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 20

System / cell line: donor ✕ Assay: cell-type ✕ Clear

Immune profiling in a living human recipient of a gene-edited pig kidney.

PMID 41507576 · PMC12823403 · Nature medicine · 2026 · 8 claims · 8 setups

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Xenograft experienced early T cell-mediated rejection (Banff grade 2A) within 1 week post-transplant despite profound circulating T cell depletion, likely driven by subtherapeutic immunosuppression and residual CD8+ T cells in lymph nodes.

xenotransplant recipient kidney integrative single-cell flow
Single-cell analysis of signalling and transcriptional responses to type I interferons.

PMID 41896367 · PMC13172048 · EMBO reports · 2026 · 7 claims · 6 setups

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Different immune cell types show cell-type-specific patterns of STAT phosphorylation and gene expression changes in response to type I IFN

freshly pbmcs mass rt-qpcr bulk
Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

PMID 41714655 · PMC13039149 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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scRNA-seq and spatial transcriptomics data provide a rich, underused source of information for calibrating tissue-scale PDE models of ligand dynamics.

skin combined annotated scrna-seq single-cell spatial cell2location
FUNCellA: A Tool for Single-Sample Enrichment Analysis and Relative Pathway Activity Estimation in Single-Cell RNA Sequencing Data.

PMID 42021835 · PMC13096679 · Computational and structural biotechnology journal · 2026 · 7 claims · 8 setups

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FUNCellA integrates 7 single-sample enrichment algorithms with novel relative activation thresholding methods to identify active, inactive, and intermediate cellular states in scRNA-Seq data

pbmcs bone liver blood scrna-seq simulated microarray
Single-cell RNA-sequencing of dermal fibroblasts demonstrates culture-induced changes and variable persistence of keloid disease features.

PMID 42058918 · PMC13123497 · iScience · 2026 · 7 claims · 6 setups

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Fibroblast culture leads to subtype assimilation, with in vivo heterogeneity persisting only minimally by passage 4

dermal mesenchymal stromal patient-matched single-cell bulk qpcr
Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 8 setups

Has reproduction · 75

CLAD exhibits specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

clad covid-19 million formalin-fixed single-cell single-nucleus integrated
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
Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

PMID 33958982 · PMC8093778 · Frontiers in neuroscience · 2021 · 8 claims · 6 setups

Has reproduction · 59

Fourteen gene modules were consistently (Bonferroni-corrected) associated with ReHo across a discovery sample and two independent replication samples (including one non-Chinese HCP cohort).

healthy postmortem ahba neocortex resting-state microarray weighted
Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles.

PMID 29907695 · PMC6068466 · The EMBO journal · 2018 · 8 claims · 8 setups

Has reproduction · 46

B16F1 and B16F10 melanoma subclones functionally exchange EVs in vivo, transferring Cre mRNA cargo detectable via a Cre-LoxP color-switch reporter system

co-injected b16f1 locally 16.5k intravital cre-loxp rt-pcr
Predictive modeling of molecular activity underlying physical cell-cell interactions.

PMID 41672069 · PMC12946745 · Cell reports methods · 2026 · 8 claims · 5 setups

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Gloss, an overlapping group lasso regression combining single-gene and curated pathway features, predicts LIPSTIC interaction intensity from scRNA-seq data

tumor intestine mediastinal organs lipsticv1 ulipstic cite-seq
Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples.

PMID 41844163 · PMC13030975 · Cell reports methods · 2026 · 8 claims · 7 setups

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Cell lysis (CL) nuclei isolation yields substantially more nuclei and less biased immune cell proportions than mechanical separation (MS)

frozen paxgene cl-derived thawed single-nucleus confocal brightfield
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
comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups

Has reproduction · 65

comBO is a single iPSC-derived organoid differentiation that generates osteolineage, vascular, lymphoid, and myeloid compartments together

hipsc-derived combo combo-derived healthy-donor flow single-cell confocal
Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

tissues genomic gtex hgmd long-read variant splice
Multi-cohort and single-cell profiling of aging genes reveals prognostic and therapeutic targets in breast cancer.

PMID 41732271 · PMC12924738 · iScience · 2026 · 8 claims · 7 setups

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The eight-gene MLAG signature outperforms 100 previously published prognostic models across 12 independent breast cancer cohorts

tcga-brca senescent normal single-cell machine univariate gene
PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

PMID 41790620 · PMC12965534 · PloS one · 2026 · 7 claims · 7 setups

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PAH-former, a Geneformer model fine-tuned on public PAH scRNA-seq data, can perform in silico perturbation to identify and rank candidate PAH disease-associated genes

pah scrna-seq pah-former candidate scrna-seq transfer perturbation
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 87

Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

airway asm most single rna-seq quantitative qrt-pcr
Immunopeptidome profiling in pulmonary fibrosis provides a platform for identifying therapeutic targets.

PMID 42010059 · PMC13132728 · Nature immunology · 2026 · 6 claims · 8 setups

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IPF fibrotic lung tissue shows an expanded and distinct HLA class I immunopeptidome compared to non-IPF lung tissue, enriched for peptides from fibroblast/macrophage-derived proteins involved in tissue remodeling

ipf tabula lung blm hla high-resolution scrna-seq
In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

PMID 16995940 · PMC1590028 · BMC genomics · 2006 · 8 claims · 6 setups

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In silico ESE-prediction algorithms (ESEfinder, RescueESE, PESX) do not reliably predict actual in vivo splicing behavior of missense mutations

hmlh1 same cos-7 hela ese splice minigene
A spatially coordinated keratinocyte-fibroblast circuit recruits MMP9(+) myeloid cells to drive type I interferon-driven inflammation in photosensitive autoimmunity.

PMID 42032302 · PMC13226071 · Nature immunology · 2026 · 8 claims · 8 setups

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MMP9+CD14+ myeloid cells are critical mediators of photosensitivity, expanding in lesional skin, producing IFNβ, and colocalizing with cytotoxic CD4+ T cells at the dermal-epidermal junction

skin blister punch donor scrna-seq 250-plex seqfish

Experiments

Immune profiling in a living human recipient of a gene-edited pig kidney.

Single-cell analysis of signalling and transcriptional responses to type I interferons.

Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

FUNCellA: A Tool for Single-Sample Enrichment Analysis and Relative Pathway Activity Estimation in Single-Cell RNA Sequencing Data.

Single-cell RNA-sequencing of dermal fibroblasts demonstrates culture-induced changes and variable persistence of keloid disease features.

Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

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

Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles.

Predictive modeling of molecular activity underlying physical cell-cell interactions.

Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples.

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

comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

Multi-cohort and single-cell profiling of aging genes reveals prognostic and therapeutic targets in breast cancer.

PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

Immunopeptidome profiling in pulmonary fibrosis provides a platform for identifying therapeutic targets.

In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

A spatially coordinated keratinocyte-fibroblast circuit recruits MMP9(+) myeloid cells to drive type I interferon-driven inflammation in photosensitive autoimmunity.