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)

Identification of metabolic network models from incomplete high-throughput datasets. - Sara Berthoumieux; Matteo Brilli; Hidde de Jong; Daniel Kahn; Eugenio Cinquemani (Bioinform., 2011)

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome. - Marco Galardini; Matteo Brilli; Giulia Spini; Matteo Rossi; Bianca Roncaglia; Alessia Bani; Manuela Chiancianesi; Marco Moretto; Kristof Engelen; Giovanni Bacci 002; Francesco Pini; Emanuele G. Biondi; et al. (PLoS Comput. Biol., 2015)

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. - Marco Moretto; Paolo Sonego; Nicolas Dierckxsens; Matteo Brilli; Luca Bianco; Daniela Ledezma-Tejeida; Socorro Gama-Castro; Marco Galardini; Chiara Romualdi; Kris Laukens; Julio Collado-Vides; Pieter Meysman; et al. (Nucleic Acids Res., 2016)