SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent. - Nicola De Maio; Chieh-Hsi Wu; Daniel J. Wilson 001 (PLoS Comput. Biol., 2016)

Bayesian reconstruction of transmission within outbreaks using genomic variants. - Nicola De Maio; Colin J. Worby; Daniel J. Wilson 001; Nicole Stoesser (PLoS Comput. Biol., 2018)

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. - Remco R. Bouckaert; Timothy G. Vaughan; Joëlle Barido-Sottani; Sebastián Duchêne; Mathieu Fourment; Alexandra Gavryushkina; Joseph Heled; Graham Jones; Denise Kühnert; Nicola De Maio; Michael Matschiner; Fábio K. Mendes; et al. (PLoS Comput. Biol., 2019)

A phylogenetic approach for weighting genetic sequences. - Nicola De Maio; Alexander V. Alekseyenko; William J. Coleman-Smith; Fabio Pardi; Marc A. Suchard; Asif U. Tamuri; Jakub Truszkowski; Nick Goldman (BMC Bioinform., 2021)

Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk. - Antanas Kalkauskas; Umberto Perron; Yuxuan Sun; Nick Goldman; Guy Baele; Stéphane Guindon; Nicola De Maio (PLoS Comput. Biol., 2021)

phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets. - Nicola De Maio; William R. Boulton; Lukas Weilguny; Conor R. Walker; Yatish Turakhia; Russell Corbett-Detig; Nick Goldman (PLoS Comput. Biol., 2022)

VGsim: Scalable viral genealogy simulator for global pandemic. - Vladimir Shchur; Vadim Spirin; Dmitry Sirotkin; Evgeni Burovski; Nicola De Maio; Russell Corbett-Detig (PLoS Comput. Biol., 2022)