SEA-AD Impact

Browse a comprehensive list of studies citing SEA-AD publications or data, illustrating SEA-AD's research community impact

2026

2025

2024

2023

2026

Title

Author

Year

Source

Type

CSF proteomics of semorinemab Alzheimer’s disease trials identifies cell-type specific signatures

Abdel-Haleem et al

2026

Brain

Journal article

Somatostatin interneurons and the pathogenesis of Alzheimer’s disease

Almeida et al

2026

Neural Regeneration Research

Journal article

LRP4+ Astrocytes: A Unique Subpopulation Crucial for Blood Vessel Maintenance and Function in the Somatosensory Cortex of Normal and 5xFAD Mice

Arzola et al

2026

Glia

Journal article

Pharmacologic reversal of advanced Alzheimer’s disease in mice and identification of potential therapeutic nodes in human brain

Chaubey et al

2026

Cell Reports Medicine

Journal article

NRF2 activation by CDDO-Im regulates inflammatory and autophagy pathways in human microglial cells

Chu et al

2026

Free Radical Biology and Medicine

Journal article

Human Neocortical Glutamatergic Neurons Revealed Through Multimodal Profiling

Dalley et al

2026

‍

Preprint

Stack: In-Context Learning of Single-Cell Biology

Dong et al

2026

‍

Preprint

Brain Region-Specific Oligodendrocyte States Highlight Mitochondrial Gene Upregulation and Loss of Canonical Identity Signatures in Alzheimer’s Disease

Drummer et al

2026

‍

Preprint

OMG! A proteomic determinant of neurodegenerative resiliency

Duggan et al

2026

Molecular Neurodegeneration

Journal article

The Caudate Nucleus Exhibits Distinct Pathology and Cell Type-Specific Responses Across Alzheimer’s Disease

Kana et al

2026

‍

Preprint

SCALPEL: A pipeline for processing large-scale spatial transcriptomics data

Kunst et al

2026

‍

Preprint

Mapping multipathology via spatial omic integration

Palaganas et al

2026

Current Opinion in Biotechnology

Journal article

Factorization of Alzheimer’s disease genetic risk influences allow patient stratification, predicting disease onset, cognitive decline, and cell-type specific responses

Pelletier et al

2026

‍

Preprint

Neuronal subtype governs amyloid structure, cellular response, and cognitive outcome in genetically targeted APP mouse models

Perez et al

2026

Molecular Neurodegeneration

Journal article

Spatial transcriptomics in epilepsy research: Early successes, opportunities, and challenges

Phillips et al

2026

Epilepsia

Journal article

Semaglutide Attenuates Neuroinflammation in Mice

Rausch et al

2026

‍

Preprint

Cell type-specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease

Ren et al

2026

Genome Research

Journal article

Reply to: a quantitative trait locus for reduced microglial APOE expression associates with reduced cerebral amyloid angiopathy

Schade et al

2026

Nature Genetics

Journal article

Uncovering the signatures of aging and senescence in the human dorsolateral prefrontal cortex

Sloan et al

2026

Cell Genomics

Journal article

Transcriptomic Divergence Between Prefrontal Cortex and Limbic Circuits in Human Aging

Somkin et al

2026

‍

Preprint

From genes to lifestyle: A multi-dimensional framework for Alzheimer’s disease prevention and therapy

Su et al

2026

Ageing Research Reviews

Journal article

Exploring phenotype-related single-cells through attention-enhanced representation learning

Wu et al

2026

Genome Medicine

Journal article

Natural glycosides as multi-target neuroprotective agents in Alzheimer’s disease: Bridging mechanistic insights and translational potential

Zhou et al

2026

Phytomedicine

Journal article

Dysregulated RNA G-quadruplex binding proteins reveal shifted stress responses in Alzheimer’s Disease

Zhou et al

2026

‍

Preprint

2025

Title

Author

Year

Source

Type

Inhibition of Bone Morphogenetic Protein Signaling Prevents Tau Pathology in iPSC Derived Neurons and PS19 Mice

Affaneh et al

2025

Annals of Neurology

Journal article

AutoDiscovery: Open-ended Scientific Discovery via Bayesian Surprise

Agarwal et a

2025

‍

Preprint

Explainable Gated Recurrent Unit with Hybrid Attention and Memory-Augmented Network for Cell Types Classification in Alzheimer’s Disease Using Single-Nucleus Transcriptomics

Ahammad et al

2025

Brain Informatics

Book section

Popari: Modeling multisample variation in spatial transcriptomics

Alam et al

2025

‍

Preprint

Microglial response to amyloid-β pathology is modulated by X chromosome dosage

Arancibia-Carcamo et al

2025

‍

Preprint

An integrated view of the relationships between amyloid, tau, and inflammatory pathophysiology in Alzheimer's disease

Arnsten et al

2025

Alzheimer's & Dementia

Journal article

Dysregulated calcium signaling in the aged primate association cortices: vulnerability to Alzheimer’s disease neuropathology

Arnsten et al

2025

Frontiers in Aging Neuroscience

Journal article

scConcept: Contrastive pretraining for technology-agnostic single-cell representations beyond reconstruction

Bahrami et al

2025

‍

Preprint

Amyloid-β Dysregulates Oligodendroglial Lineage Cell Dynamics and Myelination via PKC in the Zebrafish Spinal Cord

Balantzategi et al

2025

Glia

Journal article

PKC-dependent MYRF dysregulation links Aβ pathology to oligodendrocyte, myelin and cognitive alterations in Alzheimer’s disease

Balantzategi et al

2025

‍

Preprint

Analysis of changes in intercellular communications in Alzheimer’s disease reveals conserved changes in glutamatergic transmission in mice and humans

Bartas et al

2025

Scientific Reports

Journal article

Multi-region spatial transcriptomics reveals region specific differences in response to amyloid beta (Aβ) plaque induced changes in Alzheimer’s disease (AD)

Bayaraa et al

2025

Human Genomics

Journal article

A neuroimmune cerebral assembloid model to study the pathophysiology of familial Alzheimer’s disease

Becerra-Calixto et al

2025

Journal of Neuroinflammation

Journal article

A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

Ben-Simon et al

2025

Cell

Journal article

Human stem cell-derived GABAergic interneuron development reveals early emergence of subtype diversity and gradual electrochemical maturation

Bershteyn et al

2025

Neuron

Journal article

Deep learning-based cell type profiles reveal signatures of Alzheimer’s disease resilience and resistance

Berson et al

2025

Brain

Journal article

Cell type transcriptomics reveal shared genetic mechanisms in Alzheimer’s and Parkinson’s disease

Bhattacharya et al

2025

‍

Preprint

Kat5 cKO Biological Domain Signatures Align with Human Alzheimer’s Disease

Cary et al

2025

‍

Preprint

Mapping cross-domain drivers of Alzheimer’s disease risk through integrated network analysis

Cary et al

2025

‍

Preprint

A Single-Cell Omics Technical Guide for Advancing Neuropsychiatric Research

Casmey et al

2025

Genes

Journal article

Molecular hallmarks of excitatory and inhibitory neuronal resilience to Alzheimer’s disease

Castanho et al

2025

Molecular Neurodegeneration

Journal article

Refining the interactions between microglia and astrocytes in Alzheimer’s disease pathology

Chen et al

2025

Neuroscience

Journal article

Interneuron transcriptomics reveals pathologic markers of Alzheimer's disease progression

Chen et al

2025

Neurobiology of Disease

Journal article

Hyperactivity of subicular parvalbumin interneurons drives early amyloid pathology and cognitive deficits in Alzheimer’s disease

Chen et al

2025

Molecular Psychiatry

Journal article

Systematic characterization of cell type-specific master metabolic regulators in Alzheimer's disease

Cheng et al

2025

‍

Preprint

Functional insight into East Asian–specific genetic risk loci for Alzheimer's disease

Cho et al

2025

Alzheimer's & Dementia

Journal article

Cooperative multi-view integration with a scalable and interpretable model explainer

Choi et al

2025

Nature Machine Intelligence

Journal article

CoTF-reg reveals cooperative transcription factors in oligodendrocyte gene regulation using single-cell multi-omics

Choi et al

2025

Communications Biology

Journal article

MicroRNA cargo in neuron-derived vesicles as peripheral biomarkers of brain insulin dysregulation

Cleary et al

2025

Alzheimer's & Dementia

Journal article

The Energetic Collapse of the Alzheimer's Brain: Metabolic Inflexibility Across Cells and Networks

Constantino et al

2025

Journal of Neurochemistry

Journal article

Systematic analysis of cellular cross-talk reveals a role for SEMA6D-TREM2 regulating microglial function in Alzheimer’s disease

D’Oliveira Albanus et al

2025

Science Translational Medicine

Journal article

Bridging BioSciences and technology: The impact of AI & GenAI in life sciences and agribusiness

Da Cunha et al

2025

Gene

Journal article

Novel Pathological Mechanisms Revealed by Spatial Transcriptomic Analysis of Hippocampus in Aged Control, Primary Age-Related Tauopathy, and Alzheimer's Disease

Deng et al

2025

Research Square

Journal article

Cytoplasmic dynamics are overlooked in single nuclei RNA-seq but can be rescued by CytoRescue, a generative AI model to recover cytoplasm enriched gene

Deng et al

2025

‍

Preprint

Benchmarking and optimizing organism wide single-cell RNA alignment methods

Diaz-Mejia et al

2025

‍

Preprint

Understanding and Enhancing Mask-Based Pretraining towards Universal Representations

Dong et al

2025

‍

Preprint

Causal differential expression analysis under unmeasured confounders with causarray

Du et al

2025

‍

Preprint

Multimodal analysis identifies pericyte-centered signaling programs altered by sex and brain region in Alzheimer’s Disease

El-Ghazawi et al

2025

‍

Preprint

Layer-Specific Colocalization of Microglia with Amyloid Plaques in the Middle Temporal Gyrus Predicts Cognitive Decline in Alzheimer's Disease

Escariao et al

2025

Aging and Disease

Journal article

Inhibition of CGRP receptor ameliorates AD pathology by reprogramming lipid metabolism through HDAC11/LXRβ/ABCA1 signaling

Fan et al

2025

‍

Preprint

CIA: unveiling cellular identities with cluster-independent annotation in single-cell RNA sequencing data for comprehensive cell type characterization and exploration

Ferrari et al

2025

BMC bioinformatics

Journal article

Celebrating neuropathology's contributions to Alzheimer's Disease Research Centers

Fischer et al

2025

Alzheimer's & Dementia

Journal article

ROSMAP-Compass: A data-harmonised, AI-ready atlas of 22 million single nuclei from the ROSMAP cohort

Flotho et al

2025

‍

Preprint

Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer’s disease

Flotho et al

2025

‍

Preprint

Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution

Fullard et al

2025

Scientific Data

Journal article

Regulation of input excitability in human and mouse parvalbumin interneurons by Kir potassium channels

Furdan et al

2025

‍

Preprint

Disruption of hnRNP A2-mediated RNA dynamics by amyloid-β drives MBP increase in Alzheimer’s disease

Gaminde-Blasco et al

2025

Cellular and Molecular Life Sciences

Journal article

Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals key associations with AD pathology

Gaur et al

2025

Nature Communications

Journal article

Neuroimmune Dysregulation and AI-Driven Therapeutic Strategies in Alzheimer’s Disease

Ghosh et al

2025

Cellular and Molecular Neurobiology

Journal article

Integrating Brain Metabolism Research into Big Data Human Neuroscience

Goyal et al

2025

Metabolic Neuropsychiatry

Book section

Single-cell Spatial Transcriptomics Reveals Disease-specific Microenvironmental Niches in Neurodegeneration and COVID-19

Graf et ak

2025

‍

Preprint

A single-cell atlas to map sex-specific gene-expression changes in blood upon neurodegeneration

Grandke et al

2025

Nature Communications

Journal article

DeepDynamics resolves cell-subtype and clinicopathological dynamics from bulk RNA-seq to identify mediators of Alzheimer’s disease risk

Haddad et al

2025

‍

Preprint

Single-nucleus epigenomic dysregulation unmasks genetic risk-associated neurodegenerative glia states

Han et al

2025

‍

Preprint

Simultaneous analysis of single-cell gene expression and morphology provides new insight into how microglia change with age

Henze et al

2025

‍

Preprint

Integrative analysis reveals generalizable human neurodegenerative disease-associated glial states

Horan-Portelance et al

2025

‍

Preprint

Predicting emergent phenotypes from single cell populations using CELLECTION

Hu et al

2025

‍

Preprint

scBIT: Integrating Single-cell Transcriptomic Data into fMRI-based Prediction for Alzheimer's Disease Diagnosis

Huang et al

2025

‍

Preprint

Computational whole-body-exposome models for global precision brain health

Ibáñez et al

2025

Nature Communications

Journal article

SingleBrain: A Meta-Analysis of Single-Nucleus eQTLs Linking Genetic Risk to Brain Disorders

Jang et al

2025

‍

Preprint

Neuronal subtype-specific metabolic changes in neurodegenerative and neuropsychiatric diseases predicted via a systems biology-based approach

Jiang et al

2025

‍

Preprint

Reconstructing developmental and disease progression with sample-level embeddings

Jiang et al

2025

‍

Preprint

Single-Cell Multi-Modal Differential Analysis of the Human Neo-Cortex in HIV Infection Reveals Similarities with Hallmarks of Alzheimer’s Disease

Joshi et al

2025

‍

Preprint

Comprehensive molecular characterization of craniopharyngiomas using whole transcriptome and spatial transcriptomics approaches

Kert et al

2025

Brain Tumor Pathology

Journal article

Whole-genome sequencing analyses suggest novel genetic factors associated with Alzheimer’s disease and a cumulative effects model for risk liability

Kim et al

2025

Nature Communications

Journal article

The DREAM complex links somatic mutation, lifespan, and disease

Koch et al

2025

‍

Preprint

Multiomic analyses direct hypotheses for Creutzfeldt-Jakob disease risk genes

Küçükali et al

2025

Brain

Journal article

Spatial-Omics Methods and Applications

Kulasinghe et al

2025

Methods in Molecular Biology

Journal article

Cell-weighted polygenic risk scores are associated with β-amyloid and tau biomarkers in Alzheimer’s disease

Kumar et al

2025

Brain Communications

Journal article

Single-Cell Cortical Transcriptomics Reveals Common and Distinct Changes in Cell-Cell Communication in Alzheimer’s and Parkinson’s Disease

Le Bars et al

2025

Molecular Neurobiology

Journal article

Neuroferroptosis in health and diseases

Lei et al

2025

Nature Reviews Neuroscience

Journal article

Microglial States Are Susceptible to Senescence and Cholesterol Dysregulation in Alzheimer's Disease

Li et al

2025

Aging Cell

Journal article

Integrated multi-omics analysis identifies potential therapeutic targets for Alzheimer’s disease

Li et al

2025

Neural Regeneration Research

Journal article

Targeting ceramide-induced microglial pyroptosis: Icariin is a promising therapy for Alzheimer's disease

Li et al

2025

Journal of Pharmaceutical Analysis

Journal article

Transcript-guided targeted cell enrichment for scalable single-nucleus RNA sequencing

Liao et al

2025

Cell Genomics

Journal article

EnrichSci: Transcript-guided Targeted Cell Enrichment for Scalable Single-Cell RNA Sequencing

Liao et al

2025

‍

Preprint

Cell-death pathways and tau-associated neuronal vulnerability in Alzheimer’s disease

Lin et al

2025

Cell Reports

Journal article

Hv1 inhibition rescues AD pathology by restoring microglial mitochondrial function and enhancing mitochondrial transfer

Lin et al

2025

Experimental & Molecular Medicine

Journal article

Linking spatial omics to patient phenotypes at the population scale by BSNMani: Bayesian scalar-on-network regression with manifold learning

Liu et al

2025

‍

Preprint

Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience

Liu et al

2025

Cell

Journal article

Integrated Cross-Disease Atlas of Human And Mouse Astrocytes Reveals Heterogeneity and Conservation of Astrocyte Subtypes in Neurodegeneration

Lucas et al

2025

‍

Preprint

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

Luques et al

2025

‍

Preprint

The Fate and Dynamics of Neural Stem Cells (NSCs) and Their Neurogenic Decline in Alzheimer’s Disease

M Naffaa et al

2025

Lifespan Development and Mental Health

Journal article

HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data

Madhu et al

2025

‍

Preprint

Apolipoprotein E: Historical Perspective on Isoform Structure and Function in Cardiovascular and Neurological Diseases

Mahley et al

2025

Apolipoprotein E

Book section

Microglial BIN1 deficiency elicits enhanced microglial inflammatory responses that mimic early AD pathology

Margariti et al

2025

‍

Preprint

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

Marshe et al

2025

‍

Preprint

MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics

Martin et al

2025

‍

Preprint

Cell Type–Specific Studies of Human Tissue for Investigation of the Molecular Cell Biology of Late-Onset Neurodegenerative Disease

Mätlik et al

2025

Annual Review of Neuroscience

Journal article

Single-nucleus transcriptome atlas of orbitofrontal cortex in ALS with a deep learning-based decoding of alternative polyadenylation mechanisms

McKeever et al

2025

Cell Genomics

Journal article

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

Meir et al

2025

‍

Preprint

Annotation Comparison Explorer (ACE): connecting brain cell types across studies of health and Alzheimer's Disease

Miller et al

2025

‍

Preprint

HMGA1 deficiency: a pathogenic link between tau pathology and insulin resistance

Mirabelli et al

2025

eBioMedicine

Journal article

Human Brain Cell-Type-Specific Aging Clocks Based on Single-Nuclei Transcriptomics

Muralidharan et al

2025

Advanced Science

Journal article

Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegeneration

Murray etal

2025

Neuron

Journal article

A Reproducibility Focused Meta-Analysis Method for Single-Cell Transcriptomic Case-Control Studies Uncovers Robust Differentially Expressed Genes

Nakatsuka et al

2025

‍

Preprint

GABA-activated slow spontaneous inhibitory postsynaptic currents are decreased in dorsal hippocampal dentate gyrus granule cells in an aged mouse model of Alzheimer's disease

Netsyk et al

2025

Journal of Alzheimer’s Disease

Journal article

Complement biosynthesis in human brain: Insights from single-nucleus transcriptomics of hippocampus

Nguyen et al

2025

‍

Preprint

Quantification of Alzheimer disease neuropathology using tissue microarrays

Nguyen-Hao et al

2025

Journal of Neuropathology & Experimental Neurology

Journal article

The new frontier in understanding human and mammalian brain development

Nowakowski et al

2025

Nature

Journal article

Multi-omic derived cell-type specific Alzheimer disease polygenic risk scores

O’Neill et al

2025

Neurobiology of Aging

Journal article

A cerebrospinal fluid synaptic protein biomarker for prediction of cognitive resilience versus decline in Alzheimer’s disease

Oh et al

2025

Nature Medicine

Journal article

Transcriptomic analysis of the TRP gene family in human brain physiopathology

Olejniczak et al

2025

Frontiers in Molecular Neuroscience

Journal article

Single-nucleus RNA-seq reveals no increase in T cells in Alzheimer’s disease prefrontal cortex or hippocampus

Oxendine et al

2025

Frontiers in Cellular Neuroscience

Journal article

Fate mapping of peripherally-derived macrophages after traumatic brain injury in mice reveals a long-lasting population with a distinct transcriptomic signature

Paladini et al

2025

Nature Communications

Journal article

Adult human subventricular zone microglia promote a pro-neurogenic niche for neuronal progenitors in Parkinson’s disease

Pecoraro et al

2025

Brain, Behavior, and Immunity

Journal article

Distinct Cellular Phenotypes of Language and Executive Decline in Amyotrophic Lateral Sclerosis

Petrescu et al

2025

‍

Preprint

Exploring inflammation-related protein expression and its relationship with TSPO PET in Alzheimer's disease

Pola et al

2025

Alzheimer's & Dementia

Journal article

All the single cells: Single-cell transcriptomics/epigenomics experimental design and analysis considerations for glial biologists

Prater et al

2025

Glia

Journal article

GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models

Qiu et al

2025

‍

Preprint

Systematic characterization of cell type-specific master metabolic regulators in Alzheimer's disease

Qiu et al

2025

Research Square

Journal article

Cell type-specific master metabolic regulators of Alzheimer’s disease

Qiu et al

2025

‍

Preprint

Brief sleep disruption alters synaptic structures among hippocampal and neocortical somatostatin-expressing interneurons

Raven et al

2025

‍

Preprint

Human brain vascular multi-omics elucidates disease-risk associations

Reid et al

2025

Neuron

Journal article

Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions

Ren et al

2025

Acta Pharmaceutica Sinica B

Journal article

Single-cell digital twins identify drug targets and repurposable medicine in Alzheimer’s disease

Ren et al

2025

‍

Preprint

Utilization of precision medicine digital twins for drug discovery in Alzheimer's disease

Ren et al

2025

Neurotherapeutics

Journal article

Powerful and accurate case-control analysis of spatial molecular data with deep learning-defined tissue microniches

Reshef et al

2025

‍

Preprint

STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics

Rocha et al

2025

‍

Preprint

Digital neuropathology of neurodegenerative disorders: Foundations, research advances, and future directions

Rosado et al

2025

Alzheimer's & Dementia

Journal article

Cysteine string protein α and a link between rare and common neurodegenerative dementias

Rosene et al

2025

npj Dementia

Journal article

High-Resolution Spatial Profiling of Microglia Reveals Proximity Associated Immunometabolic Reprogramming in Alzheimer’s Disease

Saito et al

2025

‍

Preprint

Radiophobia Harm, Its Main Cause, and a Proposed Solution

Scott et al

2025

Dose-Response

Journal article

A novel computational analysis integrating social determinants information from EHR and literature with Alzheimer’s disease biological knowledge through large language models and knowledge graphs

Shang et al

2025

Innovation in Aging

Journal article

Differences in transcriptome characteristics and drug repositioning of Alzheimer's disease according to sex

Shi et al

2025

Neurobiology of Disease

Journal article

Leveraging multiomic approaches to elucidate mechanisms of heterogeneity in Alzheimer's disease: Neuropsychiatric symptoms, co-pathologies, and sex differences

Shwab et al

2025

Alzheimer's & Dementia

Journal article

Accurate tiling of spatial single-cell data with Tessera

Stein et al

2025

‍

Preprint

Polygenic risk for Alzheimer’s disease shapes microglial inflammatory and antigen-presentation programs in vivo

Strooper et al

2025

‍

Preprint

Synapse vulnerability and resilience across the clinical spectrum of dementias

Taddei et al

2025

Nature Reviews Neurology

Journal article

NVUAtlas: A Comprehensive Single-Nucleus RNA-Seq Resource for the Human Neurovascular Unit in Alzheimer’s Disease

Tang et al

2025

‍

Preprint

Searching for the cellular underpinnings of the selective vulnerability to tauopathic insults in Alzheimer’s disease

Torok et al

2025

Communications Biology

Journal article

Reduced triacylglycerols and lipid droplets are associated with resilience to Alzheimer’s disease

Van Der Vliet et al

2025

‍

Preprint

Production of Amyloid-β in the Aβ-Protein-Precursor Proteolytic Pathway Is Discontinued or Severely Suppressed in Alzheimer’s Disease-Affected Neurons: Contesting the ‘Obvious’

Volloch et al

2025

Genes

Journal article

Alzheimer’s Is a Multiform Disease of Sustained Neuronal Integrated Stress Response Driven by the C99 Fragment Generated Independently of AβPP; Proteolytic Production of Aβ Is Suppressed in AD-Affected Neurons: Evolution of a Theory

Volloch et al

2025

International Journal of Molecular Sciences

Journal article

CRISPR-based epigenetic editing of Gad1 improves synaptic inhibition and cognitive behavior in a Tauopathy mouse model

Wan et al

2025

Neurobiology of Disease

Journal article

The impact of apolipoprotein E, type ∊4 allele on Alzheimer’s disease pathological biomarkers: a comprehensive post-mortem pilot-analysis

Wan et al

2025

PLOS ONE

Journal article

scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics

Wang et al

2025

‍

Preprint

Multi-omics integration reveals key miRNAs, immune inflammation, and signaling pathways in Alzheimer's disease: Implications for targeted therapy

Wang et al

2025

International Journal of Biological Macromolecules

Journal article

Neuronal ABCA7 deficiency aggravates mitochondrial dysfunction and neurodegeneration in Alzheimer's disease

Wang et al

2025

Alzheimer's & Dementia

Journal article

CellMemory: hierarchical interpretation of out-of-distribution cells using bottlenecked transformer

Wang et al

2025

Genome Biology

Journal article

Glial changes and gene expression in Alzheimer's disease from snRNA-Seq and spatial transcriptomics

Wei et al

2025

Journal of Alzheimer’s Disease

Journal article

Aged brain multi-omic integration captures immunometabolic and sex variation

Whalley et al

2025

‍

Preprint

Single Cell Landscape of Sex-specific Drivers of Alzheimer’s Disease

Wu et al

2025

‍

Preprint

Benchmarking large language models for cell typing in single-cell RNA-Seq

Xiao et al

2025

Briefings in Bioinformatics

Journal article

Single-cell-level condition-related signal estimation with batch effect removal through neural discrete representation learning

Xiao et al

2025

‍

Preprint

Inferring spatial single-cell-level interactions through interpreting cell state and niche correlations learned by self-supervised graph transformer

Xiao et al

2025

Nature Machine Intelligence

Journal article

Brain network dynamics determine tau presence while regional vulnerability governs tau load in Alzheimer’s disease

Xiao et al

2025

‍

Preprint

Fast evolutionary turnover and overlapping variances of sex-biased gene expression patterns defy a simple binary sex classification of somatic tissues

Xie et al

2025

eLife

Journal article

Patterns of extreme outlier gene expression suggest an edge of chaos effect in transcriptomic networks

Xie et al

2025

Genome Biology

Journal article

DSCT: a novel deep-learning framework for rapid and accurate spatial transcriptomic cell typing

Xu et al

2025

National Science Review

Journal article

Single-cell, multi-region profiling of the macaque brain across the lifespan

Yang et al

2025

‍

Preprint

Attention Graphical Neural Networks-based Single-cell Multi-omics Fusion Analysis of Chromatin Accessibility and Transcriptome Characterization in Alzheimer's Disease

Ye et al

2025

Current Bioinformatics

Journal article

Construction of ROS-responsive cascade-targeted liposomes and investigation of their anti-AD effects

Yu et al

2025

International Immunopharmacology

Journal article

Brain-wide interpolation and conditioning of gene expression in the human brain using Implicit Neural Representations

Yu et al

2025

‍

Preprint

CompBioAgent: An LLM-powered agent for single-cell RNA-seq data exploration

Zhang et al

2025

‍

Preprint

OmniCellTOSG: The First Cell Text-Omic Signaling Graphs Dataset for Joint LLM and GNN Modeling

Zhang et al

2025

‍

Preprint

DiSC: a Statistical Tool for Fast Differential Expression Analysis of Individual-level Single-cell RNA-seq Data

Zhang et al

2025

Bioinformatics

Journal article

Single-cell multiomics reveals disrupted glial gene regulatory programs in Alzheimer’s disease via interpretable machine learning

Zhang et al

2025

‍

Preprint

Multimodal brain cell atlas across the adult macaque lifespan

Zhang et al

2025

‍

Preprint

Multi-omics reveals changes in astrocyte fatty acid metabolism during early stages of Alzheimer's disease

Zhong et al

2025

Neurochemistry International

Journal article

Microglia networks within the tapestry of alzheimer’s disease through spatial transcriptomics

Zhou et al

2025

Molecular Neurodegeneration

Journal article

Recurrent patterns of widespread neuronal genomic damage shared by major neurodegenerative disorders

Zhou et al

2025

‍

Preprint

2024

Title

Author

Year

Source

Type

Systematic Analysis of Biological Processes Reveals Gene Co-expression Modules Driving Pathway Dysregulation in Alzheimer’s Disease

Adeoye et al

2024

Aging and disease

Journal article

B-BIND: BIOPHYSICAL BAYESIAN INFERENCE FOR NEURODEGENERATIVE DYNAMICS

Agrawal et al

2024

‍

Preprint

A Case for the Use of Open Data as a Tool to Incorporate Socioscientific Topics into Neuroscience Education

Allen Institute

2024

Journal of Undergraduate Neuroscience Education

Journal article

The single-cell opioid responses in the context of HIV (SCORCH) consortium

Ament et al

2024

Molecular Psychiatry

Journal article

Characterization of covalent inhibitors that disrupt the interaction between the tandem SH2 domains of SYK and FCER1G phospho-ITAM

Bashore et al

2024

PLOS ONE

Journal article

Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

Bonev et al

2024

Nature Neuroscience

Journal article

gsQTL: Associating genetic risk variants with gene sets by exploiting their shared variability

Bouland et al

2024

‍

Preprint

A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations

Chandrashekar et al

2024

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Preprint

Personalized Single-cell Transcriptomics Reveals Molecular Diversity in Alzheimer’s Disease

Chandrashekar et al

2024

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Preprint

Switch of innate to adaptative immune responses in the brain of patients with Alzheimer’s disease correlates with tauopathy progression

Costa et al

2024

npj Aging

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Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level

Deng et al

2024

Genome Research

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ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution

Flotho et al

2024

Nucleic Acids Research

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The broken Alzheimer’s disease genome

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Cell Genomics

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SEA-AD is a multimodal cellular atlas and resource for Alzheimer’s disease

Hawrylycz et al

2024

Nature Aging

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Phenotype Scoring of Population Scale Single-Cell Data Dissects Alzheimer’s Disease Complexity

He et al

2024

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Preprint

Antibody-mediated targeting of human microglial leukocyte Ig-like receptor B4 attenuates amyloid pathology in a mouse model

Hou et al

2024

Science Translational Medicine

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Identification of distinct and shared biomarker panels in different manifestations of cerebral small vessel disease through proteomic profiling

Hristovska et al

2024

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scEMB: Learning context representation of genes based on large-scale single-cell transcriptomics

Hsieh et al

2024

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Preprint

Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer's disease microglia

Huang et al

2024

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5-HT4 receptor agonists treatment reduces tau pathology and behavioral deficit in the PS19 mouse model of tauopathy

Jiang et al

2024

Frontiers in Cellular Neuroscience

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Transcriptional Patterns in Stages of Alzheimer's Disease Are Cell-Type–Specific and Partially Converge with the Effects of Alcohol Use Disorder in Humans

Joshi et al

2024

eNeuro

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Spatial Transcriptomic Analysis Identifies a SERPINA3-Expressing Astrocytic State Associated with the Human Neuritic Plaque Microenvironment

Karaahmet et al

2024

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Preprint

Cerebrospinal fluid reference proteins increase accuracy and interpretability of biomarkers for brain diseases

Karlsson et al

2024

Nature Communications

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Beyond the usual suspects: multi-factorial computational models in the search for neurodegenerative disease mechanisms

Khan et al

2024

Translational Psychiatry

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eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings

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Lin et al

2024

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Spatial Multi-Omics in Alzheimer’s Disease: A Multi-Dimensional Approach to Understanding Pathology and Progression

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Current Issues in Molecular Biology

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Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS

Marghi et al

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Nature Computational Science

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Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics

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2024

Briefings in Bioinformatics

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Single-cell multiregion dissection of Alzheimer’s disease

Mathys et al

2024

Nature

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An exhausted-like microglial population accumulates in aged and APOE4 genotype Alzheimer’s brains

Millet et al

2024

Immunity

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2024

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2024

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Proteomic changes in Alzheimer’s disease associated with progressive Aβ plaque and tau tangle pathologies

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Nature Neuroscience

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Gene networks and systems biology in Alzheimer's disease: Insights from multi-omics approaches

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CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis

Samelson et al

2024

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Single-cell investigation of lead toxicity from neurodevelopment to neurodegeneration: Current review and future opportunities

Sampson et al

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Current Opinion in Toxicology

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Astrocyte transcriptomic changes along the spatiotemporal progression of Alzheimer’s disease

Serrano-Pozo et al

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Shan et al

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Cell Reports Methods

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Sun et al

2024

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Hippocampal transcriptome-wide association study and pathway analysis of mitochondrial solute carriers in Alzheimer’s disease

Tian et al

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Translational Psychiatry

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Wang et al

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Hierarchical Interpretation of Out-of-Distribution Cells Using Bottlenecked Transformer

Wang et al

2024

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Preprint

CD8+ T cells exacerbate AD-like symptoms in mouse model of amyloidosis

Wang et al

2024

Brain, Behavior, and Immunity

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Weighted Diversified Sampling for Efficient Data-Driven Single-Cell Gene-Gene Interaction Discovery

Wu et al

2024

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Preprint

Cell States and Interactions of CD8 T Cells and Disease-Enriched Microglia in Human Brains with Alzheimer’s Disease

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Biomedicines

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Yang et al

2024

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Zhao et al

2024

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Preprint

Genetic influences on brain and cognitive health and their interactions with cardiovascular conditions and depression

Zhukovsky et al

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Nature Communications

Journal article

2023

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Author

Year

Source

Type

Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature

Berson et al

2023

Nature Communications

Journal article

Single-cell RNA sequencing data reveals rewiring of transcriptional relationships in Alzheimer’s Disease associated with risk variants

Bouland et al

2023

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Preprint

Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

Chartrand et al

2023

Science

Journal article

siVAE: interpretable deep generative models for single-cell transcriptomes

Choi et al

2023

Genome Biology

Journal article

Interindividual variation in human cortical cell type abundance and expression

Johansen et al

2023

Science

Journal article

Human disease-specific cell signatures in non-lesional tissue in Multiple Sclerosis detected by single-cell and spatial transcriptomics

Lam et al

2023

‍

Preprint

Microglial REV-ERBα regulates inflammation and lipid droplet formation to drive tauopathy in male mice

Lee et al

2023

Nature Communications

Journal article

A comparative atlas of single-cell chromatin accessibility in the human brain

Li et al

2023

Science

Journal article

LRRC37B is a human modifier of voltage-gated sodium channels and axon excitability in cortical neurons

Libé-Philippot et al

2023

Cell

Journal article

A computational method for cell type-specific expression quantitative trait loci mapping using bulk RNA-seq data

Little et al

2023

Nature Communications

Journal article

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2023

Genome Biology

Journal article

Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer’s disease pathology

Mathys et al

2023

Cell

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Comparative gene regulatory network analysis in Alzheimer’s disease and major depressive disorder identifies shared core regulatory circuits

Puype et al

2023

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Preprint

Transcriptomic signatures of Aβ- and tau-induced neuronal dysfunction reveal inflammatory processes at the core of Alzheimer’s disease pathophysiology

Sanchez-Rodriguez et al

2023

‍

Preprint

An astrocyte BMAL1-BAG3 axis protects against alpha-synuclein and tau pathology

Sheehan et al

2023

Neuron

Journal article

Sex-specific declines in cholinergic-targeting tRNA fragments in the nucleus accumbens in Alzheimer's disease

Shulman et al

2023

Alzheimer's & Dementia

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