Can Koçkan

Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution

The paper introduces LRAA, a framework for accurate isoform discovery and quantification in long-read RNA-seq data, outperforming existing methods across multiple benchmarks.

Learning-Augmented Sketching Offers Improved Performance for Privacy Preserving and Secure GWAS

The paper improves the SkSES method for privacy-preserving GWAS by integrating a learning-augmented approach, achieving up to 40% higher accuracy under memory constraints.

Homomorphic Encryption: An Application to Polygenic Risk Scores

This paper applies fully homomorphic encryption to compute polygenic risk scores securely, showing high accuracy and feasibility with synthetic and real data.

Privacy-Preserving Genotype Imputation in a Trusted Execution Environment

This paper introduces a privacy-preserving genotype imputation method using a Trusted Execution Environment to protect genetic data while maintaining accuracy comparable to existing tools.

Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave

SkSES enables secure and privacy-preserving SNP analysis across encrypted genomic data using sketching algorithms in Intel SGX enclaves, demonstrating efficient SNP querying in a large dataset.