Christopher Dirk Keene

This study uses single-nucleus RNA-seq, ATAC-seq, and Multiome to analyze Alzheimer's disease across multiple brain regions, revealing shared and region-specific cellular vulnerabilities.

This paper performs a large-scale GWAS meta-analysis of neuropathologic lesions in Alzheimer's disease and related dementias, identifying both known and novel genetic associations.

The paper introduces MOSAIC, a multimodal adaptive optical microscope that enables non-invasive imaging across biological scales in live specimens.

This study uses somatic mutations to track marrow-derived cell infiltration into the human brain, finding widespread microglia replenishment and a protective link between clonal hematopoiesis and Alzheimer's disease.

The paper introduces a pipeline to create 3D spatial atlases for brain tissue samples, enabling standardized referencing and integration across biorepositories and neuroimaging data.

The paper uses multiomic single-cell and spatial data to identify gene regulatory networks and transcription factors driving cortical regionality in the human brain.

This paper presents a single-cell multiome atlas of the human basal ganglia, linking chromatin states and transcriptomes to cell-type identity and disease-associated variants.

The paper maps AD-related pathological changes in the caudate nucleus at cellular resolution, identifying distinct features and cell type-specific responses.

This study creates a multi-modal atlas of choroid plexus pathology across aging and Alzheimer's disease, identifying fibrosis, calcification, and macrophage abnormalities as key features.

The paper describes a multi-institutional program for collecting neurotypical human brains to support multiomic brain cell atlas studies, highlighting challenges and opportunities for donor recruitment.

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

This study identifies sex-specific gene expression associations with Alzheimer's disease neuropathology and cognitive decline using single-nucleus RNA sequencing from human brain tissue.

This paper creates a cross-species spatial transcriptomic atlas of the basal ganglia in human, rhesus macaque, and common marmoset, revealing conserved molecular organization and cell type-specific compartments.

The paper presents a spatial multi-omics workflow for Alzheimer's neuropathology, resolving spatially distinct molecular domains and establishing analytical guidelines.

The paper shows that Huntingtin (HTT) helps maintain mitochondrial DNA integrity by organizing a repair complex, which is disrupted by mutant HTT in Huntington's disease, leading to DNA damage and motor deficits in a fly model.

The paper identifies sex-specific genetic loci associated with memory, executive functioning, and language performance in older adults through genome-wide meta-analyses.

This study identifies genetic risk factors for FTLD-TDP subtypes using whole-genome sequencing and meta-analysis across multiple cohorts.

This study examines the association between APOE genotype and cognitive resilience in SuperAgers, finding lower APOE-ε4 and higher APOE-ε2 frequencies in non-Hispanic White SuperAgers compared to controls and Alzheimer's cases.

This study shows that AQP4 mis-localization impairs glymphatic clearance of α-synuclein and promotes its aggregation and spread in neurodegenerative diseases.

This study uses MD-MRI to map cortical astrogliosis and distinguishes cognitive resilience from dementia in Alzheimer's disease despite significant neuropathology.

The paper introduces DART-FISH, a multiplexed RNA in situ hybridization technique for high-resolution profiling of human tissues, demonstrating its application on brain and kidney samples.

The paper develops open-source tools for 3D analysis of brain dissection photographs and surface scans, achieving accurate reconstructions and segmentations comparable to MRI.

The paper uses single nucleus RNA-sequencing to analyze human cortical areas, revealing cell type proportions and gene expression patterns that correlate with functional connectivity and areal specialization.

The paper identifies transcriptomic and morpho-electric diversity in human neocortical layer 1 interneurons, revealing greater subclass distinction compared to mouse.

The paper constructs a single-cell chromatin accessibility atlas of the human brain, identifies cell-type-specific regulatory elements, and develops models to predict regulatory function of disease risk variants.

This study uses single nucleus transcriptomics to compare human and non-human primate cortical tissues, identifying human-specific gene expression patterns and their potential functional roles.

This study identifies 461 cell clusters and 3313 subclusters in the adult human brain using single-nucleus RNA sequencing, revealing regional diversity in neurons and astrocytes.

The paper uses viral labeling and Patch-seq to define morpho-electric properties of GABAergic interneurons in human neocortex, revealing functional insights and reclassifying some SST neurons into PVALB subclass.

The paper identifies transcriptomically distinct microglia populations in Alzheimer's disease and aged human brains using single-nucleus RNA-seq and trajectory inference.

The paper presents a high-quality quantitative proteomics dataset for Alzheimer's disease, including samples from different brain regions and clinical groups.