Author

Shawn M. Simpson

CHU Sainte-Justine Research Center

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 1 Genetic & Genomic Medicine· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:benchmark study· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Organism:human· 1 Assay:long-read sequencing· 1 Approach:machine learning (classical)· 1 Approach:statistical model· 1

Frequent Co-Authors

Bastien Paré· 3 shared Martin A. SmithiD· 3 shared Marieke J. RozendaaliD· 2 shared Mélanie Sagniez· 2 shared Alexandre RouetteiD· 1 shared Anshul BudhrajaiD· 1 shared Benoîte BourdiniD· 1 shared Clément Vinet-Ouellette· 1 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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Curved chords = mutual co-authorship

3 shared papersGenomics

Bastien Paré

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Epistatic evolution drives HLA-dependent CD8+ T Cell escape risk in diverse populations

David J. Hamelin, Jean‐Christophe Grenier, Raphaël Poujol, Benoîte Bourdin, Bastien Paré, Shawn M. Simpson, Martin A. Smith, Hélène Decaluwe, Étienne Caron, Julie Hussin

The paper models HLA diversity and viral evolution to assess T cell escape risk across populations, finding that escape mutations gain fitness with additional mutations.

bioRxiv · May 26, 2026 · PreprintGenomics

Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing

Mélanie Sagniez, Anshul Budhraja, Bastien Paré, Shawn M. Simpson, Clément Vinet-Ouellette, Marieke J. Rozendaal, Martin A. Smith

The paper benchmarks RNA isoform reconstruction algorithms using nanopore sequencing data to evaluate their accuracy in transcriptome assembly.

bioRxiv · Mar 21, 2024 · PreprintBioinformatics

Real-time molecular classification of leukemias

Mélanie Sagniez, Shawn M. Simpson, Maxime Caron, Marieke J. Rozendaal, Bastien Paré, Thomas Sontag, Sylvie Langlois, Alexandre Rouette, Vincent‐Philippe Lavallée, Sonia Cellot, Daniel Sinnett, Thai Hoa Tran, Martin A. Smith

This study demonstrates real-time transcriptomic profiling using nanopore sequencing and a neural network classifier to classify childhood acute lymphoblastic leukemia subtypes efficiently.

medRxiv · Jun 22, 2022 · PreprintGenetic & Genomic Medicine