Jamie Allen

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

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

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.

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.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

SUsPECT improves variant annotation by using custom long-read transcriptomes to better predict variant effects in clinical settings.

The paper assesses breast cancer risks linked to rare missense variants in five susceptibility genes using logistic and mixture models, finding varying risk contributions across genes.

This study fine-maps 150 breast cancer risk regions to identify 178 high confidence target genes using genomic and functional annotations.