Haoyu Cheng

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

The complete genome of a songbird

This paper presents the first fully phased, diploid, telomere-to-telomere genome of the zebra finch, revealing new genes and structural features.

A near-complete human pancreatic cancer genome

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Benchmarking scRNA-seq Copy Number Inference: A Comprehensive Evaluation and Practitioner Guide

This study benchmarks 12 scRNA-seq CNV inference methods across 28 datasets, finding allele-aware tools perform better with high-quality allelic data, while expression-centric tools are reliable with raw data.

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads

The paper introduces hifiasm (ONT), an algorithm that enables near telomere-to-telomere genome assembly using standard ONT Simplex reads, reducing computational demands and improving chromosome reconstruction.

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

The paper presents T2T reference genomes from a multi-generational pedigree to study genetic and epigenetic inheritance across the complete genome.

Targeted sequencing and iterative assembly of near-complete genomes

The paper introduces Cornetto, a method using targeted long-read sequencing to improve genome assembly quality and completeness, particularly for challenging regions and sample types.

Advancing Human Population Genomics with DNA Foundation Models

This study introduces a DNA foundation model to assess functional genetic variation across diverse populations, demonstrating its utility in understanding Alzheimer's disease risk and ancestry-specific gene expression.

Complex genetic variation in nearly complete human genomes

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

The paper presents a scalable pipeline for reference genome assembly and evaluation, demonstrating its effectiveness across 51 vertebrate species using Galaxy.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

A Draft Human Pangenome Reference

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

Recombination between heterologous human acrocentric chromosomes

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

Automated assembly of high-quality diploid human reference genomes

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The complete sequence of a human genome

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes

This paper creates a comprehensive benchmark for challenging medically-relevant autosomal genes, improving variant recall from 8% to 100% by addressing reference-specific false duplications.

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.

Accurate chromosome-scale haplotype-resolved assembly of human genomes

This paper introduces a method for chromosome-scale haplotype-resolved genome assembly using long reads and long-range data, achieving high accuracy and contiguity in three human genomes.

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing

BitMapperBS is a fast and accurate aligner for whole-genome bisulfite sequencing, outperforming existing tools in speed while maintaining sensitivity and precision.