Barış Ekim

ralphi: a deep reinforcement learning framework for haplotype assembly

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

Designing efficient randstrobes for sequence similarity analyses

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

Efficient minimizer orders for large values of k using minimum decycling sets

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

mapquik: Efficient low-divergence mapping of long reads in minimizer space

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.

Minimizer-space de Bruijn graphs

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.

A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets

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.