Inferring Human Phenotype Networks from Genome-Wide Genetic Associations. - Christian Darabos; Kinjal Desai; Richard Cowper-Sallari; Mario Giacobini; Britney E. Graham; Mathieu Lupien; Jason H. Moore (EvoBIO, 2013)

ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments. - Swneke D. Bailey; Carl Virtanen; Benjamin Haibe-Kains; Mathieu Lupien (Bioinform., 2015)

PharmacoGx: an R package for analysis of large pharmacogenomic datasets. - Petr Smirnov; Zhaleh Safikhani; Nehme Hachem; Dong Wang; Adrian She; Catharina Olsen; Mark Freeman 002; Heather Marie Selby; Deena M. A. Gendoo; Patrick Grossmann; Andrew H. Beck; Hugo J. W. L. Aerts; et al. (Bioinform., 2016)

Variant Set Enrichment: an R package to identify disease-associated functional genomic regions. - Musaddeque Ahmed; Richard C. Sallari; Haiyang Guo; Jason H. Moore; Housheng H. He; Mathieu Lupien (BioData Min., 2017)

SMuRF: a novel tool to identify regulatory elements enriched for somatic point mutations. - Paul Guilhamon; Mathieu Lupien (BMC Bioinform., 2018)

C3D: a tool to predict 3D genomic interactions between cis-regulatory elements. - Tahmid Mehdi; Swneke D. Bailey; Paul Guilhamon; Mathieu Lupien (Bioinform., 2019)