Bida Gu

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.

A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

A global view of human centromere variation and evolution

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

Long-read sequencing maps transposable element variation and its regulatory and epigenetic effects in the human brain

This study uses long-read sequencing to map transposable element variation in human brain tissue, revealing regulatory and epigenetic effects across cell types and ancestries.

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.

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.

Defining a tandem repeat catalog and variation clusters for genome-wide analyses

The paper introduces a new TR catalog, TRExplorer v1.0, containing 4.86 million loci, designed for both short-read and long-read analyses and includes variation clusters identified using long-read HiFi data.

A population-scale map of human tandem repeat composition and mutation dynamics from long-read assemblies

The paper constructs TRCompDB, a database of 4.4 million tandem repeat loci across 832 human genomes, revealing mutation rates and dynamics influenced by recombination and duplication context.

Benchmarking of small and large variants across tandem repeats

The paper benchmarks small and large variants in tandem repeats across 86 samples, creating a benchmark dataset and comparison method for TR variant calling.

vamos: VNTR annotation using efficient motif sets

The paper introduces vamos, a method to annotate VNTRs by selecting representative motifs, and applies it to 32 haplotype-resolved human genomes, finding an average of 3.1-4.0 alleles per locus.