John F. Crary

Parkinson's disease genetic risk converges on Lewy body pathology-associated microglial states

The paper identifies microglial states associated with Parkinson's disease genetic risk and Lewy body pathology using single-cell profiling and integrates data with AMP PD.

Exploring transcriptomic and genomic latent variable correction approaches in differential expression analysis.

This paper evaluates combining expression-based surrogate variables and genotype-based principal components in differential expression analysis, finding the combined approach improves replicability and biological recall in ALS datasets.

Structural Compression and Entorhinal Vulnerability: Linking Tentorial Adjacency to Tau Burden and Dementia Progression

The paper links entorhinal cortex-tentorial proximity to tau burden and dementia progression using multimodal imaging data from ADNI.

Perfusion quality does not necessarily predict ultrastructural preservation after hyperosmotic brain perfusion

This paper shows that macroscopic and radiological perfusion metrics do not reliably predict ultrastructural preservation in brain tissue after hyperosmotic perfusion.

A canine brain bank for comparative neuroscience and brain aging research

The paper describes methods for establishing a canine brain bank and presents preliminary findings on brain aging using lipofuscin burden analysis.

Aldehyde-based cryopreservation of whole brains

This paper presents a protocol for preserving fixed whole brains using aldehyde-based cryopreservation, showing preserved cellular architecture after long-term storage.

Endothelial type I interferon signaling modulates the vascular response to ischemic brain injury

This study identifies endothelial type I interferon signaling as a regulator of vascular normalization after ischemic brain injury, showing it reduces BBB disruption and promotes junctional stability.

A study of gene expression in the living human brain

This study compares gene expression in living and postmortem human brain tissue, finding significant differences that challenge the assumption that postmortem data accurately represents living brain gene expression.

Evaluating ultrastructural preservation quality in banked brain tissue

The paper evaluates ultrastructural preservation quality in postmortem brain tissue using EM and light microscopy to identify artifacts and assess their impact on research applications.

Single-cell transcriptomic and neuropathologic analysis reveals dysregulation of the integrated stress response in progressive supranuclear palsy

The paper uses single-nucleus RNA sequencing to analyze PSP brains and identifies dysregulation of the integrated stress response in vulnerable cell types.

Incorporating FDR into the assessment of nanopore sequencing for the reliable detection of DNA modifications in real applications

This paper introduces modFDR, a framework to assess nanopore sequencing for DNA modification detection, showing it reliably detects abundant modifications but has high false positives for rare ones.

Genetic, transcriptomic, histological, and biochemical analysis of progressive supranuclear palsy implicates glial activation and novel risk genes

This study identifies six genetic loci associated with progressive supranuclear palsy, including a novel locus, and links them to oligodendrocytic dysfunction and C4A expression.

Whole-Genome Sequencing Analysis Reveals New Susceptibility Loci and Structural Variants Associated with Progressive Supranuclear Palsy

This study uses whole-genome sequencing to identify new genetic loci and structural variants associated with progressive supranuclear palsy, including novel signals in APOE and H1/H2 haplotype region variants.

Proteomic profiling of intracranial atherosclerotic plaque in the human brain

This study uses proteomic profiling of intracranial atherosclerotic plaques to identify differentially expressed proteins associated with ICAD, revealing potential biomarkers and biological pathways involved in the disease.

Disruption of lysosomal proteolysis in astrocytes facilitates midbrain proteostasis failure in an early-onset PD model.

This study shows that impaired lysosomal proteolysis in astrocytes leads to proteostasis failure in midbrain neurons in an early-onset PD model.

Transcriptome deregulation of peripheral monocytes in GBA-related Parkinson's disease

The paper identifies transcriptomic changes in monocytes from GBA mutation carriers with Parkinson's disease, highlighting dysregulated pathways related to alpha-synuclein degradation and lysosomal function.

17q21.31 sub-haplotypes underlying H1-associated risk for Parkinsons disease are associated with LRRC37A/2 expression in astrocytes

The paper identifies three H1 sub-haplotypes at the 17q21.31 locus associated with Parkinson's disease risk and links them to LRRC37A/2 expression in astrocytes.

A single closed head injury in mice induces chronic, progressive white matter atrophy and increased phospho-tau expressing oligodendrocytes

This study shows that a single closed head injury in mice causes chronic white matter atrophy and increased phospho-tau in oligodendrocytes, differing from chronic traumatic encephalopathy from repeated injuries.

Cell environment shapes TDP-43 function: implications in neuronal and muscle disease

The paper compares TDP-43's transcriptional and splicing effects in muscle and neuronal cells, showing tissue-specific roles in disease.

Single-cell Transcriptomic Atlas of the Human Substantia Nigra in Parkinson's Disease

This study generates a large single-cell RNA sequencing dataset of the human substantia nigra in Parkinson's disease, identifies DA neuron subtypes, and reveals molecular changes associated with PD.

The impact of genomic structural variation on the transcriptome, chromatin, and proteome in the human brain

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

Dysregulated coordination of MAPT exon 2 and exon 10 splicing underlies different tau pathologies in PSP and AD

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.

Genome-wide association study and functional validation implicates JADE1 in tauopathy

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

Discordant transcriptional signatures of mitochondrial genes in Parkinson's disease human myeloid cells

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

Single-cell atlas of progressive supranuclear palsy reveals a distinct hybrid glial cell population

The paper analyzes single-cell transcriptomic data from PSP brains to identify hybrid glial cell populations and their role in disease progression.

Glutamatergic dysfunction precedes neuron loss in cerebral organoids with MAPT mutation.

This study shows that glutamatergic dysfunction occurs before neuron loss in cerebral organoids with MAPT mutations, suggesting therapeutic targets for FTD.

The landscape of human brain immune response in patients with severe COVID-19

The paper analyzes single-nucleus transcriptomes from brain regions of COVID-19 patients to show increased neuroinflammation and microglial transcriptome changes, without evidence of viral brain tropism.

Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia

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