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 13

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

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
Comparative multi-omic analysis reveals conserved and derived mechanisms of fin and limb regeneration.

PMID 41571662 · PMC12923738 · Nature communications · 2026 · 8 claims · 8 setups

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Fin and limb regeneration share conserved proximal and distal blastema territory markers, DNA damage repair activation, hif1a-mediated hypoxia response, and sequential pro-/anti-inflammatory gene programs.

polypterus axolotl zebrafish regenerating single-nucleus spatial single-cell
Single-cell and spatial transcriptomic profiling of cardiac fibroblasts following myocardial infarction.

PMID 41526391 · PMC12890913 · Scientific data · 2026 · 7 claims · 6 setups

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Cthrc1+ Reparative Cardiac Fibroblasts (RCFs) are the primary driver of the cardiac healing process after myocardial infarction

col1α1-gfp+ heart frozen bulk single-cell spatial
Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

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Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

apc-deficient heart ileum fresh-frozen spatial high-resolution bulk
Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

PMID 41031483 · PMC13242933 · Genomics, proteomics & bioinformatics · 2026 · 7 claims · 8 setups

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The human decidua contains two coherent spatial domains, the implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the decidua compacta and spongiosa

first-trimester decidual spots dnk 10x h&e type
sCellST predicts single-cell gene expression from H& E images.

PMID 41513659 · PMC12858858 · Nature communications · 2026 · 7 claims · 6 setups

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sCellST is a weakly supervised (Multiple Instance Learning) deep learning framework that predicts single-cell gene expression from H&E images alone, trained using paired spatial transcriptomics (Visium) and H&E slides

ovarian kidney prostate breast simulation spot-level nucleus
Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer.

PMID 41723121 · PMC12932787 · Nature communications · 2026 · 8 claims · 8 setups

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Different tumor cell transcriptomic states organize into distinct spatial clusters, or 'villages', each supported by a unique surrounding microenvironment

liver malignant non-malignant tumor single-cell immunofluorescence non-negative
Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

PMID 40233745 · PMC12143324 · Cell genomics · 2025 · 8 claims · 6 setups

Has reproduction

SGS is a user-friendly, collaborative, versatile browser for integrative visualization of single-cell and spatial multimodal (scMulti-omics) data

dorsal hematopoietic brain onek1k sn-m3c-seq scatac-seq spatial
scSurv: a deep generative model for single-cell survival analysis.

PMID 41429574 · PMC12797213 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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scSurv combines a Cox proportional hazards model with a deep generative model (VAE) of single-cell transcriptomes to estimate individual cellular contributions to clinical outcomes

simulated tcga melanoma renal scrna-seq bulk single-cell
Deciphering immune and cellular reprogramming during the progression from inflammatory bowel disease to colorectal cancer using multi-omics single-cell and spatial transcriptomics.

PMID 42001187 · PMC13122952 · Journal of translational medicine · 2026 · 8 claims · 5 setups

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CEACAM5 is consistently upregulated across Crohn's disease and ulcerative colitis samples and links epithelial activation in IBD to tumorigenic processes in CRC

intestinal colorectal single-cell serum bulk single-cell spatial
SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.

PMID 41615289 · PMC12856952 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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WGCNA's reliance on a scale-free topology assumption is problematic because real co-expression networks do not consistently exhibit scale-free properties

gse114007 gse261545 dryad.37pvmcvsg prjna762466 bulk spatial merfish
Novel fatty acid metabolism-related molecular subtyping and prognostic signature for breast cancer.

PMID 41674979 · PMC12885896 · Translational cancer research · 2026 · 8 claims · 8 setups

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A FAM-related gene prognostic model (FAMGM) built using CoxBoost and random survival forest was identified as the optimal model among 101 machine learning combinations, based on highest average C-index across TCGA-BRCA and GSE96058 cohorts

tcga-brca gse96058 brca breast bulk single-cell spatial
Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

tcga-luad best brain advanced bulk kaplan-meier pearson

Experiments

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

Comparative multi-omic analysis reveals conserved and derived mechanisms of fin and limb regeneration.

Single-cell and spatial transcriptomic profiling of cardiac fibroblasts following myocardial infarction.

Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

sCellST predicts single-cell gene expression from H& E images.

Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer.

Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

scSurv: a deep generative model for single-cell survival analysis.

Deciphering immune and cellular reprogramming during the progression from inflammatory bowel disease to colorectal cancer using multi-omics single-cell and spatial transcriptomics.

SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.

Novel fatty acid metabolism-related molecular subtyping and prognostic signature for breast cancer.

Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.