3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. - Allegra Via; Daniele Peluso; Pier Federico Gherardini; Emanuele de Rinaldis; Teresa Colombo; Gabriele Ausiello; Manuela Helmer-Citterich (Nucleic Acids Res., 2007)

PatentMatrix: an automated tool to survey patents related to large sets of genes or proteins. - Armin Lahm; Emanuele de Rinaldis (Source Code Biol. Medicine, 2007)

CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments. - Paolo Uva; Emanuele de Rinaldis (BMC Bioinform., 2008)

Scaling up single-cell RNA-seq data analysis with CellBridge workflow. - Nima Nouri; Andre H. Kurlovs; Giorgio Gaglia; Emanuele de Rinaldis; Virginia Savova (Bioinform., 2023)