A Knowledge-Based Query System for Biological Databases. - Paolo Bresciani; Paolo Fontana (FQAS, 2002)

TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts. - Stefano Toppo; Nicola Cannata; Paolo Fontana; Chiara Romualdi; Paolo Laveder; Emanuela Bertocco; Gerolamo Lanfranchi; Giorgio Valle (Bioinform., 2003)

The SSEA server for protein secondary structure alignment. - Paolo Fontana; Eckart Bindewald; Stefano Toppo; Riccardo Velasco; Giorgio Valle; Silvio C. E. Tosatto (Bioinform., 2005)

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. - Carlotta De Filippo; Matteo Ramazzotti; Paolo Fontana; Duccio Cavalieri (Briefings Bioinform., 2012)

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. - Francesca Finotello; Enrico Lavezzo; Paolo Fontana; Denis Peruzzo; Alessandro Albiero; Luisa Barzon; Marco Falda; Barbara Di Camillo; Stefano Toppo (Briefings Bioinform., 2012)

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms. - Marco Falda; Stefano Toppo; Alessandro Pescarolo; Enrico Lavezzo; Barbara Di Camillo; Andrea Facchinetti; Elisa Cilia; Riccardo Velasco; Paolo Fontana (BMC Bioinform., 2012)

Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data. - Luca Beltrame; Luca Bianco; Paolo Fontana; Duccio Cavalieri (Bioinform., 2013)

keeSeek: searching distant non-existing words in genomes for PCR-based applications. - Marco Falda; Paolo Fontana; Luisa Barzon; Stefano Toppo; Enrico Lavezzo (Bioinform., 2014)

Reducing bias in RNA sequencing data: a novel approach to compute counts. - Francesca Finotello; Enrico Lavezzo; Luca Bianco; Luisa Barzon; Paolo Mazzon; Paolo Fontana; Stefano Toppo; Barbara Di Camillo (BMC Bioinform., 2014)

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms. - Luca Bianco; Samantha Riccadonna; Enrico Lavezzo; Marco Falda; Elide Formentin; Duccio Cavalieri; Stefano Toppo; Paolo Fontana (Bioinform., 2017)

FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms. - Federico Bianca; Emilio Ispano; Ermanno Gazzola; Enrico Lavezzo; Paolo Fontana; Stefano Toppo (Bioinform., 2023)