Sinem Demirkaya-Budak

This paper shows that using pangenome references improves biomarker estimation in tumor sequencing, reducing bias in TMB calculations for non-European populations.

This paper presents an informatic method to identify germline de novo mutations in family trios using consensus across variant callers, achieving high precision and recall.

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

This study develops population-specific genome graphs to improve sequencing data analysis, showing reduced mapping errors and better variant calling in African ancestry samples.