Laksh Malik

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

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.

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

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

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

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

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.

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

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.

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.

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.

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.