A New Approach for the Identification of Processed Pseudogenes. - Ivan Molineris; Gabriele Sales; Federico Bianchi 007; Ferdinando Di Cunto; Michele Caselle (J. Comput. Biol., 2010)

MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. - Gabriele Sales; Alessandro Coppe; Andrea Bisognin; Marta Biasiolo; Stefania Bortoluzzi; Chiara Romualdi (Nucleic Acids Res., 2010)

parmigene - a parallel R package for mutual information estimation and gene network reconstruction. - Gabriele Sales; Chiara Romualdi (Bioinform., 2011)

Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies. - Paolo G. V. Martini; Davide Risso; Gabriele Sales; Chiara Romualdi; Gerolamo Lanfranchi; Stefano Cagnin (BMC Bioinform., 2011)

graphite - a Bioconductor package to convert pathway topology to gene network. - Gabriele Sales; Enrica Calura; Duccio Cavalieri; Chiara Romualdi (BMC Bioinform., 2012)

MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). - Andrea Bisognin; Gabriele Sales; Alessandro Coppe; Stefania Bortoluzzi; Chiara Romualdi (Nucleic Acids Res., 2012)

Graphite Web: web tool for gene set analysis exploiting pathway topology. - Gabriele Sales; Enrica Calura; Paolo G. V. Martini; Chiara Romualdi (Nucleic Acids Res., 2013)

timeClip: pathway analysis for time course data without replicates. - Paolo G. V. Martini; Gabriele Sales; Enrica Calura; Stefano Cagnin; Monica Chiogna; Chiara Romualdi (BMC Bioinform., 2014)

metaGraphite-a new layer of pathway annotation to get metabolite networks. - Gabriele Sales; Enrica Calura; Chiara Romualdi (Bioinform., 2019)

NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data. - Federico Agostinis; Chiara Romualdi; Gabriele Sales; Davide Risso (Bioinform., 2022)