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)

graphite - a Bioconductor package to convert pathway topology to gene network. - Gabriele Sales; Enrica Calura; Duccio Cavalieri; Chiara Romualdi (BMC Bioinform., 2012)

Graphite Web: web tool for gene set analysis exploiting pathway topology. - Gabriele Sales; Enrica Calura; Paolo G. V. Martini; Chiara Romualdi (Nucleic Acids Res., 2013)

timeClip: pathway analysis for time course data without replicates. - Paolo G. V. Martini; Gabriele Sales; Enrica Calura; Stefano Cagnin; Monica Chiogna; Chiara Romualdi (BMC Bioinform., 2014)

metaGraphite-a new layer of pathway annotation to get metabolite networks. - Gabriele Sales; Enrica Calura; Chiara Romualdi (Bioinform., 2019)

A pan-cancer landscape of pathogenic somatic copy number variations. - Tommaso Becchi; Luca Beltrame; Laura Mannarino; Enrica Calura; Sergio Marchini; Chiara Romualdi (J. Biomed. Informatics, 2023)

Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions. - Giulia Cesaro; James Shiniti Nagai; Nicolò Gnoato; Alice Chiodi; Gaia Tussardi; Vanessa Klöker; Carmelo Vittorio Musumarra; Ettore Mosca; Ivan G. Costa; Barbara Di Camillo; Enrica Calura; Giacomo Baruzzo (Briefings Bioinform., 2025)