Davide Bolognini

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.

This study presents a pan-pangenome of humans, chimpanzees, and bonobos, revealing structural variation, selection patterns, and adaptations related to immunity and malaria resistance.

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

This study identifies distinct gene regulatory networks driving naive and memory B cell differentiation, showing IRF4's role in both GC and plasma cell development independently of PRDM1.

COSIGT improves genotyping accuracy at low sequencing depths by matching coverage patterns to pangenome haplotypes using cosine similarity, enabling population-scale analysis of complex variation.

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.

SAFE-LD estimates linkage disequilibrium from GWAS summary statistics using pseudo-genotypes that preserve in-sample LD while protecting privacy.

This study examines amylase structural haplotypes in humans, finding increased copy numbers in agricultural populations and evidence of recent selection over the last 12,000 years.

GASOLINE detects germline and somatic structural variants from long-read sequencing data with high accuracy, outperforming existing methods in synthetic and real datasets.

The paper uses nanopore sequencing to map DNA methylation in AMLs, revealing hypermethylation at CpG-poor regions drives chemoresistance through transcription factor networks.

This study demonstrates that long-read sequencing using Oxford Nanopore Technologies can rapidly and accurately detect pathogenic unbalanced structural variants with resolution comparable to traditional methods.

NanoR is an R package that simplifies nanopore sequencing data visualization and comparison between MinION and GridION X5 platforms.