Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. - Valerio Bianchi; Pier Federico Gherardini; Manuela Helmer-Citterich; Gabriele Ausiello (BMC Bioinform., 2012)

DBATE: database of alternative transcripts expression. - Valerio Bianchi; Alessio Colantoni; Alberto Calderone; Gabriele Ausiello; Fabrizio Ferrè; Manuela Helmer-Citterich (Database J. Biol. Databases Curation, 2013)

webPDBinder: a server for the identification of ligand binding sites on protein structures. - Valerio Bianchi; Iolanda Mangone; Fabrizio Ferrè; Manuela Helmer-Citterich; Gabriele Ausiello (Nucleic Acids Res., 2013)

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)

PhenoFeatureFinder: a python package for linking developmental phenotypes to omics features. - Lissy-Anne M. Denkers; Marc D. Galland; Annabel Dekker; Valerio Bianchi; Petra M. Bleeker (J. Open Source Softw., 2024)