School of Biomedical Sciences cordially invites you to join the following Post-doctoral Fellow (PDF) Seminar:

Date: 25 March 2025 (Tuesday)
Time: 4:00 pm – 4:30 pm
Venue: Lecture Theatre 1, G/F, William M.W Mong Block, 21 Sassoon Road
Host: Dr. Haifeng Fu

Light refreshments will be served. Please register via the below link by 24 March 2025 (Monday):
Registration: https://hku.au1.qualtrics.com/jfe/form/SV_0fAfspp6TinWtka

Bridging individual variation in gene expression prediction: challenges and opportunities with sequence models
Dr. Shumin Li (Post-doctoral Fellow)
[Supervisor: Professor Yuanhua Huang & Professor Ruibang Luo]

Recent advances in genomic sequence models demonstrate remarkable capability in predicting genome-wide gene expression levels and epigenomic signals directly from DNA sequences across diverse cell types. While these models perform well in predicting population-average expression from reference genomes, they fail to account for expression variability among individuals. In this study, we explore the potential of fine-tuning state-of-the-art models—including Enformer, Borzoi, and genomic foundation models such as Evo2, and Caduceus—using paired DNA and RNA sequencing data to predict individual-specific gene expression. Preliminary findings reveal that fine-tuned models effectively predicting expression of seen genes in held-out individuals. However, it does not contribute to the performance for unseen genes, presenting a challenge in the field and suggesting that multi-omics training data or a new training strategy is needed to address this problem.

All are welcome.