Kimberley J. Billingsley

Cell-type-resolved somatic variant discovery from bulk long-read sequencing

SniffCell assigns somatic variants to cell types using DNA methylation from bulk long-read sequencing, revealing cell-type-specific mutations in human tissues.

SALRR: Scalable Analysis of Long-Read RNA-Seq Enables Comprehensive Transcriptome Profiling in Human Brain

SALRR provides a scalable platform for long-read RNA-seq analysis, identifying novel splice variants in human brain tissue.

Long-read sequencing maps transposable element variation and its regulatory and epigenetic effects in the human brain

This study uses long-read sequencing to map transposable element variation in human brain tissue, revealing regulatory and epigenetic effects across cell types and ancestries.

Haplotype-Resolved DNA Methylation at the APOE Locus identifies Allele-Specific Epigenetic Signatures Relevant to Alzheimer's Disease Risk

This paper uses long-read sequencing to analyze haplotype-resolved DNA methylation at the APOE locus in brain samples, identifying allele-specific methylation patterns linked to Alzheimer's disease risk.

The complete genome of the KOLF2.1J reference iPSC line

The paper generates and characterizes a custom genome assembly for the KOLF2.1J iPSC line to improve genomic analysis accuracy compared to standard references.

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.

Long-read sequencing identifies FGF14 repeat expansions in Parkinson's disease

The paper identifies FGF14 GAA repeat expansions in Parkinson's disease using long-read sequencing and finds they occur in both patients and controls.

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.

Long-Read epigenetic clocks identify improved brain aging predictions

The paper develops epigenetic clocks using long-read DNA methylation data from diverse ancestries, showing improved aging predictions and identifying ancestry-specific aging pathways.

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories

The paper uses long-read sequencing to analyze genomic and epigenomic changes in melanoma subclones, revealing parallel evolutionary paths and lineage-specific methylation patterns.

Dissecting the biological impact of GBA1 mutations using multi-omics in an isogenic setting

The paper investigates the biological impact of GBA1 mutations using multi-omics in isogenic iPSC lines, finding limited overlapping results across cell types and suggesting RNA-based quantitation may not be optimal for characterizing GCase mechanisms.

APOE stratified genome-wide association studies provide novel insights into the genetic etiology of Alzheimers's disease

This study performs APOE-stratified GWAS to uncover genetic mechanisms underlying Alzheimer's disease risk and response to therapies.

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.

African ancestry neurodegeneration risk variant disrupts an intronic branchpoint in GBA1

The paper identifies a non-coding risk variant in GBA1 associated with Parkinson's disease in African ancestry populations, showing it disrupts splicing and reduces glucocerebrosidase activity.

Genetic regulation of TERT splicing contributes to reduced or elevated cancer risk by altering cellular longevity and replicative potential

This study identifies VNTR6-1 and rs10069690 as regulators of TERT splicing and expression, influencing cancer risk and telomere dynamics through altered telomerase isoform ratios.

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.

Assessing methylation detection for primary human tissue using Nanopore sequencing

This study compares 5mC detection accuracy between Nanopore R9 and R10 chemistries using human datasets, finding high concordance and strong correlation with Illumina bisulfite methods.

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.

Exploring the Genetic and Genomic Connection Underlying Neurodegeneration with Brain Iron Accumulation and the Risk for Parkinson's Disease

This study investigates the genetic and genomic links between NBIA and PD, finding no strong association and suggesting they may be distinct conditions.

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.

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

This paper develops a scalable protocol for Oxford Nanopore long-read sequencing, achieving high SNP and structural variant detection with haplotype-resolved methylation calls, suitable for large-scale genomics projects.

Identification and prediction of Parkinson's disease subtypes and progression using machine learning in two cohorts.

This study uses machine learning to identify Parkinson's disease subtypes and predict progression in two cohorts, finding three subtypes with distinct progression rates and high prediction accuracy.

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

Genome-wide contribution of common short-tandem repeats to Parkinson's disease genetic risk

This study identifies 34 genome-wide significant short-tandem repeat (STR) loci associated with Parkinson's disease risk and shows their functional impact on gene expression and disease pathways.

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.

REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats

REViewer visualizes sequencing data around long repeat expansions by reconstructing haplotypes and aligning reads, improving the assessment of repeat genotype calls and detecting interruptions.

Human-lineage-specific genomic elements: relevance to neurodegenerative disease and APOE transcript usage

The paper identifies human-lineage-specific genomic elements, called CNCRs, and shows their enrichment in neurological disease genes and APOE intron-3 retention transcripts in Alzheimer's disease.

The Parkinson's Disease GWAS Locus Browser

The paper presents a GWAS locus browser for Parkinson's disease that helps prioritize genes associated with risk variants from multiple GWAS studies.

Transcriptomic analysis of dystonia-associated genes reveals functional convergence within specific cell types and shared neurobiology with psychiatric disorders

This study identifies cell-type-specific expression of dystonia-associated genes and links them to shared genetic and biological mechanisms with psychiatric disorders.

Regulatory sites for known and novel splicing in human basal ganglia are enriched for disease-relevant information

The paper identifies disease-relevant regulatory loci in human basal ganglia using genomic and transcriptomic data from 117 brains, highlighting splicing eQTLs and ASE analyses as sources of cell-specific regulatory information.