Andrea Guarracino

The paper introduces Yruler, a tool to measure Y chromosome satellite arrays from sequencing reads without alignment, revealing lineage-specific variations in satellite length and composition.

This study evaluates the impact of an individual-specific pangenome on somatic variant calling in a pediatric AML patient, finding reduced false positives and altered phylogenetic branching.

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

The paper identifies evolutionary processes in acrocentric chromosomes of great apes, including repeat enrichment, inversion, and gene family amplification, with implications for human genomic instability.

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

The paper analyzes subtelomeric regions across 465 human genomes to show widespread sequence exchange and recombination, revealing a population-scale pattern of concerted evolution.

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.

Panomap maps raw nanopore signals to pangenome variation graphs, improving mapping accuracy and reducing reference bias compared to linear-reference methods.

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

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

KaryoScope annotates genome assemblies at base-pair resolution across multiple feature classes quickly and without alignment, revealing structural variation in centromeres and subtelomeres.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

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

This paper introduces adaptive tracepoints for compressing pangenome alignments, achieving significant compression ratios while maintaining alignment accuracy.

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.

The paper analyzes structural variants in three North American jay species using pangenome tools and long-read assemblies, revealing rapid genome evolution and population size effects on SV dynamics.

The paper presents a mouse pangenome with 17 strains, resolving structural complexity and improving RNA-Seq analysis by identifying non-reference genes and VNTR polymorphisms.

The paper generates a complete diploid genome assembly for RPE-1 cells and uses it as a matched reference to improve multi-omics data analysis and identify haplotype-specific epigenetic variation.

This study assembles human Robertsonian chromosomes, identifies a common breakpoint and centromere epigenetic changes, and explores structural features enabling their formation.

GNQA, a retrieval-augmented GPT question-answering system over 3000 GeneNetwork, aging and diabetes papers, cites source paragraphs; RAGAS rated answer relevance above human thumbs-up ratings (89% vs 76%).

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

This study constructs a reference-free pangenome of Arabidopsis thaliana using 93 assemblies, revealing gene and pseudogene diversity across geographic regions.

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

This study quantifies protein expression in rat brains, identifies pQTLs, and links them to behavioral traits and human disorders.

This study constructs a rat pangenome from linked-read data to enhance variant discovery and genotype-phenotype mapping in recombinant inbred strains.

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.