2025
DJ Hamelin, M Scicluna, I Saadie, F Mostefai, JC Grenier, C Baron, E Caron, JG Hussin. 2025. Predicting pathogen evolution and immune evasion in the age of artificial intelligence. Computational and Structural Biotechnology Journal

Cantin Baron, Pamela Mehanna, Caroline Daneault, Leslie Hausermann, David Busseuil, Jean-Claude Tardif, Jocelyn Dupuis, Christine Des Rosiers, Matthieu Ruiz, Julie G Hussin. 2025. Insights into heart failure metabolite markers through explainable machine learning. Computational and Structural Biotechnology Journal.

2024
Gilbert Jabbour, Alexis Nolin-Lapalme, Olivier Tastet, Denis Corbin, Paloma Jordà, Achille Sowa, Jacques Delfrate, David Busseuil, Julie G Hussin, Marie-Pierre Dubé, Jean-Claude Tardif, Léna Rivard, Laurent Macle, Julia Cadrin-Tourigny, Paul Khairy, Robert Avram, Rafik Tadros. 2024. Prediction of incident atrial fibrillation using deep learning, clinical models, and polygenic scores. European Heart Journal.

Fatima Mostefai, Jean-Christophe Grenier, Raphaël Poujol, Julie Hussin. 2024. Refining SARS-CoV-2 intra-host variation by leveraging large-scale sequencing data. NAR genomics and bioinformatics.

Kevin A Kovalchik, David J Hamelin, Peter Kubiniok, Benoîte Bourdin, Fatima Mostefai, Raphaël Poujol, Bastien Paré, Shawn M Simpson, John Sidney, Éric Bonneil, Mathieu Courcelles, Sunil Kumar Saini, Mohammad Shahbazy, Saketh Kapoor, Vigneshwar Rajesh, Maya Weitzen, Jean-Christophe Grenier, Bayrem Gharsallaoui, Loïze Maréchal, Zhaoguan Wu, Christopher Savoie, Alessandro Sette, Pierre Thibault, Isabelle Sirois, Martin A Smith, Hélène Decaluwe, Julie G Hussin, Mathieu Lavallée-Adam, Etienne Caron. 2024. Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines. Nature communications.

Erin E Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Nithu Sara John, Justin Richardsson, Ashley Hobb, Abayomi S Olabode, Alexandru Lepsa, Ana T Duggan, Andrea D Tyler, Arnaud N’Guessan, Atul Kachru, Brandon Chan, Catherine Yoshida, Christina K Yung, David Bujold, Dusan Andric, Edmund Su, Emma J Griffiths, Gary Van Domselaar, Gordon W Jolly, Heather KE Ward, Henrich Feher, Jared Baker, Jared T Simpson, Jaser Uddin, Jiannis Ragoussis, Jon Eubank, Jörg H Fritz, José Héctor Gálvez, Karen Fang, Kim Cullion, Leonardo Rivera, Linda Xiang, Matthew A Croxen, Mitchell Shiell, Natalie Prystajecky, Pierre-Olivier Quirion, Rosita Bajari, Samantha Rich, Samira Mubareka, Sandrine Moreira, Scott Cain, Steven G Sutcliffe, Susanne A Kraemer, Yelizar Alturmessov, Yann Joly, CPHLN Consortium**, CanCOGeN Consortium**, VirusSeq Data Portal Academic and Health Network**, Marc Fiume, Terrance P Snutch, Cindy Bell, Catalina Lopez-Correa, Julie G Hussin, Jeffrey B Joy, Caroline Colijn, Paul MK Gordon, William WL Hsiao, Art FY Poon, Natalie C Knox, Mélanie Courtot, Lincoln Stein, Sarah P Otto, Guillaume Bourque, B Jesse Shapiro, Fiona SL Brinkman. 2024. The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. Microbial Genomics.

Pascal Theriault-Lauzier, Denis Cobin, Olivier Tastet, Elodie Labrecque Langlais, Bahareh Taji, Guson Kang, Aun-Yeong Chong, Derek So, An Tang, Judy Wawira Gichoya, Sarath Chandar, Pierre-Luc Déziel, Julie G Hussin, Samuel Kadoury, Robert Avram. 2024. A responsible framework for applying artificial intelligence on medical images and signals at the point of care: the PACS-AI platform. Canadian Journal of Cardiology.

Alexis Nolin-Lapalme, Pascal Theriault-Lauzier, Denis Corbin, Olivier Tastet, Abhinav Sharma, Julie G Hussin, Samuel Kadoury, River Jiang, Andrew D Krahn, Richard Gallo, Robert Avram. 2024. Maximising large language model utility in cardiovascular care: a practical guide. Canadian Journal of Cardiology.

Nolin-Lapalme A, Cobin D, Tastet O, Avram R, Hussin JG. 2024. Advancing Fairness in Cardiac Care: Strategies for Mitigating Bias in Artificial Intelligence Models within Cardiology. Canadian Journal of Cardiology.

Dominique Fournelle, Fatima Mostefai, Elsa Brunet-Ratnasingham, Raphaël Poujol, Jean-Christophe Grenier,Javier Hector Gálvez, Amélie Pagliuzza, Inès Levade, Sandrine Moreira, Mehdi Benlarbi, Guillaume Beaudoin-Bussières, Gabrielle Gendron-Lepage, Catherine Bourassa,Alexandra Tauzin, Simon Grandjean Lapierre, Nicolas Chomont, Andres Finzi, Daniel E. Kaufmann, Morgan Craig, Hussin JG*. 2024. Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis. Viruses 16(3), 342. (*corresponding)

Alex Richard-St-Hilaire, Isabel Gamache, Justin Pelletier, Jean-Christophe Grenier, Raphaël Poujol, Julie G Hussin*. Signatures of Co-evolution and Co-regulation in the CYP3A and CYP4F Genes in Humans, Genome Biology and Evolution, Volume 16, Issue 1, January 2024. (*corresponding)

2023
Baron C, Cherkaoui S, Therrien-Laperriere S, Ilboudo Y, Poujol R, Mehanna P, Garrett ME, Telen MJ, Ashley-Koch AE, Bartolucci P, Rioux JD, Lettre G, Des Rosiers C, Ruiz M, Hussin JG*. 2023. Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results. iScience. (*corresponding)

Nolin-Lapalme A, Avram R, Hussin JG*. 2023. PrivECG: generating private ECG for end-to-end anonymization. Machine Learning for Healthcare Conference, NY, USA. Proceedings of Machine Learning Research, JMLR Proceedings track. (*corresponding)

Scicluna M, Grenier JC, Poujol R, Lemieux S, Hussin JG*. 2023. Towards Computing Attributions for Dimensionality Reduction Techniques. Bioinformatics Advances. (*corresponding)

Gazeau S, Deng X, Ooi JHK, Mostefai F, Hussin JG, Heffernan J, Jenner AL, Craig M. 2023. The race to understand immunopathology in COVID-19: perspectives on the impact of quantitative approaches understanding within-host interactions. Immunoinformatics.

Legault MA, Barhdadi A, Gamache I, Lemaçon A, Lemieux Perreault LP, Grenier JC, Sylvestre MP, Hussin JG, Rhainds D, Tardif JC, Dubé MP. 2023. Study of effect modifiers of genetically predicted CETP reduction. Genetic Epidemiology 47(2):198-212

N’Guessan A, Kailasam S, Mostefai F, Poujol R, Grenier JC, Contini P, De Palma R, Haber C, Stadler V, Bourque G, Hussin JG, Shapiro BJ, Fritz JH, Piccirillo CA. 2023. Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis. iScience. 26(8)

Trochet H, Pelletier J, Tadros R, Hussin JG. 2023. Comparison of polygenic risk scores for heart disease highlights obstacles to overcome for clinical use. GLBIO Conference paper.

Cristina T Pop, Julie Hussin, Christine Des Rosiers, Nadia Bouabdallaoui. 2023. Phenomapping Of Patients With HFpEF Using Unsupervised Learning Analyses. Journal of Cardiac Failure, Volume 29, Issue 4, Pages 665-666.

2022

Castro E, Schweinfurth L, Mostefai F, Scicluna M, Ni S, Wolf G, Hussin JG, Krishnaswamy S. Evolution of SARS-CoV-2 ACE2-Binding Through the Lens of ReLSO. Machine Learning in Computational Biology (MLCB) 2022 (conference paper)

Besse S°, Poujol R, Hussin JG*. 2022. Comparative study of protein aggregation propensity and mutation tolerance between the naked mole-rat and mouse. Gen Biol Evol. (°corresponding, *senior author)

Pesaranghader A, Matwin S, Sokolova M, Beiko RG, Grenier JC, Hussin JG*. 2022. deepSimDEF: deep neural embeddings of gene products and Gene Ontology terms for functional analysis of genes. Bioinformatics. (*corresponding)

Mostefai F, Gamache I, Huang J, N’Guessan A, Pelletier J, Pesaranghader A, Hamelin D, Murall CL, Poujol R, Grenier JC, Smith M, Craig M, Wolf G, Krishnaswamy S, Shapiro J and Hussin JG*. 2022. Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages. Frontiers in Medicine. (*corresponding)

Levinsson A, de Denus S, Sandoval J, Lemieux Perreault LP, Rouleau J, Tardif JC, Hussin JG, Dubé MP. 2022. Construction of a femininity score in the UK Biobank and its association with angina diagnosis prior to myocardial infarction. Scientific Reports.

Kuchroo M, Huang J, Wong P, Grenier JC, Shung D, Tong A, Lucas C, Klein J, Burkhardt D, Gigante S, Godavarthi A, Israelow B, Mao T, Eun Oh J, Silva J, Takahashi T, Odio CD, Casanovas-Massana A, Fournier J, Yale IMPACT Team, Farhadian S, Dela Cruz C, Ko AI, Wilson FP, Hussin JG*, Wolf G*, Iwasaki A*, Krishnaswamy S*. 2022. Multiscale PHATE identifies multimodal signatures of COVID-19. Nature Biotechnology. (*co-senior)

2021

Hamelin D, Fournelle D, Grenier JC, Schockaert J, Kovalchik K, Kubiniok P, Mostefai F, Duquette JD, Saab F, Sirois I, Smith MA, Pattijn S, Soudeyns H, Decaluwe H, Hussin JG*, Caron E* (*co-senior). The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner. Cell Systems.

Gamache I, Legault MA, Grenier JC, Sanchez R, Rhéaume E, Asgari S, Barhdadi A, Feroz Zada Y, Trochet H, Luo Y, Lecca L, Murray M, Raychaudhuri S, Tardif JC, Dubé MP, Hussin JG*. 2021. A sex-specific evolutionary interaction between ADCY9 and CETP. eLife (*corresponding)

Ben Ali W°, Pesaranghader A°, Avram R, Overtchouk P, Perrin N, Laffite S, Cartier R, Ibrahim, R, Modine T*, Hussin JG*. 2021. Implementing Machine Learning in Interventional Cardiology: The Benefits are Worth the Trouble. Frontiers in Cardiovascular Medicine. (°co-first authors, *co-senior)

Paré B, Rozendaal M, Morin S, Kaufmann L, Simpson SM, Poujol R, Mostefai F, Grenier JC, Xing H, Sanchez M, Yechouron A, Racette R, Hussin JG, Wolf G, Pavlov I, Smith MA. 2021. Patient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes. PLoS ONE

Samman K, Mehanna P, Takla E, Grenier JC, Chan MY, Lopes RD, Lee Neely M, Wang TY, Newby LK, Becker RC, Lordkipanidzé M, Ruiz M, Hussin JG°,* and Jolicoeur ME°. 2021. Differential modulation of polyunsaturated fatty acids in patients with myocardial infarction treated with ticagrelor or clopidogrel. Cell Reports Medicine, 2, 1002999 (°co-senior, *corresponding)

Dubé MP, Lemaçon A, Barhdadi A, Lemieux Perreault LP, [25 authors], Hussin JG, Boivin G, Busseuil D, Tardif JC. 2021. Genetics of symptom remission in outpatients with COVID-19. Scientific Reports, 11,10847

Tremblay J, Haloui M, Attaoua R, Tahir R, Hishmih C, Harvey F, Marois-Blanchet FC, Long C , Simon P, Santucci L, Hizel C, Chalmers J, Marre M, Harrap S, Cífková R, Krajčoviechová A, Matthews D, Williams B, Poulter N, Zoungas S, Colagiuri S, Mancia G, Grobbee DE, Rodgers A, Liu L, Agbessi M, Bruat V, Favé M-J, Harwood M, Awadalla P, Woodward M, Hussin JG, Hamet P. 2021. Polygenic risk scores predict diabetes complications and their response to intensive blood pressure and glucose control. Diabetologia.

2020

Tremblay-Gravel M, Fortier A, Baron C, Mehanna P, Ducharme A, Hu Q, Hussin JG, Tardif JC, Des Rosiers C, Dupuis J, Ruiz M. 2020 Long-chain acylcarnitines and monounsaturated fatty acids discriminate heart failure patients according to pulmonary hypertension status. Metabolites. 11(4), 196

Pesaranghader A, Pelletier J, Grenier JC, Poujol R, Hussin JG*. 2020. ImputeCoVNet: 2D ResNet Autoencoder for Imputation of SARS-CoV-2 Sequences. 15th Machine Learning in Computational Biology (MLCB) proceedings. (*corresponding)

Hamet P, Pausova Z, Attaoua R, Hishmih C, Haloui M, Shin J, Paus T, Michal A, Gaudet D, Santucci L, Kotchen T. A., Cowley A.W, Hussin JG, Tremblay J. 2020. SARS-CoV-2 receptor ACE2 gene is associated with hypertension and severity of COVID-19 interaction with sex, obesity and smoking. American Journal of Hypertension.

2019

Rochefort-Boulanger C, Choiniere L, Grenier JC, Carrier PL and Hussin JG*. 2019. Generalization Capability of the Diet Network Model on Genomic Data. 14th Machine Learning in Computational Biology (MLCB) proceedings  (*corresponding)

2018

Hilary C Martin*, Elizabeth M Batty*, Julie G Hussin*, Portia Westall, Tasman Daish, Stephen Kolomyjec, Paolo Piazza, Rory Bowden, Margaret Hawkins, Tom Grant, Craig Moritz, Frank Grutzner, Jaime Gongora, Peter Donnelly. (2018) Insights into platypus population structure and history from whole-genome sequencing. Molecular biology and evolution. (*co-first)

2017

Isabel Alves, Armande Ang Houle, Julie G Hussin, Philip Awadalla. (2017) The impact of recombination on human mutation load and disease. Phil. Trans. R. Soc. B.

Adriana Romero, Pierre Luc Carrier, Akram Erraqabi, Tristan Sylvain, Alex Auvolat, Etienne Dejoie, Marc-André Legault, Marie-Pierre Dubé, Julie G Hussin, Yoshua Bengio. (2016) Diet networks: thin parameters for fat genomics. 5th International Conference on Learning Representations (ICLR) 2017.

2016

Benjamin Davies, Edouard Hatton, Nicolas Altemose, Julie G Hussin, Florencia Pratto, Gang Zhang, Anjali Gupta Hinch, Daniela Moralli, Daniel Biggs, Rebeca Diaz, Chris Preece, Ran Li, Emmanuelle Bitoun, Kevin Brick, Catherine M Green, R Daniel Camerini-Otero, Simon R Myers, Peter Donnelly. (2016) Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice. Nature.

2015

Hilary C Martin, Ryan Christ, Julie G Hussin, Jared O’Connell, Scott Gordon, Hamdi Mbarek, Jouke-Jan Hottenga, Kerrie McAloney, Gonnecke Willemsen, Paolo Gasparini, Nicola Pirastu, Grant W Montgomery, Pau Navarro, Nicole Soranzo, Daniela Toniolo, Veronique Vitart, James F Wilson, Jonathan Marchini, Dorret I Boomsma, Nicholas G Martin, Peter Donnelly. (2015) Multicohort analysis of the maternal age effect on recombination. Nature communications.

Julie G Hussin, Alan Hodgkinson, Youssef Idaghdour, Jean-Christophe Grenier, Jean-Philippe Goulet, Elias Gbeha, Elodie Hip-Ki, Philip Awadalla. (2015) Recombination affects accumulation of damaging and disease-associated mutations in human populations. Nature genetics.

2014

Benjamin Davies, Edouard Hatton, Julie Hussin, Nicolas Altemose, Florencia Pratto, Daniela Moralli, Anjali Gupta, Daniel Biggs, Kevin Brick, Catherine Green, Daniel Camerini-Otero, Simon Myers, Peter Donnelly. (2014) Reprogramming meiotic recombination in the mouse. TRANSGENIC RESEARCH.

2013

Ferran Casals, Alan Hodgkinson, Julie Hussin, Youssef Idaghdour, Vanessa Bruat, Thibault de Maillard, Jean-Cristophe Grenier, Elias Gbeha, Fadi F Hamdan, Simon Girard, Jean-François Spinella, Mathieu Larivière, Virginie Saillour, Jasmine Healy, Isabel Fernández, Daniel Sinnett, Jacques L Michaud, Guy A Rouleau, Elie Haddad, Françoise Le Deist, Philip Awadalla. (2013) Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans. PLoS Genetics.

Marc-Phillip Hitz, Louis-Philippe Lemieux-Perreault, Christian Marshall, Yassamin Feroz-Zada, Robbie Davies, Shi Wei Yang, Anath Christopher Lionel, Guylaine D’Amours, Emmanuelle Lemyre, Rebecca Cullum, Jean-Luc Bigras, Maryse Thibeault, Philippe Chetaille, Alexandre Montpetit, Paul Khairy, Bert Overduin, Sabine Klaassen, Pamela Hoodless, Philip Awadalla, Julie Hussin, Youssef Idaghdour, Mona Nemer, Alexandre FR Stewart, Cornelius Boerkoel, Stephen W Scherer, Andrea Richter, Marie-Pierre Dubé, Gregor Andelfinger. (2013) Rare Copy Number Variants Contribute to Congenital Left-Sided Heart Disease. PLoS Genetics.

2012

Julie Hussin, Daniel Sinnett, Ferran Casals, Youssef Idaghdour, Vanessa Bruat, Virginie Saillour, Jasmine Healy, Jean-Christophe Grenier, Thibault De Malliard, Jean-Francois Spinella, Mathieu Lariviere, Stephan Busche, Greg Gibson, Anna Andersson, Linda Holmfeldt, Jing Ma, Lei Wei, Jinghui Zhang, Gregor Andelfinger, James Downing, Charles Mullighan, Phillip Awadalla. (2012) Rare allelic forms of PRDM9 associated with childhood leukemogenesis. Genome Research.

Ferran Casals, Youssef Idaghdour, Julie Hussin, Philip Awadalla. (2012) Next-generation sequencing approaches for genetic mapping of complex diseases. Journal of Neuroimmunology.

Reed A Cartwright, Julie Hussin, Jonathan EM Keebler, Eric A Stone, Philip Awadalla. (2012) A family-based probabilistic method for capturing de novo mutations from high-throughput short-read sequencing data. Statistical applications in genetics and molecular biology.

2011

Julie Hussin, Marie-Hélène Roy-Gagnon, Roxanne Gendron, Gregor Andelfinger, Philip Awadalla. (2011) Age-dependent recombination rates in human pedigrees. PLoS Genetics.

Rachel A Myers, Ferran Casals, Julie Gauthier, Fadi F Hamdan, Jon Keebler, Adam R Boyko, Carlos D Bustamante, Amelie M Piton, Dan Spiegelman, Edouard Henrion, Martine Zilversmit, Julie Hussin, Jacklyn Quinlan, Yan Yang, Ronald G Lafrenière, Alexander R Griffing, Eric A Stone, Guy A Rouleau, Philip Awadalla. (2011) A population genetic approach to mapping neurological disorder genes using deep resequencing. PLoS Genetics.

Julie Hussin, Philippe Nadeau, Jean-François Lefebvre, Damian Labuda. (2011) Haplotype allelic classes for detecting ongoing positive selection. BMC Bioinformatics.

2010

OraLee H Branch, Patrick L Sutton, Carmen Barnes, Juan Carlos Castro, Julie Hussin, Philip Awadalla, Gisely Hijar. (2010) Plasmodium falciparum genetic diversity maintained and amplified over 5 years of a low transmission endemic in the Peruvian Amazon. Molecular biology and evolution.

Duane L Guernsey, Haiyan Jiang, Julie Hussin, Marc Arnold, Khalil Bouyakdan, Scott Perry, Tina Babineau-Sturk, Jill Beis, Nadine Dumas, Susan C Evans, Meghan Ferguson, Makoto Matsuoka, Christine Macgillivray, Mathew Nightingale, Lysanne Patry, Andrea L Rideout, Aidan Thomas, Andrew Orr, Ingrid Hoffmann, Jacques L Michaud, Philip Awadalla, David C Meek, Mark Ludman, Mark E Samuels. (2010) Mutations in centrosomal protein CEP152 in primary microcephaly families linked to MCPH4. The American Journal of Human Genetics.