Kensuke Daida

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.

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.

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.

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.

Complementarity of long-read sequencing and optical genome mapping in Parkinson's disease

This study compares long-read sequencing and optical genome mapping in detecting structural variants in Parkinson's disease, finding OGM better detects large variants while ONT provides high-resolution refinement.

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.

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.

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.