JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. - Jan Christian Bryne; Eivind Valen; Man-Hung Eric Tang; Troels Torben Marstrand; Ole Winther; Isabelle da Piedade; Anders Krogh; Boris Lenhard; Albin Sandelin (Nucleic Acids Res., 2008)

DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices. - Isabelle da Piedade; Man-Hung Eric Tang; Olivier Elemento (BMC Bioinform., 2009)

MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles. - Matteo Tiberti; Thilde Terkelsen; Kristine Degn; Ludovica Beltrame; Tycho Canter Cremers; Isabelle da Piedade; Miriam Di Marco; Emiliano Maiani; Elena Papaleo (Briefings Bioinform., 2022)