An open letter to the scientific journals. - Catherine A. Ball; Gavin Sherlock; Helen E. Parkinson; Philippe Rocca-Serra; Catherine Brooksbank; Helen C. Causton; Duccio Cavalieri; Terry Gaasterland; Pascal Hingamp; Frank C. P. Holstege; Martin Ringwald; Paul T. Spellman; et al. (Bioinform., 2002)

Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. - Duccio Cavalieri; Cinzia Castagnini; Simona Toti; Karolina Maciag; Thomas Kelder; Luca Gambineri; Samuele Angioli; Piero Dolara (Bioinform., 2007)

Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. - Andrea Splendiani; Michaela Gündel; Jonathan M. Austyn; Duccio Cavalieri; Ciro Scognamiglio; Marco Brandizi (Briefings Bioinform., 2011)

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. - Luca Beltrame; Enrica Calura; Razvan R. Popovici; Lisa Rizzetto; Damariz Rivero Guedez; Michele Donato; Chiara Romualdi; Sorin Draghici; Duccio Cavalieri (Bioinform., 2011)

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

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

Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting. - Davide Albanese; Carlotta De Filippo; Duccio Cavalieri; Claudio Donati (PLoS Comput. Biol., 2015)

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)

OBO Foundry Food Ontology Interconnectivity. - Damion M. Dooley; Liliana Andrés-Hernández; Georgeta Bordea; Leigh Carmody; Duccio Cavalieri; Lauren E. Chan; Pol Castellano-Escuder; Carl Lachat; Fleur Mougin; Francesco Vitali; Chen Yang 022; Magalie Weber; et al. (JOWO, 2021)

ONS Modeling of Diet Concepts: Further Development Required by the Objective Definition of "Western Diet". - Ana Reis-Costa; Francesco Vitali; Agnese Gori; Giovanni Bacci 002; Carlotta De Filippo; Duccio Cavalieri (JOWO, 2021)

OBO Foundry food ontology interconnectivity. - Damion M. Dooley; Liliana Andrés-Hernández; Georgeta Bordea; Leigh Carmody; Duccio Cavalieri; Lauren E. Chan; Pol Castellano-Escuder; Carl Lachat; Fleur Mougin; Francesco Vitali; Chen Yang 022; Magalie Weber; et al. (Semantic Web, 2024)