MotifScorer: using a compendium of microarrays to identify regulatory motifs. - Matteo Brilli; Renato Fani; Pietro Liò (Bioinform., 2007)

On the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the Common Pathway genes. - Marco Fondi; Matteo Brilli; Renato Fani (BMC Bioinform., 2007)

The CAI Analyser Package: Inferring Gene Expressivity from Raw Genomic Data. - Matteo Ramazzotti; Matteo Brilli; Renato Fani; Giampaolo Manao; Donatella Degl'Innocenti (Silico Biol., 2007)

Topological Metrics in Blast Data Mining: Plasmid and Nitrogen-Fixing Proteins Case Studies. - Pietro Liò; Matteo Brilli; Renato Fani (BIRD, 2008)

Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes. - Matteo Brilli; Renato Fani; Pietro Liò (Briefings Bioinform., 2008)

Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network. - Matteo Brilli; Alessio Mengoni; Marco Fondi; Marco Bazzicalupo; Pietro Liò; Renato Fani (BMC Bioinform., 2008)

The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis. - Matteo Brilli; Marco Fondi; Renato Fani; Alessio Mengoni; Lorenzo Ferri; Marco Bazzicalupo; Emanuele G. Biondi (BMC Syst. Biol., 2010)

MeDuSa: a multi-draft based scaffolder. - Emanuele Bosi; Beatrice Donati; Marco Galardini; Sara Brunetti; Marie-France Sagot; Pietro Liò; Pierluigi Crescenzi; Renato Fani; Marco Fondi (Bioinform., 2015)