Mark Cookson

The paper generates isogenic iPSC lines with CAG repeats and HTT KO for Huntington's disease study, showing differentiation potential and altered gene expression in neurons and astrocytes.

This study profiles proteomic changes in iPSC-derived neurons exposed to Aβ42A, revealing AD-related pathways and validating findings in postmortem AD brain tissue.

ProtPipe2 provides a unified framework for downstream proteomics analysis across mass spectrometry, Olink, and SomaScan platforms, enabling consistent workflows and reusable analyses.

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

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

This study shows APOE genotypes alter astrocytic lipid droplet proteomes and dynamics, with APOE4 showing resistance to lipophagy, suggesting impaired clearance as a mechanism for AD risk.

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

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.

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.

This study shows that DJ-1 deficiency impairs autophagosome-lysosome fusion and lysosomal degradation, leading to autophagic substrate accumulation through ROS-dependent modulation of the AMPK/mTORC1 axis in Parkinson's disease.

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

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

This study investigates the role of SORL1 genetic variants in AD, RD, and PD across diverse populations, identifying variants associated with risk but no significant cumulative effect.

This paper presents a xeno-free protocol to rapidly differentiate human iPSCs into microglia using the KOLF2.1J line, resulting in functional microglia with immune markers and phagocytic activity.

The paper uses single-cell RNA sequencing to assess the impact of Lrrk2 mutations on neuroinflammation in mice, finding limited transcriptional effects.

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

MoVUS, a random forest model, classifies variants of uncertain significance in Alzheimer's and neurological disorders with high accuracy, prioritizing potentially pathogenic variants.

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

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

This study shows the PD-risk GBA1 variant E326K reduces lysosomal GCase activity by disrupting LIMP2 interaction and causes lysosomal and mitochondrial dysfunction.

The paper identifies JIP4 and RILPL1 as opposing motor adaptors regulating lysosomal tubulation through differential microtubule transport.

The paper presents the cryo-EM structure of the LRRK2:14-3-32 complex, showing how 14-3-3 binding inhibits LRRK2 activity and how PD mutations disrupt this interaction.

This study shows that triglyceride metabolism is essential for microglial activation and disease states in APOE4 microglia, with implications for modulating immune responses.

This study identifies sex-biased gene expression patterns across multiple cortical regions and cell types in the human brain using single-cell transcriptomics.

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.

This study identifies cell-type-specific RNA isoform changes in aging mouse brain using single-cell and long-read sequencing, revealing altered coding potential and senescence markers in immune cells.

This paper develops 3D brain organoids with endothelial and neural cells using sequential differentiation of iPSC-derived embryoid bodies, showing enhanced angiogenesis and SARS-CoV-2 receptor expression.

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

The paper profiles HLA immunopeptidomes and interactomes in microglia, identifying disease-associated epitopes and their interactions.