Barış Ekim

ralphi uses deep reinforcement learning to improve haplotype assembly, achieving lower error rates than existing methods on standard benchmarks.

This paper introduces new randstrobe construction methods, identifies biases in previous approaches, and improves accuracy in short-read mapping.

The paper introduces new minimizer orders for large k-values using decycling sets, improving efficiency in DNA sequencing analysis.

mapquik accelerates long-read mapping by using minimizer-space seeding and a pseudo-chaining algorithm, achieving high sensitivity and speed on human and maize genomes.

This paper introduces a new method for DNA sequence analysis using minimizer-space de Bruijn graphs, achieving faster and more memory-efficient genome and metagenome assembly with high accuracy.

This paper introduces PASHA, a randomized parallel algorithm for generating near-optimal universal hitting sets, which is significantly faster and more memory-efficient than existing methods.