pyGeno: A Python package for precision medicine and proteogenomics. - Tariq Daouda; Claude Perreault; Sébastien Lemieux (F1000Research, 2016)

Warp: a method for neural network interpretability applied to gene expression profiles. - Assya Trofimov; Sébastien Lemieux; Claude Perreault (CoRR, 2017)

Holographic Neural Architectures. - Tariq Daouda; Jeremie Zumer; Claude Perreault; Sébastien Lemieux (CoRR, 2018)

Towards the Latent Transcriptome. - Assya Trofimov; Francis Dutil; Claude Perreault; Sébastien Lemieux; Yoshua Bengio; Joseph Paul Cohen (CoRR, 2018)

The SysteMHC Atlas project. - Wenguang Shao; Patrick G. A. Pedrioli; Witold Wolski; Christian Scurtescu; Emanuel Schmid; Juan Antonio Vizcaíno; Mathieu Courcelles; Heiko Schuster; Daniel Kowalewski; Fabio Marino; Cecilia S. Lindestam Arlehamn; Kerrie Vaughan; et al. (Nucleic Acids Res., 2018)

Factorized embeddings learns rich and biologically meaningful embedding spaces using factorized tensor decomposition. - Assya Trofimov; Joseph Paul Cohen; Yoshua Bengio; Claude Perreault; Sébastien Lemieux (Bioinform., 2020)

CAMAP: Artificial neural networks unveil the role of codon arrangement in modulating MHC-I peptides presentation. - Tariq Daouda; Maude Dumont-Lagacé; Albert Feghaly; Yahya Benslimane; Rébecca Panes; Mathieu Courcelles; Mohamed Benhammadi; Lea Harrington; Pierre Thibault; François Major; Yoshua Bengio; Etienne Gagnon; et al. (PLoS Comput. Biol., 2021)