ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. - Ricardo Roberto da Silva; Fabien Jourdan; Diego M. Salvanha; Fabien Létisse; Emilien L. Jamin; Simone Guidetti-Gonzalez; Carlos A. Labate; Ricardo Z. N. Vêncio (Bioinform., 2014)

Propagating annotations of molecular networks using in silico fragmentation. - Ricardo Roberto da Silva; Mingxun Wang 001; Louis-Félix Nothias; Justin J. J. van der Hooft; Andrés Mauricio Caraballo-Rodríguez; Evan Fox; Marcy J. Balunas; Jonathan L. Klassen; Norberto Peporine Lopes; Pieter C. Dorrestein (PLoS Comput. Biol., 2018)

ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization. - Gustavo Tamasco; Manish Kumar; Karsten Zengler; Rafael Silva-Rocha; Ricardo Roberto da Silva (BMC Bioinform., 2022)

Improving annotation propagation on molecular networks through random walks: introducing ChemWalker. - Tiago Cabral Borelli; Gabriel Santos Arini; Luís G. P. Feitosa; Pieter C. Dorrestein; Norberto Peporine Lopes; Ricardo Roberto da Silva (Bioinform., 2023)