CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. - Marco Galardini; Emanuele G. Biondi; Marco Bazzicalupo; Alessio Mengoni (Source Code Biol. Medicine, 2011)

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)

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)

pyseer: a comprehensive tool for microbial pangenome-wide association studies. - John A. Lees; Marco Galardini; Stephen D. Bentley; Jeffrey N. Weiser; Jukka Corander (Bioinform., 2018)

ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling. - Hannah M. Doherty; George Kritikos; Marco Galardini; Manuel Banzhaf; Danesh Moradigaravand (Bioinform., 2023)