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Predicting emergent phenotypes from single cell populations using CELLECTION
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Novel insights into brain lipid metabolism in Alzheimer's disease: Oligodendrocytes and white matter abnormalities
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B cell analysis in SARS-CoV-2 versus malaria: Increased frequencies of plasmablasts and atypical memory B cells in COVID-19
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Dysregulation of energy metabolism in Alzheimer's disease
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Radial glia and neural stem cells
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A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease
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Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
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Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer’s disease pathology
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Conserved brain myelination networks are altered in Alzheimer's and other neurodegenerative diseases
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Implications of glial metabolic dysregulation in the pathophysiology of neurodegenerative diseases
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The Cellular and Molecular Landscapes of the Developing Human Central Nervous System
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New insights into the dynamic development of the cerebral cortex in childhood and adolescence: Integrating macro- and microstructural MRI findings
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Tissue morphology influences the temporal program of human brain organoid development
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Microglial activation states and their implications for Alzheimer's Disease
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Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units
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The ethics of experimenting with human brain tissue
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Markers of microglia in post-mortem brain samples from patients with Alzheimer’s disease: a systematic review
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Molecular networks as sensors and drivers of common human diseases
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Myelination and support of axonal integrity by glia
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A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex
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Systems genetics approaches to understand complex traits
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The use of brain organoids to investigate neural development and disease
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Role of neuroinflammation in neurodegeneration development
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Ecological drivers of global gradients in avian dispersal inferred from wing morphology
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Monocyte-driven atypical cytokine storm and aberrant neutrophil activation as key mediators of COVID-19 disease severity
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scPair: Boosting single cell multimodal analysis by leveraging implicit feature selection and single cell atlases
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Cerebral organoids display dynamic clonal growth and tunable tissue replenishment
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Beyond the neuron–cellular interactions early in Alzheimer disease pathogenesis
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Single-cell transcriptomic analysis of Alzheimer’s disease
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Dense sampling of bird diversity increases power of comparative genomics
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Autism genes converge on asynchronous development of shared neuron classes
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Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy
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APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes
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Complexity of avian evolution revealed by family-level genomes
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Single-cell multiregion dissection of Alzheimer’s disease
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An integrated transcriptomic cell atlas of human neural organoids
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Consensus prediction of cell type labels in single-cell data with popV
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SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
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Single-cell multi-omics analysis of the immune response in COVID-19
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Microglial mechanisms drive amyloid-β clearance in immunized patients with Alzheimer’s disease
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scGPT: toward building a foundation model for single-cell multi-omics using generative AI
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Imbalance between firing homeostasis and synaptic plasticity drives early-phase Alzheimer’s disease
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A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation
inferredcites →https://doi.org/10.1038/s41593-024-01774-5openalex-snapshot
Integrated multimodal cell atlas of Alzheimer’s disease
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DNA language model GROVER learns sequence context in the human genome
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Loss of astrocyte cholesterol synthesis disrupts neuronal function and alters whole-body metabolism
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Inflammation and neurodegenerative diseases
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DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
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ProtoCell4P: an explainable prototype-based neural network for patient classification using single-cell RNA-seq
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Postnatal Development of Radial Glia and the Ventricular Zone (VZ): a Continuum of the Neural Stem Cell Compartment
inferredcites →https://doi.org/10.1101/2025.01.28.635153openalex-snapshot
sciLaMA: A Single-Cell Representation Learning Framework to Leverage Prior Knowledge from Large Language Models
inferredcites →https://doi.org/10.1109/tpami.2020.3005434openalex-snapshot
Deep Learning for 3D Point Clouds: A Survey
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AVONET: morphological, ecological and geographical data for all birds
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Systems Biology: A Brief Overview
inferredcites →https://doi.org/10.1126/science.aap8809openalex-snapshot
Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex
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Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus
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Evolutionary-scale prediction of atomic-level protein structure with a language model
inferredcites →https://doi.org/10.1126/science.adf1226openalex-snapshot
Comprehensive cell atlas of the first-trimester developing human brain
inferredcites →https://doi.org/10.1126/science.ado9336openalex-snapshot
Sequence modeling and design from molecular to genome scale with Evo
inferredcites →https://doi.org/10.1142/9789811250477_0031openalex-snapshot
CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq
inferredcites →https://doi.org/10.1146/annurev-animal-090414-014900openalex-snapshot
The Genome 10K Project: A Way Forward
inferredcites →https://doi.org/10.1172/jci133737openalex-snapshot
Type I interferon response drives neuroinflammation and synapse loss in Alzheimer disease
inferredcites →https://doi.org/10.1177/1073858407313512openalex-snapshot
Radial Glia Cells in the Developing Human Brain
inferredcites →https://doi.org/10.1177/10943420231201154openalex-snapshot
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
inferredcites →https://doi.org/10.1186/s12883-021-02407-1openalex-snapshot
Cell type-specific potential pathogenic genes and functional pathways in Alzheimer’s Disease
inferredcites →https://doi.org/10.1186/s12974-024-03296-0openalex-snapshot
Fueling neurodegeneration: metabolic insights into microglia functions
inferredcites →https://doi.org/10.1186/s13059-023-03123-4openalex-snapshot
Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets
inferredcites →https://doi.org/10.1186/s13075-025-03560-5openalex-snapshot
Bioinformatic analysis and experimental verification reveal expansion of monocyte subsets with an interferon signature in systemic lupus erythematosus patients
inferredcites →https://doi.org/10.1186/s40478-018-0515-3openalex-snapshot
White matter changes in Alzheimer’s disease: a focus on myelin and oligodendrocytes
inferredcites →https://doi.org/10.1186/s41232-022-00193-yopenalex-snapshot
Central nervous system regeneration: the roles of glial cells in the potential molecular mechanism underlying remyelination
inferredcites →https://doi.org/10.1214/11-aoas495openalex-snapshot
Prototype selection for interpretable classification
inferredcites →https://doi.org/10.1242/dev.166074openalex-snapshot
Brain organoids: advances, applications and challenges
inferredcites →https://doi.org/10.1371/journal.pbio.3002912openalex-snapshot
Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue
inferredcites →https://doi.org/10.1609/aaai.v32i1.11771openalex-snapshot
Deep Learning for Case-Based Reasoning Through Prototypes: A Neural Network That Explains Its Predictions
inferredcites →https://doi.org/10.26508/lsa.202402774openalex-snapshot
Clonal landscape of autoantibody-secreting plasmablasts in COVID-19 patients
inferredcites →https://doi.org/10.3233/jad-180098openalex-snapshot
Role of Blood-Brain Barrier in Alzheimer’s Disease
inferredcites →https://doi.org/10.3389/fimmu.2021.720109openalex-snapshot
Monocytes and Macrophages in COVID-19
inferredcites →https://doi.org/10.3389/fnana.2018.00104openalex-snapshot
Neural Progenitor Cell Terminology
inferredcites →https://doi.org/10.3389/fnins.2021.662242openalex-snapshot
Glycolytic Metabolism, Brain Resilience, and Alzheimer’s Disease
inferredcites →https://doi.org/10.3390/ijms18091965openalex-snapshot
Blood-Brain Barrier Dysfunction and the Pathogenesis of Alzheimer’s Disease
inferredcites →https://doi.org/10.3390/neuroglia4030015openalex-snapshot
The Role of Astrocytes and Blood–Brain Barrier Disruption in Alzheimer’s Disease
inferredcites →https://doi.org/10.4049/jimmunol.204.supp.64.2openalex-snapshot
Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and -independent cellular responses in Alzheimer’s disease
inferredcites →https://doi.org/10.4230/oasics.dx.2026.15openalex-snapshot
AutoResearch Lite: a reproducible paper-inspired experiment runner (Adam mechanism reproduction and convergence-speed comparison)
inferredcites →https://doi.org/10.48550/arxiv.1502.03167openalex-snapshot
Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift
inferredcites →https://doi.org/10.48550/arxiv.1503.01161openalex-snapshot
The Bayesian Case Model: A Generative Approach for Case-Based Reasoning and Prototype Classification
inferredcites →https://doi.org/10.48550/arxiv.1802.03426openalex-snapshot
UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction
inferredcites →https://doi.org/10.48550/arxiv.2311.12570openalex-snapshot
BEND: Benchmarking DNA Language Models on biologically meaningful tasks
inferredcites →https://doi.org/10.48550/arxiv.2501.07737openalex-snapshot
Multi-megabase scale genome interpretation with genetic language models
inferredcites →https://doi.org/10.5281/zenodo.17575540openalex-snapshot
Neuromodulatory Control Networks (NCNs): A Biologically Inspired Architecture for Dynamic LLM Processing
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/s44320-026-00197-7openalex-snapshot
Progress and new challenges in image-based profiling.
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