hypeR: an R package for geneset enrichment workflows. - Anthony Federico; Stefano Monti (Bioinform., 2020)

nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline. - Zeyuan Song; Anastasia Gurinovich; Anthony Federico; Stefano Monti; Paola Sebastiani (J. Open Source Softw., 2021)

Contextualized Protein-Protein Interactions. - Anthony Federico; Stefano Monti (Patterns, 2021)

Development of methods for Omics Network inference and analysis and their application to disease modeling - Anthony Federico (2022)

Structure learning for gene regulatory networks. - Anthony Federico; Joseph Kern; Xaralabos Varelas; Stefano Monti (PLoS Comput. Biol., 2023)