Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 9

System / cell line: single-cell ✕ Assay: local ✕ Clear

Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.

PMID 41555918 · PMC12812404 · Frontiers in genetics · 2025 · 7 claims · 5 setups

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LiVAE, a dual-pathway VAE with Lorentzian geometric regularization between a primary Euclidean pathway and an information-bottleneck pathway, balances local fidelity with global topology coherence in single-cell embeddings

single-cell same dapp1 benchmarking umap component-wise
GRAMD1B is a regulator of lipid homeostasis, autophagic flux and phosphorylated tau.

PMID 40204713 · PMC11982250 · Nature communications · 2025 · 8 claims · 7 setups

Has reproduction · 91

GRAMD1B is increased in excitatory neurons of human neural organoids (HNOs) carrying the MAPT R406W mutation

neural hno single-cell immunofluorescence western
Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact
Determination of complete chromosomal haplotypes by bulk DNA sequencing.

PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups

Has reproduction · 97

A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts

rpe-1 na12878 aneuploid linked-read hi-c bulk
Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

Has reproduction · 92

Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

skeletal merged myogenic muscle scrnaseq batch-correction differential
Multiomics and deep learning dissect regulatory syntax in human development.

PMID 41951735 · PMC13216069 · Nature · 2026 · 8 claims · 8 setups

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The Human Development Multiomic Atlas (HDMA) is a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types

fetal annotated embryo chrombpnet share-seq chromvar activity-by-contact
Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.

PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups

Has reproduction · 83

Vascular macrophages form a spatiotemporal niche in direct contact with mural cells across microvascular and macrovascular beds

cx3cr1-mφ rfp-rep coronary peritoneal intravital confocal single-cell
IFN signaling is associated with radiotherapy response in malignant peripheral nerve sheath tumors.

PMID 41766654 · PMC12948414 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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MPNST cells are more radioresistant than benign plexiform neurofibroma (pNF) cells in vitro

mpnst st88-14 nf9511.b jh-2-002 flow fractionated bulk
CLK1 Promotes Myeloid-Derived Suppressor Cell Trafficking and Reprograms the Tumor Microenvironment by Activating Hippo/YAP Signaling in Colorectal Cancer.

PMID 41686262 · PMC13136879 · Cancer immunology research · 2026 · 8 claims · 8 setups

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CLK1 is markedly upregulated in immune-cold colorectal tumors and correlates with increased MDSC infiltration and CD8+ T-cell exclusion

colorectal tcga-coad ct26 tumor scrna-seq bulk multiplex

Experiments

Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.

GRAMD1B is a regulator of lipid homeostasis, autophagic flux and phosphorylated tau.

Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

Determination of complete chromosomal haplotypes by bulk DNA sequencing.

Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

Multiomics and deep learning dissect regulatory syntax in human development.

Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.

IFN signaling is associated with radiotherapy response in malignant peripheral nerve sheath tumors.

CLK1 Promotes Myeloid-Derived Suppressor Cell Trafficking and Reprograms the Tumor Microenvironment by Activating Hippo/YAP Signaling in Colorectal Cancer.