Alan DenAdel

Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance

This study evaluates how pre-training dataset size and diversity affect single-cell foundation model performance on zero-shot and fine-tuned tasks using 22.2 million cells.

A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing

This paper introduces a method to prevent over-clustering in scRNA-seq by controlling double-dipping, improving differential expression analysis accuracy.

Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease

This study identifies mutation and transcriptional state compatibility in Ph+ ALL MRD, showing that targeting these interactions can overcome BCR::ABL1 independence and improve MRD monitoring.

Leveraging the Genetic Correlation between Traits Improves the Detection of Epistasis in Genome-wide Association Studies

This paper introduces mvMAPIT, a method to detect epistasis in GWAS by jointly modeling multiple traits, showing improved power over single-trait approaches.