Dan Vitale

Repeat expansions in Parkinson's disease and parkinsonism across ancestries: insights from a global genetic cohort

This study identifies pathogenic and intermediate repeat expansions in Parkinson's disease and parkinsonism across 11 ancestries, highlighting ATXN2's role in PD risk and ancestry-specific patterns.

The Global Parkinson's Disease Genetics (GP2) Genome Browser

The paper introduces a genome browser for Parkinson's disease genomic data, integrating WGS and CES samples with variant annotations and ancestry stratification.

Genetic Contributions to Alzheimer's Disease and Frontotemporal Dementia in Admixed Latin American Populations

This study identifies genetic variants associated with Alzheimer's disease and frontotemporal dementia in admixed Latin American populations using whole-genome sequencing and ancestry analysis.

CNV-Finder: Streamlining Copy Number Variation Discovery

CNV-Finder uses deep learning to detect copy number variations from array data, improving accuracy and reducing manual workload for downstream analyses.

CARDBiomedBench: A Benchmark for Evaluating Large Language Model Performance in Biomedical Research

CARDBiomedBench evaluates LLM performance in biomedical research using a benchmark focused on neurodegenerative diseases, revealing significant limitations in response quality and safety.

Large-scale genetic characterization of Parkinson's disease in the African and African admixed populations

This study identifies genetic variants associated with Parkinson's disease in African and African admixed populations, highlighting differences from European and Asian populations.

Random forest model improves annotation and discovery of variants of uncertain significance in Alzheimer's and other neurological disorders

MoVUS, a random forest model, classifies variants of uncertain significance in Alzheimer's and neurological disorders with high accuracy, prioritizing potentially pathogenic variants.

The Global Landscape of Genetic Variation in Parkinson's disease: Multi-Ancestry Insights into Established Disease Genes and their Translational Relevance

This paper analyzes genetic variation in Parkinson's disease across multiple ancestries, revealing ancestry-specific patterns and highlighting the importance of diverse populations in genetic research.

Insights into Ancestral Diversity in Parkinsons Disease Risk: A Comparative Assessment of Polygenic Risk Scores

This study compares polygenic risk scores for Parkinson's disease across seven ancestries, finding varying predictive accuracy and highlighting the need for ancestry-specific models.

The Neurodegenerative Disease Knowledge Portal: Propelling Discovery Through the Sharing of Neurodegenerative Disease Genomic Resources

The paper introduces the Neurodegenerative Disease Knowledge Portal (NDKP), an open-science platform aggregating genomic datasets for neurodegenerative diseases to enable collaborative analysis and discovery.

Haplotype-Resolved Long-Read Sequencing in Hundreds of Diverse Brains Identifies Structural Variant Impacts on Expression and Allele-Specific Methylation

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

GenoTools: An Open-Source Python Package for Efficient Genotype Data Quality Control and Analysis

GenoTools provides a Python package for genotype data QC, ancestry estimation, and GWAS, enabling scalable and reproducible analysis of large genetic datasets.

NeuroBooster Array: A Genome-Wide Genotyping Platform to Study Neurological Disorders Across Diverse Populations

The paper introduces the NeuroBooster Array, a genome-wide genotyping platform designed to study neurological disorders across diverse populations by capturing genetic variation and enabling imputation of disease-related variants.

Cluster Buster: A Machine Learning Algorithm for Genotyping SNPs from Raw Data

Cluster Buster improves SNP genotyping quality by reducing no-calls and enhancing genotype accuracy for neurodegenerative disease research.

Federated Learning for multi-omics: a performance evaluation in Parkinson's disease

This study evaluates federated learning models for multi-omics Parkinson's disease prediction, finding they perform comparably to centrally trained models with minor performance differences.

omicSynth: an Open Multi-omic Community Resource for Identifying Druggable Targets across Neurodegenerative Diseases

The paper identifies druggable target genes for neurodegenerative diseases using Mendelian Randomization and provides a web platform for exploring therapeutic targets.

Multi-ancestry genome-wide meta-analysis in Parkinson's disease

This paper conducts a multi-ancestry genome-wide meta-analysis of Parkinson's disease, identifying 78 independent loci and 23 genes associated with PD risk.

Genome-wide Association Identifies Novel Etiological Insights Associated with Parkinsons Disease in African and African Admixed Populations

Intronic GBA1 variant rs3115534-G, common in African and African admixed ancestry but rare elsewhere, raises Parkinson's disease risk (OR 1.58) and lowers onset age.

Global Parkinson's Genetics Program (GP2) Complex Network Protocol: Defining the causes of sporadic Parkinson's disease

The paper outlines the protocol for integrating genetic and clinical data from a global cohort of over 150,000 participants to study the genetic causes of sporadic Parkinson's disease.

Multi-ancestry meta-analysis and fine-mapping in Alzheimer's Disease

This study conducts a multi-ancestry GWAS meta-analysis of Alzheimer's disease, identifies two novel loci, and assesses polygenic risk score generalizability across populations.

Genetic risk factor clustering within and across neurodegenerative diseases

This study clusters patients with neurodegenerative diseases based on genetic risk variants, revealing overlapping genetic etiology and subsets with no common risk factors.

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson's disease data

The paper describes a virtual hackathon event that brought together early career scientists to develop tools for Parkinson's disease research using open science principles.

Polygenic Parkinson's disease genetic risk score as risk modifier of parkinsonism in Gaucher disease

The paper examines how a polygenic Parkinson's disease genetic risk score modifies the risk of parkinsonism in Gaucher disease patients.

A reference induced pluripotent stem cell line for large-scale collaborative studies

The paper identifies and characterizes a reference iPSC line, KOLF2.1J, for standardized use in collaborative studies across multiple differentiation protocols and assays.

Large-scale Rare Variant Burden Testing in Parkinson's Disease Identifies Novel Associations with Genes Involved in Neuro-inflammation

Genome-wide analysis of Structural Variants in Parkinson's Disease using Short-Read Sequencing data

This study identifies 3,154 high-confidence structural variants in Parkinson's disease using short-read sequencing and validates some with long-read data, highlighting limitations of short-read methods.

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.

fuNTRp: Identifying protein positions for variation driven functional tuning

The paper introduces funtrp, a method to classify protein positions as neutral, rheostat, or toggle based on mutational impact, showing these types correlate with functional effects and improve variant effect prediction.