Yan Ping Gao

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

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.

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

LongcallD jointly calls and phases small, structural, and mosaic variants from long reads, improving SV discovery and mosaic variant accuracy.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

This paper introduces Patho-DBiT, a method for spatial transcriptomics in FFPE tissues, enabling RNA biology analysis including splicing, variants, and regulatory networks in clinical samples.

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.

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

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

abPOA is a fast partial order alignment library using SIMD acceleration, achieving 15x speed improvement over SPOA with similar accuracy.

cuteSV improves structural variation detection in long-read sequencing by combining signature-based methods with clustering and refinement, achieving better performance on real datasets.

deGSM constructs large de Bruijn graphs efficiently in limited memory, handling terabase-pair datasets on standard hardware.