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).

• 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

• 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

• Identification of a new population of Tnn(+) progenitors to form tendon enthesis fibrocartilage.

  PMID 42009636 · PMC13096267 · Bone research · 2026 · 8 claims · 8 setups

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  A novel Tnn+ progenitor cell population resides in the tendon enthesis and serves as a cellular origin of fibrocartilage lineages

  tendon developing spatial single-cell visium single-cell stamp

• 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

• 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

• 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 reveals altered communities and drivers of aberrant epithelia and pro-fibrotic fibroblasts in interstitial lung diseases.

  PMID 41576947 · PMC12985369 · Cell genomics · 2026 · 7 claims · 7 setups

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  snRNA-seq census of 227,680 nuclei across 48 cell types reveals altered cellular states and compositional rewiring of the distal lung in ILD

  frozen lung flash-frozen spatial single-nucleus scrna-seq 10x

• Dissecting glioblastoma risk signatures in the tumor immune microenvironment based on multi-dimensional transcriptomics.

  PMID 41880523 · PMC13154832 · GigaScience · 2026 · 7 claims · 8 setups

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  Hallmarks of malignancy and cell cycle regulatory pathways are consistently enriched across single-cell, bulk, and spatial transcriptomic modalities, promoting tumor cell proliferation and progression.

  tumor gbm normal wild-type single-cell bulk microarray

• Single-cell and spatial profiling of peripheral blood and synovium unveils pro-arthritis CNBP(+) myeloid cells.

  PMID 41928282 · PMC13169754 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  Peripheral CNBP+ monocytes are expanded and show elevated 'inflammatory response' pathway scores in arthritis patients

  peripheral blood synovial arthritis single-cell bulk immunofluorescence

• Single-cell and spatial transcriptome analysis reveals the potential therapeutic targets for testicular sex cord-stromal cell tumor.

  PMID 42057139 · PMC13130799 · Biomarker research · 2026 · 8 claims · 8 setups

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  Tumor areas of TSCST show significantly low expression of immune cell genes, indicating an immune-cold tumor microenvironment

  fresh fetal paraffin-embedded paraffin single-nucleus scrna-seq spatial

• 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

• Benchmarking tools for deciphering cellular crosstalk in spatially-resolved transcriptomics.

  PMID 41952215 · PMC13174004 · Genome biology · 2026 · 8 claims · 5 setups

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  No prior systematic, quantitative benchmark exists for CCI inference methods specifically developed for spatial transcriptomics across multiple platforms

  synthetic real simulated simulation spot-purity real-data

• 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

• 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

• 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

• LIMCH1-enriched extracellular vesicles promote vascular permeability in early-onset preeclampsia.

  PMID 41604492 · PMC12851021 · Science advances · 2026 · 8 claims · 8 setups

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  LIMCH1 is identified as an Eo-PE-associated EV protein via serum sEV proteomics combined with GEO placental transcriptome datasets

  serum placenta jar huvecs lc-ms exoview nanoflow

• Identification of cycling regulatory T cell precursors as conductors of immune escape during breast carcinoma progression.

  PMID 41997138 · PMC13213619 · Cancer cell · 2026 · 8 claims · 8 setups

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  A novel proliferative Treg precursor state, cycling Treg (cycTreg: FOXP3^int, MKI67^hi, IKZF2/4^int-hi), is absent in normal breast, low in DCIS, and strongly expanded in IBC

  normal mammary dcis tumor-draining scrna-seq spatial multiplex

• 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