Vilas Menon

brisc: a multithreaded CPU toolkit for single-cell analysis

brisc is a multithreaded CPU toolkit for single-cell analysis that is faster and more reproducible than existing tools like Scanpy and Seurat.

Disrupted glial-mediated synaptic refinement in Fragile X syndrome

This study identifies impaired glial-mediated synaptic refinement in FXS model mice, showing enhanced astrocyte-microglia signaling and synaptic over-engulfment as key features.

Dissecting cellular and molecular networks of aging and senescence in the human hippocampus

This study identifies spatially resolved aging and senescence signatures in the human hippocampus using multi-omics approaches, revealing cell-type and sex-specific gene expression changes.

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.

Integrating dorsolateral prefrontal cortex multi-omics and GWAS summary data enhances gene-mapping of Parkinson's disease

This study integrates multi-omics data from DLPFC with GWAS summary data to identify PD risk genes, finding significant overlaps between bulk and cell-type-aware TWAS and PWAS results.

Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights

A free Meta Quest virtual reality app harmonizes CODEX, Visium, Xenium, volumetric immunofluorescence and electron microscopy data from 5 organs into 4 scale levels using the Human Reference Atlas.

High-Dimensional Multi-omic Mapping of Post-Mortem Human Brain Using Iterative Indirect Immunofluorescence Imaging on Xenium-Processed Tissues

The paper develops a post-processing workflow combining Xenium spatial technology with 4i imaging to enable multi-omic mapping of post-mortem human brain tissue, focusing on pathological microenvironments.

Altered microglial communication in brains with Alzheimers Disease pathology

The paper analyzes microglial communication in Alzheimer's disease using single-nucleus RNA sequencing to identify altered signaling pathways and cell interactions associated with disease pathology.

Modulating the Novel miR-23b-Wnt/β-catenin Axis Strengthens Endothelial Barrier Properties

This study identifies miR-23b as a negative regulator of BBB integrity and shows that anti-miR-23b enhances barrier function through multiple signaling pathways and improves outcomes in a stroke model.

A p53-ΔNp73 signaling axis drives selective motor neuron degeneration in spinal muscular atrophy

This study identifies a p53-ΔNp73 signaling axis that drives motor neuron degeneration in SMA, revealing a context-dependent switch in p53 family signaling that promotes neurodegeneration.

Brain shuttle target expression levels vary by individual, not by brain region, disease, age, or sex

The paper shows brain shuttle target expression varies between individuals but not by brain region, disease, age, or sex.

Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity

This study integrates multi-omics data from aged human brains to identify cross-system biological factors and molecular subtypes associated with Alzheimer's disease heterogeneity.

Single-cell Transcriptomic Variance Analysis Reveals Intercellular Circadian Desynchrony in the Alzheimer's Affected Human Brain

The paper introduces ORPHEUS, a method to quantify circadian desynchrony in single-cell data, finding reduced synchrony in AD-affected human brain excitatory neurons.

Electrophysiologically Targeted Biopsies Reveal the Transcriptional Landscape of Focal Epilepsy

This study uses electrophysiologically guided biopsies and single-nucleus RNA sequencing to identify transcriptional differences between seizure focus and ictal penumbra in focal epilepsy.

HEXIM1/P-TEFb complex controls RNA polymerase II pause release and immediate early gene induction following neuronal depolarization

This study investigates the role of the HEXIM1/P-TEFb complex in regulating RNA polymerase II pause release and immediate early gene induction in neurons during depolarization.

Th17 effector cytokines induce shared and distinct microglial and endothelial cell responses in post-streptococcal encephalitis

This study identifies IL-17A-IL-17RA signaling in microglia as a critical driver of BBB dysfunction after GAS infections using single-cell RNA sequencing and spatial transcriptomics.

Ontogeny of the spinal cord dorsal horn

This paper investigates how the dorsal horn of the spinal cord develops, showing that neurons are diversified by time and spatial-molecular gradients, leading to the formation of laminae.

Post-translational modifications in the brain are critical contributors to Alzheimers disease neuropathology and cognitive decline

This study identifies novel post-translational modifications in Alzheimer's disease brains linked to neuropathology and cognition using mass spectrometry data from 101 participants.

Single Cell Landscape of Sex-specific Drivers of Alzheimers Disease

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.

Gene module-trait network analysis uncovers cell type specific systems and genes relevant to Alzheimers Disease

The paper identifies cell type-specific gene modules associated with Alzheimer's Disease traits using snRNASeq data from human brain tissues.

Cytokine expression profile in the human brain of older adults

This study examines cytokine gene expression in human brain tissue from elderly individuals with and without Alzheimer's disease to identify biomarkers and understand disease mechanisms.

Reconstructed Cell-Type Specific Rhythms in Human Brain link Alzheimer's Pathology, Circadian Stress, and Ribosomal Disruption

The paper estimates circadian phases in human brain cells using single-nucleus RNA sequencing and finds disrupted ribosomal rhythms in Alzheimer's patients.

Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord

The paper identifies microglia subsets in ALS brain and spinal cord, finding an undifferentiated phenotype and enrichment of interferon response microglia in aggressive cases.

Early neuronal reprogramming and cell cycle reentry shape Alzheimer's disease progression

The paper identifies early transcriptional changes in neuronal subtypes in Alzheimer's disease using single-nucleus RNA data, revealing distinct programs linked to vulnerability and resilience.

Cell-type-specific Transcriptomic-wide Association Studies Detected 91 Independent Risk Genes for Alzheimer's Disease Dementia

The paper uses an omnibus xWAS pipeline to integrate snRNA-seq and GWAS data, identifying 91 independent cell-type-specific risk genes for Alzheimer's disease dementia.

Corticothalamic Neurons in Motor Cortex Have a Permissive Role in Motor Execution

The paper identifies corticothalamic neurons in the motor cortex as having a permissive role in motor execution by suppressing inhibition of corticospinal neurons during movement.

Brain Multi-Omic Subtypes of Neuroticism Reveal Molecular Signatures linked to Alzheimer's Disease

The paper identifies three brain multi-omic molecular subtypes of neuroticism linked to Alzheimer's disease traits, with subtype N1 showing the strongest associations.

The Role of Alpha Synuclein in Synucleinopathy: Impact on Lipid Regulation at Mitochondria ER Membranes

This paper investigates the role of alpha-synuclein in lipid regulation at MAM domains in synucleinopathies, showing disease-specific lipid alterations and Syn's impact on phosphatidylserine metabolism.

Cell type-specific associations with Alzheimer's Disease conserved across racial and ethnic groups

The paper identifies cell-type-specific and continuous gene programs associated with Alzheimer's Disease across multiple racial and ethnic groups using single-nucleus RNA-seq and ATAC-seq.

A factor-based analysis of individual human microglia uncovers regulators of an Alzheimer-related transcriptional signature

The paper uses single-cell data to identify factors regulating an Alzheimer's disease-related microglial signature and proposes a new analytic framework for microglial classification.