Towfique Raj

The paper identifies structural variants in the human brain and their associations with molecular traits and neurodegenerative diseases.

The paper analyzes the transcriptome of human microglia across brain regions, aging, and disease to identify genetic effects on gene expression and splicing, linking them to neurological disorders.

The paper identifies dysregulated coordination of MAPT exon 2 and exon 10 splicing in Alzheimer's and progressive supranuclear palsy, leading to distinct tau isoform accumulation.

This study identifies JADE1 as a novel genetic factor in tauopathy through genome-wide association and functional validation in human and Drosophila models.

This study fine-maps Parkinson's disease susceptibility loci to identify putative causal variants and their mechanisms of action.

The paper identifies discordant mitochondrial gene expression patterns in PD monocytes and microglia, revealing distinct transcriptomic alterations in these myeloid cell types.

echolocatoR provides an automated pipeline for fine-mapping causal variants using summary statistics and integrates multiple functional genomic datasets.

The paper shows that ALS/FTD risk variants in UNC13A increase sensitivity to TDP-43 depletion by promoting cryptic exon inclusion and protein loss.

The paper identifies neurodegenerative disease-specific trans-eQTLs by analyzing gene expression in stimulated monocytes and macrophages using tensor decomposition.

The paper uses unsupervised machine learning to identify three molecular subtypes in ALS cortex samples, associated with oxidative stress, retrotransposon activation, and glial activation.

This study prioritizes Parkinson’s Disease genes using transcriptomic data, identifying 29 peripheral monocyte and 44 prefrontal cortex gene associations, including novel and known genes like MAPT.

The paper identifies 129 differentially expressed genes in the PFC of alcoholics and links them to pathways and modules associated with alcohol dependence and consumption.

The paper identifies brain-derived circulating cell-free DNA as a peripheral biomarker specific to cell-type and brain-region origins in neurotrauma and neurodegeneration.

The paper identifies genetic variants influencing isoform usage in the anti-viral response, revealing ERAP2's role in balancing selection and influenza-specific regulation.

This study identifies splicing variations in aging brains linked to Alzheimer’s Disease, finds genetic regulation of splicing, and highlights shared pathways with other neurodegenerative diseases.

RolyPoly links GWAS summary statistics with single-cell RNA-seq to identify trait-relevant cell types and genes, finding associations between microglia and Alzheimer's disease, and oligodendrocytes and schizophrenia.

This study identifies a haplotype lowering PU.1 expression in myeloid cells that delays Alzheimer’s disease onset by affecting gene expression and function.

The paper uses gene expression data from schizophrenia cases and controls to show that common variants at 20% of schizophrenia risk loci regulate brain gene expression, with functional impacts on neural progenitor cells and zebrafish neuroanatomy.