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 32

Assay: multiome ✕ Clear

Interpretable and integrative analysis of single-cell multiomics with scMKL.

PMID 40770488 · PMC12328712 · Communications biology · 2025 · 7 claims · 7 setups

Has reproduction · 65

scMKL outperforms SVM, EasyMKL, MLP, and XGBoost in classification accuracy (AUROC) across multiple single-cell cancer datasets

mcf-7 t-47d small prostate 10x scrna-seq sciatac-seq
CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

PMID 41734268 · PMC12987762 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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CIRCE re-implements the Cicero co-accessibility algorithm in Python, producing near-identical results while running much faster and using far less memory

bmmc pbmc foetal cis-regulatory enhancer-promoter scalability
A multi-modal diffusion model with dual-cross-attention for multi-omics data generation and translation.

PMID 41980989 · PMC13253844 · Nature communications · 2026 · 8 claims · 7 setups

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scDiffusion-X is a multi-modal latent denoising diffusion probabilistic model for single-cell multi-omics data generation, translation, and interpretation.

openproblem 10x babel miniatlas paired modality augmentation
Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

PMID 41832957 · PMC13137218 · Cell reports · 2026 · 8 claims · 8 setups

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Generated a single-nucleus multiome (snATAC + gene expression) dataset from 357 human dorsolateral prefrontal cortex samples (ages 15-100, European and African admixed ancestry), yielding over 1.5 million cells as a public resource.

postmortem million+ pfc each single-nucleus umap pseudobulk
Single-cell resolution of an open chromatin signature in persister tumor cells.

PMID 41485222 · PMC12978573 · Cell reports · 2026 · 8 claims · 8 setups

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Single-nucleus multi-omic (snRNA-seq + snATAC-seq) profiling of fallopian tube, treatment-naive, and NACT-treated HGSOC tissue identifies a persister cell signature (PCS) defining the chemotherapy-tolerant state.

non-malignant same epithelial tumor single-nucleus mitochondrial copy-number
Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

PMID 41526381 · PMC12902073 · Nature communications · 2026 · 8 claims · 8 setups

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BioCRE, a novel bi-orientation regression algorithm, more accurately links genes to candidate cis-regulatory elements (CREs) than existing tools Signac and ArchR

gastrulating gastrula gold-standard embryo single-cell computational promoter
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
Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap.

PMID 41650244 · PMC12890892 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 7 setups

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SuperMap learns cross-modal feature mappings directly from unpaired multimodal data without requiring paired training data

pbmc bone skin embryos scrna-seq scnmt-seq asap-seq
Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

PMID 41781332 · PMC13138337 · Genome research · 2026 · 8 claims · 7 setups

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Single-nucleus multiome (RNA+ATAC) sequencing of mouse substantia nigra across four age stages (2, 6, 12, 18 months) yields a 40,125-cell atlas spanning 27 cell subclasses

substantia allen five oligodendrocyte single-nucleus scrna-seq single-cell
Multi-modal dissection of cell-type specific TDP-43 pathology in the motor cortex.

PMID 41803120 · PMC12982666 · Nature communications · 2026 · 7 claims · 4 setups

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Mainly excitatory cortical neurons are affected by TDP-43 pathology in the ALS/ALS-FTD motor cortex

post-mortem publicly als single-nucleus single-nucleus spatial genotyping
Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn
B-lineage commitment is dependent on a reversible epigenetic switch.

PMID 41266087 · PMC12863259 · Genes & development · 2026 · 8 claims · 8 setups

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B-lymphoid commitment is mediated by a transcription factor-dose-dependent epigenetic switch that suppresses inherent T-lineage potential in early lymphoid progenitors

bone expanded pax5 ebf1 combined atac-seq chip-seq
CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning.

PMID 41481570 · PMC12758788 · PLoS computational biology · 2026 · 8 claims · 7 setups

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CellPredX is a unified semi-supervised framework integrating domain adaptation and deep metric learning to align heterogeneous embeddings for cross-modality cell type annotation.

pbmc fetal pancreas gse149683 matched unmatched cross-protocol
Benchmarking component choices for unpaired single cell RNA and epigenomic integration.

PMID 41987329 · PMC13192178 · Genome biology · 2026 · 7 claims · 8 setups

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Gene activity scores (GAS) show limited correlation with actual gene expression but effectively preserve cellular neighborhood structure and support clustering.

e18 pbmc brain kidney scrna-seq share-seq gas
BiCLUM: Bilateral contrastive learning for unpaired single-cell multi-omics integration.

PMID 41632825 · PMC12904586 · PLoS computational biology · 2026 · 8 claims · 5 setups

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BiCLUM consistently outperforms or matches existing integration methods across multiple RNA+ATAC and RNA+protein datasets in visualization and quantitative benchmarks

pbmc kidney bmmc bmcite scrna-seq cite-seq
Single-cell atlas of the developing Down syndrome brain cortex.

PMID 41545595 · PMC13004680 · Nature medicine · 2026 · 8 claims · 8 setups

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RORB/FOXP1-expressing L4-like excitatory neurons are subtype-specifically and dramatically reduced in Down syndrome fetal cortex, especially at later stages (PCW16-20)

fetal excitatory neural humanized single-nucleus immunostaining compositional
Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment.

PMID 41556506 · PMC12818872 · eLife · 2026 · 8 claims · 8 setups

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Mouse TM contains three molecularly distinct, reproducible cell subtypes (TM1, TM2, TM3) identified by scRNA-seq and validated by IF/ISH

limbal lmx1b scrna-seq snatac-seq immunofluorescence
MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.

PMID 41922875 · PMC13095666 · Nature structural & molecular biology · 2026 · 8 claims · 6 setups

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MitoPerturb-Seq combines pooled CRISPR–Cas9 screening (CROP-seq) with 10x Genomics multiome (scATAC-seq + scRNA-seq) to simultaneously profile mtDNA sequence/copy number/heteroplasmy and the nuclear transcriptome/chromatin accessibility in single heteroplasmic cells

cas9-expressing heteroplasmic tfam-ko pooled tap-seq hybridization-capture-based
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.

PMID 38781959 · PMC11228554 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

Has reproduction · 76

DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs across patients and samples

fresh matched archived dsrct scrna-seq single-nucleus bulk
Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.

PMID 41821037 · PMC12983708 · Genome biology · 2026 · 8 claims · 8 setups

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Horizontal integration of scRNA-seq and snRNA-seq improves cell-type identification

renal kidney pbmc heart scrna-seq snrna-seq snatac-seq

Experiments

Interpretable and integrative analysis of single-cell multiomics with scMKL.

CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

A multi-modal diffusion model with dual-cross-attention for multi-omics data generation and translation.

Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

Single-cell resolution of an open chromatin signature in persister tumor cells.

Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

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

Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap.

Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

Multi-modal dissection of cell-type specific TDP-43 pathology in the motor cortex.

Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

B-lineage commitment is dependent on a reversible epigenetic switch.

CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning.

Benchmarking component choices for unpaired single cell RNA and epigenomic integration.

BiCLUM: Bilateral contrastive learning for unpaired single-cell multi-omics integration.

Single-cell atlas of the developing Down syndrome brain cortex.

Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment.

MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.

Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.

Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.