Ivo Violich

A Complete Genome for the Common Marmoset

The paper presents the first telomere-to-telomere genome for the common marmoset, revealing genomic features and a pangenome resource for biomedical research.

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.

Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing

This study evaluates the diagnostic yield of short-read and long-read sequencing in rare diseases, finding limited added value from long-read sequencing despite increased variant discovery.

Haplotype-resolved centromeric chromatin organization from a complete diploid human genome

The paper uses a complete diploid human genome to study centromeric chromatin organization, revealing that DNA methylation regulates centromere structure and plasticity.

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

The paper presents T2T reference genomes from a multi-generational pedigree to study genetic and epigenetic inheritance across the complete genome.

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection

This study evaluates the diagnostic yield of long-read nanopore sequencing in rare disease detection, finding it covers more genes and detects additional variants compared to short-read sequencing.

Decreased SNCA Expression in Whole-Blood RNA Analysis of Parkinson's Disease Adjusting for Lymphocytes

The paper identifies decreased SNCA expression in Parkinson's Disease blood samples after correcting for immune cell effects, suggesting it as a potential transcriptomic biomarker.

The Foundational data initiative for Parkinsons disease (FOUNDIN-PD): enabling efficient translation from genetic maps to mechanism

The paper presents a multi-layered molecular dataset from iPSC-derived dopaminergic neurons to model Parkinson's disease genetic risk and provides a data browser for accessing these resources.

Multi-Modality Machine Learning Predicting Parkinsons Disease

This paper develops an automated ML model to predict Parkinson's Disease using multi-modal data, achieving high AUC scores and constructing gene networks relevant to PD.

Deep sncRNA-seq of the PPMI cohort to study Parkinson's disease progression

The paper analyzes sncRNA-seq data from the PPMI cohort to identify miRNAs associated with Parkinson's disease progression and systemic inflammation.

Quality Control Metrics for Whole Blood Transcriptome Analysis in the Parkinson's Progression Markers Initiative (PPMI)

The paper quantifies technical variability in whole blood transcriptome data from the PPMI study using pooled reference samples and describes the dataset's availability.