Eddie Ferro

SIFT selects reference haplotypes for genome patching using compressed indexing and pseudo-MEM queries to improve T2T imputation efficiency.

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.

RAPID-PFP accelerates Prefix-Free Parsing using GPU parallelism, achieving significant speedups on genomic datasets compared to CPU implementations.

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.