Yue Hao

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 long-term organotypic slice culture model of patient high-grade glioma preserving tumor heterogeneity and architecture, and specificity of CAR T cell targeting

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.

Iron-deficiency in the tumor microenvironment reprograms tumor-immune interactions in a sex biased manner

This study shows that iron deficiency in glioblastoma tumors affects immune interactions differently in males and females.

Telomere Dysfunction in Human Astrocytes Drives Acrocentric Chromosome Instability and Nucleolar Reorganization

This study shows that telomere dysfunction in human astrocytes leads to acrocentric chromosome instability and nucleolar reorganization through a combination of cytogenetic, imaging, and chromatin-contact analyses.

Emergence of Genetic Sex Determination in an Environmentally Sex-Determined Animal

The paper identifies a genetic variant in Daphnia pulex that suppresses recombination, leading to the emergence of a mixed-mating system with both genetic and environmental sex determination.

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.

Pangenome discovery of missing autism variants

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.

Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing

The paper presents diploid genome assemblies for two human fibroblast cell lines, enabling clone-specific variant calling, improved read mapping, and accurate phasing.

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

The paper confirms a two-step hybridization model for the formation of hexaploidy in Brassiceae and shows subgenomes have distinct loss rates but functionally compatible genes.

clustifyr: An R package for automated single-cell RNA sequencing cluster classification

clustifyr assigns cell types to scRNA-seq clusters using diverse reference data and provides tools for exploratory analysis.