Finishing an M.Sc. in bioinformatics (U of C) - I adapt pretrained genomic foundation models to answer clinical questions
Hi, my name is Sasha Chernenkoff!
I am finishing an M.Sc. in bioinformatics in the Long lab at the University of Calgary. My research focuses on representation learning with genomic foundation models. A central question is whether large, pretrained models can be adapted to new prediction tasks without losing what they've already learned. I want that adaptation to point at real clinical questions rather than remain purely computational. Current work involves fine-tuning genomic foundation models for a range of molecular phenotype prediction tasks, and testing how far their learned representations generalize beyond the tasks they were originally trained on.
Before grad school, I worked as an R&D scientist at PerkinElmer Genomics, where I developed second-tier biochemical diagnostic tests for newborn screening - an LC-MS/MS biomarker panel for MPS I & II and a Western blot CRIM-status assay for Pompe disease. That work got me interested in the intersection of molecular biology and diagnostics, and inspired my work in computational genomics.
I can generally be found behind my computer screen writing code, getting lost in the Canadian Rockies with my husband and son, or designing and building websites, keyboards, and graphics!
Sasha
I am finishing an M.Sc. in bioinformatics in the Long lab at the University of Calgary. My research focuses on representation learning with genomic foundation models. A central question is whether large, pretrained models can be adapted to new prediction tasks without losing what they've already learned. I want that adaptation to point at real clinical questions rather than remain purely computational. Current work involves fine-tuning genomic foundation models for a range of molecular phenotype prediction tasks, and testing how far their learned representations generalize beyond the tasks they were originally trained on.
Before grad school, I worked as an R&D scientist at PerkinElmer Genomics, where I developed second-tier biochemical diagnostic tests for newborn screening - an LC-MS/MS biomarker panel for MPS I & II and a Western blot CRIM-status assay for Pompe disease. That work got me interested in the intersection of molecular biology and diagnostics, and inspired my work in computational genomics.
I can generally be found behind my computer screen writing code, getting lost in the Canadian Rockies with my husband and son, or designing and building websites, keyboards, and graphics!
Sasha