Jesse Raphael Gibbs

Integration of cell-specific gene expression and chromatin accessibility facilitates localization of neurodegenerative risk in microglia

The paper integrates cell-specific gene expression and chromatin accessibility to identify neurodegenerative disease risk loci specific to microglia.

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.

Semi-automated annotation refinement accelerates cell type identification in brain spatial and single-cell studies

SAHA provides a statistical framework for rapid cell type annotation by transferring labels from reference datasets to query datasets without integration.

Age-related erosion of X chromosome inactivation in human tissues

The paper investigates age-related X chromosome inactivation (XCI) erosion in human females using bulk and single-cell datasets, finding age-dependent escape from XCI in specific genes.

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.

Region-Specific Transcriptional Signatures of Brain Aging in the Absence of Neuropathology at the Single-cell Level

This study uses snRNA-seq to analyze age-related transcriptional changes in four brain regions across young and aged individuals, identifying region-specific age-associated genes and biological processes.

Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD- associated kinase LRRK2 between human and mice

The paper shows that inflammatory signaling affects LRRK2 regulation differently in human and mouse models, highlighting species-specific regulatory mechanisms.

Trans-eQTLs reveal the architecture of human gene regulatory networks

The paper maps cis- and trans-eQTLs in blood samples to infer gene regulatory networks and prioritize trait-relevant pathways.

Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus

The paper identifies USP18 as a negative regulator of interferon response at a lupus risk locus through trans-eQTL analysis in lymphoblastoid cell lines.

Integrative analysis reveals generalizable human neurodegenerative disease-associated glial states

This study identifies generalizable glial states across multiple neurodegenerative diseases using integrative single-cell transcriptomic analysis of multi-region atlases.

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.

Characterization of DNA methylation in PBMCs and donor-matched iPSCs shows methylation is reset during stem cell reprogramming

The paper shows that DNA methylation is reset in iPSCs compared to donor PBMCs, with unique methylation sites influenced by genetics in each cell type.

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.

Imaging spatial transcriptomics reveals molecular patterns of vulnerability to pathology in a transgenic α-synucleinopathy model

The paper uses imaging spatial transcriptomics to identify neuronal subtypes vulnerable to -synuclein pathology in a transgenic mouse model and finds Plk2 and hSNCA expression are key to pathology development.

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.

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.

Association of a common genetic variant with Parkinson's disease is propagated through microglia

The paper shows that a non-coding genetic variant affects LRRK2 expression specifically through microglia, highlighting the importance of cell type in understanding non-coding variation's role in Parkinson's disease.

Investigation of Autosomal Genetic Sex Differences in Parkinsons disease

This study investigates sex-specific genetic factors in Parkinson's disease using GWAS but finds no significant genetic differences between male and female cases.

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 DNA Variant Browser

The paper introduces a web browser for Parkinson's disease genomic data, aggregating results from 102,127 participants to aid in identifying risk genes and variants.

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.

Replication assessment of NUS1 variants in Parkinson's Disease

The paper assesses the association of NUS1 variants with Parkinson's Disease in European descent cohorts and finds no evidence of a link, suggesting previous findings may be due to population-specific variants.

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.

Mutations in the SPTLC1 gene are a cause of juvenile amyotrophic lateral sclerosis that may be amenable to serine supplementation

The paper identifies de-novo SPTLC1 mutations in juvenile ALS patients and suggests serine supplementation may alleviate symptoms.

Large-scale pathway-specific polygenic risk, transcriptomic community networks and functional inferences in Parkinson disease

The paper identifies pathway-specific polygenic risk factors and transcriptomic networks associated with Parkinson disease using large-scale genetic and expression data.

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.

Common variation at the LRRK2 locus is associated with survival in the primary tauopathy progressive supranuclear palsy

The paper identifies common LRRK2 locus variation associated with survival in progressive supranuclear palsy, linking it to gene expression regulation and suggesting therapeutic implications for tauopathies.

Penetrance of Parkinson’s disease in LRRK2 p.G2019S carriers is modified by a polygenic risk score

This study shows that a polygenic risk score increases the likelihood of Parkinson's disease in LRRK2 p.G2019S carriers, with stronger effects in younger individuals.