Davide Bolognini

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.

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

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

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.

Competing gene regulatory networks drive naive and memory B cell differentiation

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.

Population-scalable genotyping from low-coverage sequencing data using pangenome graphs

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.

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.

SAFE-LD: A novel method for the estimation of linkage disequilibrium from summary statistics

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

GASOLINE: detecting germline and somatic structural variants from long-reads data.

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

High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias.

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

Third Generation Cytogenetic Analysis (TGCA): diagnostic application of long-read sequencing.

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: a user-friendly R package to analyze and compare nanopore sequencing data

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