Silvia Buonaiuto

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 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.

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.

Identity-by-descent captures Shared Environmental Factors at Biobank Scale

This paper uses IBD-based clustering to reveal environmental and health disparities across subcommunities in a biobank dataset.

The Biorepository and Integrative Genomics resource for inclusive genomics: insights from a diverse pediatric and admixed cohort

The paper analyzes genomic data from a diverse cohort to highlight genetic diversity and disparities in disease prevalence linked to ancestry and environment.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

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.

A Draft Human Pangenome Reference

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

Recombination between heterologous human acrocentric chromosomes

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

A standardized approach for case selection and genomic data analysis of maternal exomes for the diagnosis of oocyte maturation and early embryonic developmental arrest in IVF

The paper develops a methodology for selecting IVF cases with oocyte maturation defects and preimplantation embryo lethality, using whole-exome sequencing and bioinformatics to identify causative genetic variants.

Prioritization of putatively detrimental variants in euploid miscarriages

The paper identifies potentially harmful genetic variants in euploid miscarriage embryos and highlights specific genes linked to miscarriage risk.