stefano de Pretis; Ryan Lister; Marco J. Morelli; Valerio Bianchi; Bruno Amati; Joseph R. Ecker; Mattia Pelizzola (BMC Bioinform., 2015)

LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. - Giorgio E. M. Melloni; Stefano de Pretis; Laura Riva; Mattia Pelizzola; Arnaud Céol; Jole Costanza; Heiko Müller 003; Luca Zammataro (BMC Bioinform., 2016)

Dynamics of transcriptional and post-transcriptional regulation. - Mattia Furlan; Stefano de Pretis; Mattia Pelizzola (Briefings Bioinform., 2021)