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)

FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes. - Alice C. L. Parodi; Laura M. Sangalli; Simone Vantini; Bruno Amati; Piercesare Secchi; Marco J. Morelli (Bioinform., 2017)