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Yannis Trakadis

Membre affilié
Professeur adjoint, McGill University, Département de médecine et Département de génétique humaine
Sujets de recherche
Apprentissage automatique médical
Apprentissage sur graphes
Modélisation moléculaire
Traitement du langage naturel

Biographie

Le Dr Yannis Trakadis est généticien médical et médecin métabolique au Département de génétique médicale du Centre universitaire de santé McGill (CUSM), et professeur adjoint au Département de génétique humaine de la Faculté de médecine et des sciences de la santé de l’Université McGill. Il est président du comité métabolique du Collège canadien des généticiens médicaux (CCGM) et membre du comité de développement des lignes directrices de pratique clinique du CCGM.

Le Dr Trakadis est un chercheur-boursier clinicien du Fonds de recherche du Québec - Santé (FRQS) pour ses recherches sur les applications de l'apprentissage automatique en santé. Son laboratoire a appliqué l'apprentissage automatique à l'analyse de données génomiques et fonctionnelles de milliers d'individus. Plus précisément, le Dr Trakadis et son équipe ont développé de nouvelles méthodes d'apprentissage automatique pour l'analyse de données cliniques, génomiques, transcriptomiques et métabolomiques afin de permettre le développement de soins médicaux plus personnalisés.

Les intérêts de recherche du Dr Trakadis incluent l'intégration clinique de nouvelles technologies et de modèles de santé numérique, avec pour objectif principal l'application de l'intelligence artificielle pour faire progresser la médecine de précision.

Publications

Disease-Specific Prediction of Missense Variant Pathogenicity with DNA Language Models and Graph Neural Networks
Mohamed Ghadie
Sameer Sardaar
Yannis Trakadis
2025-10-13
Bioengineering (publié)
doi.org
Disease-Specific Prediction of Missense Variant Pathogenicity with DNA Language Models and Graph Neural Networks
Mohamed Ghadie
Sameer Sardaar
Yannis Trakadis
2025-10-13
Bioengineering (publié)
doi.org
Disease-Specific Prediction of Missense Variant Pathogenicity with DNA Language Models and Graph Neural Networks
Mohamed Ghadie
Sameer Sardaar
Yannis Trakadis
Accurate prediction of the impact of genetic variants on human health is of paramount importance to clinical genetics and precision medicine… (voir plus). Recent machine learning (ML) studies have tried to predict variant pathogenicity with different levels of success. However, most missense variants identified on a clinical basis are still classified as variants of uncertain significance (VUS). Our approach allows for the interpretation of a variant for a specific disease and, thus, for the integration of disease-specific domain knowledge. We utilize a comprehensive knowledge graph, with 11 types of interconnected biomedical entities at diverse biomolecular and clinical levels, to classify missense variants from ClinVar. We use BioBERT to generate embeddings of biomedical features for each node in the graph, as well as DNA language models to embed variant features directly from genomic sequence. Next, we train a two-stage architecture consisting of a graph convolutional neural network to encode biological relationships. A neural network is then used as the classifier to predict disease-specific pathogenicity of variants, essentially predicting edges between variant and disease nodes. We compare performance across different versions of our model, obtaining prediction-balanced accuracies as high as 85.6% (sensitivity: 90.5%; NPV: 89.8%) and discuss how our work can inform future studies in this area.
2025-10-13
Bioengineering (publié)
doi.org
Current landscape of clinical genetics knowledge and attitudes among Non-Geneticist Physicians - the McGill genetics education survey (McGES).
Sarah Abdullah-Maklan
Yannis Trakadis
2025-10-01
Journal of Community Genetics (publié)
doi.org
Current landscape of clinical genetics knowledge and attitudes among Non-Geneticist Physicians - the McGill genetics education survey (McGES).
Sarah Abdullah-Maklan
Yannis Trakadis
2025-10-01
Journal of Community Genetics (publié)
doi.org
Current landscape of clinical genetics knowledge and attitudes among Non-Geneticist Physicians - the McGill genetics education survey (McGES)
Sarah Abdullah-Maklan
Yannis Trakadis
2025-10-01
Journal of Community Genetics (publié)
doi.org
Metabolic Control and Frequency of Clinical Monitoring Among Canadian Children With Phenylalanine Hydroxylase Deficiency: A Retrospective Cohort Study
Nataliya Yuskiv
Ammar Saad
Beth K. Potter
Sylvia Stockler‐Ipsiroglu
John J. Mitchell
Steven Hawken
Kylie Tingley
Michael Pugliese
Monica Lamoureux
Andrea J. Chow
Jonathan B. Kronick
Kumanan Wilson
Annette Feigenbaum
Sharan Goobie
Michal Inbar-Feigenberg
Julian Little
Saadet Mercimek‐Andrews
Amy Pender
Chitra Prasad
Andreas Schulze … (voir 9 de plus)
Yannis Trakadis
Gloria Ho
Hilary Vallance
Valerie Austin
Anthony Vandersteen
Andrea C. Yu
Cheryl Rockman‐Greenberg
Aizeddin Mhanni
Pranesh Chakraborty
2025-09-01
JIMD Reports (publié)
doi.org
Graph Representation Learning for the Prediction of Medication Usage in the UK Biobank Based on Pharmacogenetic Variants
Bill Qi
Yannis Trakadis
2025-05-31
Bioengineering (publié)
doi.org
Co-developing longitudinal patient registries for phenylketonuria and mucopolysaccharidoses in Canada
John Adams
Kim Angel
John J. Mitchell
Pranesh Chakraborty
Beth K. Potter
Michal Inbar-Feigenberg
Sylvia Stockler
Monica Lamoureux
Alison H. Howie
Alex Pace
Nancy J. Butcher
Cheryl Rockman-Greenberg
Robin Hayeems
Anne-Marie Laberge
Thierry Lacaze-Masmonteil
Jeff Round
Martin Offringa
Maryam Oksoui
Andreas Schulze
Kathy N. Speechley … (voir 3 de plus)
Kednapa Thavorn
Yannis Trakadis
Kumanan Wilson
2024-04-01
Molecular Genetics and Metabolism (publié)
doi.org
Co-developing longitudinal patient registries for phenylketonuria and mucopolysaccharidoses in Canada
John Adams
Kim Angel
John J. Mitchell
Pranesh Chakraborty
Beth K. Potter
Michal Inbar-Feigenberg
Sylvia Stockler
Monica Lamoureux
Alison H. Howie
Alex Pace
Nancy J. Butcher
Cheryl Rockman-Greenberg
Robin Hayeems
Anne-Marie Laberge
Thierry Lacaze-Masmonteil
Jeff Round
Martin Offringa
Maryam Oksoui
Andreas Schulze
Kathy N. Speechley … (voir 3 de plus)
Kednapa Thavorn
Yannis Trakadis
Kumanan Wilson
2024-04-01
Molecular Genetics and Metabolism (publié)
doi.org
Co-developing The Canadian MPS Registry: A longitudinal rare disease patient registry
John J. Mitchell
Michal Inbar-Feigenberg
Kim Angel
Pranesh Chakraborty
Monica Lamoureux
John Adams
Beth K. Potter
Sylvia Stockler-Ipsirolgu
Alison H. Howie
Alex Pace
Nancy J. Butcher
Cheryl Greenberg
Robin Hayeems
Anne-Marie Laberge
Jeff Round
Martin Offringa
Maryam Oskoui
Chelsea Ruth
Andreas Schulze
Kathy N. Speechley … (voir 4 de plus)
Kednapa Thavorn
Yannis Trakadis
Kumanan Wilson
Thierry Lacaze
2024-02-01
Molecular Genetics and Metabolism (publié)
doi.org
Co-developing The Canadian MPS Registry: A longitudinal rare disease patient registry
John J. Mitchell
Michal Inbar-Feigenberg
Kim Angel
Pranesh Chakraborty
Monica Lamoureux
John Adams
Beth K. Potter
Sylvia Stockler-Ipsirolgu
Alison H. Howie
Alex Pace
Nancy J. Butcher
Cheryl Greenberg
Robin Hayeems
Anne-Marie Laberge
Jeff Round
Martin Offringa
Maryam Oskoui
Chelsea Ruth
Andreas Schulze
Kathy N. Speechley … (voir 4 de plus)
Kednapa Thavorn
Yannis Trakadis
Kumanan Wilson
Thierry Lacaze
2024-02-01
Molecular Genetics and Metabolism (publié)
doi.org