Deniz Kural

Fast and Accurate Genomic Analyses using Genome Graphs

This paper introduces a graph genome reference that improves read alignment and variant calling accuracy compared to traditional haplotype-based methods.

Comparing complex variants in family trios

This paper introduces VBT, a tool for identifying Mendelian violations in family trios by solving the 3-way variant matching problem, showing improved accuracy over existing methods.

geck: trio-based comparative benchmarking of variant calls

The paper introduces a statistical model to benchmark variant calling pipelines using trio data, showing it can estimate precision and recall differences with low uncertainty.

Genome Graphs

This paper introduces genome graphs as an alternative to linear reference genomes, showing they improve read mapping and variant calling compared to the standard GRCh38 reference.

Rabix: an open-source workflow executor supporting recomputability and interoperability of workflow descriptions

The paper introduces Rabix Executor, an open-source workflow engine that enhances reproducibility through reusability and interoperability of workflow descriptions.