Haowen Zhang

Quality control of single-cell ATAC-seq data without peak calling using Chromap

This paper extends Chromap to provide peak-based quality control metrics for single-cell ATAC-seq without peak calling, improving downstream analysis by identifying low-quality cells missed by other methods.

Fast alignment and preprocessing of chromatin profiles with Chromap

Chromap provides a fast and accurate method for aligning and preprocessing chromatin profiles, outperforming existing tools in speed while maintaining alignment accuracy.

A comprehensive evaluation of long read error correction methods

This paper evaluates long read error correction methods using real data, comparing their performance on quality, runtime, memory, and impact on genome assembly.

Weighted minimizer sampling improves long read mapping

The paper introduces a weighted minimizer sampling algorithm to improve long-read mapping accuracy, particularly in repetitive regions, by reducing false positives while maintaining match guarantees.

On the Complexity of Sequence to Graph Alignment

This paper proves sequence to graph alignment is NP-complete under Hamming and edit distances for alphabets of size ≥2 and presents an efficient algorithm for when only sequence changes are allowed.

Validating paired-end read alignments in sequence graphs

The paper introduces an algorithm to validate distance constraints in graph-based genomic references using sparse matrix operations, demonstrating efficiency on real-world datasets.

Accelerating Sequence Alignment to Graphs

The paper introduces a parallel algorithm for sequence-to-graph alignment, achieving significant speedup for aligning DNA reads to variation graphs.