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 624

Assay: scrna ✕ Clear

Single-cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma.

PMID 41923630 · PMC13130666 · Cell reports. Medicine · 2026 · 8 claims · 4 setups

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A malignant cell subset expressing IFN-response and MHC-II genes (IFN/MHC-II) increases in proportion after pembrolizumab treatment and is associated with response

hnscc ffpe syngeneic independent single-cell multiplexed tumor
Single-Cell and Spatial Transcriptomics Reveal That TXNIP and BIRC3 Contribute to Human Prostate Tumor Progression.

PMID 41972735 · PMC13072731 · Cells · 2026 · 6 claims · 8 setups

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TXNIP and BIRC3 are established as spatially restricted tumor-niche genes associated with metabolic stress and inflammatory survival pathways

prostate tcga-prad integration single-cell spatial pseudotime
A sequence knowledge-guided deep learning method for single-cell multi-omics translation.

PMID 41975483 · PMC13185235 · Genome biology · 2026 · 7 claims · 7 setups

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scProTrans, a deep learning framework combining sequence knowledge (dna2vec gene embeddings, ProtT5 protein embeddings) with a cross-omics attention mechanism, translates single-cell transcriptome data into proteome profiles

multi-omics pbmcs datasets fully cite-seq cross-technology tri-omics
Deep single-cell decoding of human pancreatic islets reveals T2D β-cell gene expression defects.

PMID 41986506 · PMC13226668 · The EMBO journal · 2026 · 8 claims · 6 setups

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Single-cell transcriptome profiling of 245,878 islet cells from 48 donors (ND/PD/T2D) identifies 14 distinct, robust islet cell types detected in every donor

pancreatic aggregated endoc-βh3 subset droplet-based pseudobulk unsupervised
A multi-omic single-cell landscape of perinatal mouse skin maps lineage specification and reveals shared dynamics in human fetal skin.

PMID 41998142 · PMC13144478 · Experimental & molecular medicine · 2026 · 7 claims · 8 setups

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Integrated scATAC/scRNA multi-omics analysis of developing mouse skin identifies gene network axes underlying skin lineage specification

dorsal scrna-seq skin fibroblast scatac-seq scrna-seq spatial
Opioid-induced transcriptional reprogramming of cerebrospinal fluid immune cells is associated with neuroinflammatory signaling in antiretroviral treated SIV-infected rhesus macaques.

PMID 42010620 · PMC13227897 · Journal of neuroinflammation · 2026 · 8 claims · 5 setups

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Morphine-dependent macaques show increased CD4+ TCM and Treg cell proportions and decreased CD8+ TEM cell proportions in CSF at the pre-infection timepoint compared to saline controls

csf scrna-seq necropsy single-cell flow cell-cell
Single cell transcriptional evolution of myeloid leukemia of Down syndrome.

PMID 42026063 · PMC13106683 · Nature communications · 2026 · 8 claims · 5 setups

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Transcriptional changes induced by TAM-defining GATA1 mutations are retained in and account for most of the ML-DS transcriptome, persisting even in progressive disease that has undergone further genetic evolution.

foetal blasts leukaemias normal single-cell bulk whole-genome
Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL.

PMID 42026624 · PMC13238118 · Genome biology · 2026 · 8 claims · 6 setups

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SEAGALL combines a geometry-regularised autoencoder (GRAE) to embed cells and build a cell-cell graph with a graph attention network (GAT) classifier and GNNExplainer-based XAI to identify features driving cell type/phenotype.

count same scchip-seq ten count latent classification
Telomerase-Associated Genes as Prognostic Markers in High-Grade Serous Ovarian Cancer.

PMID 42050900 · PMC13137916 · Medical science monitor : international medical journal of experimental and clinical research · 2026 · 8 claims · 8 setups

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TAGs are linked to HGSOC progression and yield a candidate prognostic model

hgsoc tcga-ov scrna-seq-derived single-cell bulk cellchat
PSGRN: Gene regulatory network inference from single-cell perturbational data through self-training with synthetic gold standards.

PMID 42054465 · PMC13127566 · Science advances · 2026 · 8 claims · 4 setups

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PSGRN infers GRNs by generating pseudoannotations from gene-gene correlations and iteratively refining them via a self-training classifier using pre/post-intervention expression features.

k562 rpe1 processed single-cell computational biological
Impact of enteric neuronal loss on intestinal cell composition.

PMID 42063560 · PMC13127327 · iScience · 2026 · 8 claims · 7 setups

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ENS loss in ret mutant zebrafish alters the non-neuronal composition of the intestine, with increased immune cells and shifts in epithelial and ECM-producing populations

intestine ens immune phox2bb single-cell scrna-seq whole-mount
Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

PMID 42063567 · PMC13127482 · iScience · 2026 · 8 claims · 8 setups

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LUSC arising within UIP originates from AT2-derived metaplastic basal cells

fresh-frozen same scrna-seq paired single-cell copy ligand-receptor
Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

PMID 42074110 · PMC13115843 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide
Charting spatial ligand-target activity using Renoir.

PMID 42086556 · PMC13144314 · Nature communications · 2026 · 8 claims · 8 setups

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Renoir computes a neighborhood activity score for curated ligand-target pairs at each spatial spot/cell by integrating cell type abundance, cell type-specific mRNA abundance, receptor expression, gene entropy, and mutual information between ligand and target genes.

intestine triple-negative dorsolateral dlpfc semi-synthetic spatial single-cell
PRDM1 Is Associated with Chemoradiotherapy-Associated Enrichment of Adaptive NK Cells in Cervical Cancer.

PMID 42110212 · PMC13150072 · Computational and structural biotechnology journal · 2026 · 8 claims · 8 setups

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CRT enriches adaptive NK (aNK) cells within the cervical cancer immune microenvironment, with enrichment apparent after the first fraction and persisting after the second

cervical subclusters ank overlapping single-cell cluster differential
Dynamics of severity-associated immune remodeling by granulocytes and macrophages in acute lung injury.

PMID 42111184 · PMC13157102 · iScience · 2026 · 7 claims · 7 setups

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Granulocytes expand while macrophages are depleted as ALI severity progresses from intermediate to late stage

bronchoalveolar granulocytes granulocyte immune single-cell gene pseudotime
scDBic: a novel deep learning-based biclustering algorithm for analyzing scRNA-seq data.

PMID 41746287 · PMC13012890 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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scDBic improves cell clustering by combining deep autoencoder-based cell clustering, gene clustering, and reverse-strategy identification of key gene clusters

e-mtab-3321 e-mtab-2600 gse45719 gse52529 biclustering ablation
Souporcell3: robust demultiplexing for high-donor single-cell RNA-seq datasets.

PMID 41808435 · PMC13012599 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

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Souporcell3 can robustly demultiplex pooled scRNA-seq data from up to 64 donors

pooled scrna-seq doublet genotype-based umap-based
DAGFormer: A graph-based domain adaptation approach for single-cell cancer drug response prediction.

PMID 41417875 · PMC12795466 · PLoS computational biology · 2025 · 7 claims · 5 setups

Has reproduction

DAGFormer constructs cellular neighbor graphs using diverse topological strategies to represent intercellular interactions for drug response prediction

pan-cancer jhu006 scc47 pc9 bulk scrna-seq
Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals the transcriptome profile of Microtus fortis immune cells during the early phase of infection with Schistosoma japonicum.

PMID 41675929 · PMC12886473 · Frontiers in cellular and infection microbiology · 2025 · 8 claims · 2 setups

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Both innate and adaptive immune responses were activated in M. fortis peripheral blood at 10 dpi, while activation was not obvious in Kunming mice at the same time point

pbmcs single-cell qpcr

Experiments

Single-cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma.

Single-Cell and Spatial Transcriptomics Reveal That TXNIP and BIRC3 Contribute to Human Prostate Tumor Progression.

A sequence knowledge-guided deep learning method for single-cell multi-omics translation.

Deep single-cell decoding of human pancreatic islets reveals T2D β-cell gene expression defects.

A multi-omic single-cell landscape of perinatal mouse skin maps lineage specification and reveals shared dynamics in human fetal skin.

Opioid-induced transcriptional reprogramming of cerebrospinal fluid immune cells is associated with neuroinflammatory signaling in antiretroviral treated SIV-infected rhesus macaques.

Single cell transcriptional evolution of myeloid leukemia of Down syndrome.

Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL.

Telomerase-Associated Genes as Prognostic Markers in High-Grade Serous Ovarian Cancer.

PSGRN: Gene regulatory network inference from single-cell perturbational data through self-training with synthetic gold standards.

Impact of enteric neuronal loss on intestinal cell composition.

Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

Charting spatial ligand-target activity using Renoir.

PRDM1 Is Associated with Chemoradiotherapy-Associated Enrichment of Adaptive NK Cells in Cervical Cancer.

Dynamics of severity-associated immune remodeling by granulocytes and macrophages in acute lung injury.

scDBic: a novel deep learning-based biclustering algorithm for analyzing scRNA-seq data.

Souporcell3: robust demultiplexing for high-donor single-cell RNA-seq datasets.

DAGFormer: A graph-based domain adaptation approach for single-cell cancer drug response prediction.

Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals the transcriptome profile of Microtus fortis immune cells during the early phase of infection with Schistosoma japonicum.