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).

• 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

• 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

• FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis.

  PMID 41839892 · PMC13201544 · Nature communications · 2026 · 8 claims · 6 setups

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  FineST, a bimodal contrastive learning model integrating histology (Virchow2 ViT features) and spatial gene expression, enables nuclei-resolved high-resolution RNA imputation.

  colorectal crc breast he-stained spatial type ccc

• VISTA uncovers missing gene expression and spatial-induced information for spatial transcriptomic data analysis.

  PMID 41507434 · PMC12891734 · Communications biology · 2026 · 8 claims · 6 setups

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  VISTA predicts unmeasured gene expression in subcellular spatial transcriptomic data by integrating scRNA-seq and SST through variational inference and geometric deep learning with built-in uncertainty quantification

  brain breast embryo muscle imaging-based sequencing spot-based

• ISG15-driven immune modulation and tumor progression in breast cancer metastasis: insights from single-cell and spatial transcriptomics.

  PMID 41639695 · PMC12958617 · BMC medicine · 2026 · 8 claims · 8 setups

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  CSC proportion is elevated in lymph node metastatic tumor tissue (BRCA_LNMT) compared to primary tumor (BRCA_PT)

  4t1 brca tcga-brca top single-cell spatial bulk

• SpaPheno: linking spatial transcriptomics to clinical phenotypes with interpretable machine learning.

  PMID 41975540 · PMC13185361 · Genome medicine · 2026 · 8 claims · 8 setups

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  SpaPheno integrates spatial transcriptomics with clinically annotated bulk RNA-seq to identify spatially resolved biomarkers predictive of patient outcomes including survival, tumor stage, and immunotherapy response

  cortex liver clear breast spatial elastic

• Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells.

  PMID 35177610 · PMC8854666 · Nature communications · 2022 · 8 claims · 7 setups

  Has reproduction · 84

  SHARC uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA

  model dipicolinic hek293t 28s crosslinking nmr crosslink

• Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies.

  PMID 41501078 · PMC12780049 · Nature communications · 2026 · 8 claims · 7 setups

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  MAGPIE is a computational framework (Snakemake workflow) that co-registers Visium spatial transcriptomics with MSI metabolomics and tissue morphology images from same or consecutive sections

  lung brain publicly rodent spatial desi h&e

• S3RL: Enhancing Spatial Single-Cell Transcriptomics With Separable Representation Learning.

  PMID 41556263 · PMC13042551 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  S3RL is a separable representation learning framework that denoises sparse spatial transcriptomic data and enhances biologically relevant signals by integrating gene expression, spatial coordinates, and histological image features.

  dorsolateral dlpfc nanostring spatial cell-type multi-platform

• Spatial transcriptomics identifies differentiation, lipid metabolism, and retinoid pathway alterations in acne vulgaris.

  PMID 41657309 · PMC12892907 · JCI insight · 2026 · 8 claims · 6 setups

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  A custom KRT5-directed segmentation pipeline improves transcript assignment accuracy in the spatially complex sebaceous gland compared with standard multimodal or nuclei-expansion segmentation

  skin inflammatory tert gtrd spatial immunohistochemistry reanalysis

• Spatial multi-omics identifies a NOTCH3-mediated capillary-mCAF crosstalk driving immune exclusion in hepatocellular carcinoma.

  PMID 42099451 · PMC13147954 · iMeta · 2026 · 8 claims · 8 setups

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  A high-resolution spatial multi-omics atlas of HCC (CosMx transcriptomics + GeoMx proteomics + pan-cancer scRNA-seq of CAFs under ICB) reveals coordinated cellular topography of the tumor microenvironment

  hcc cafs independent spontaneous spatial pan-cancer multiplex

• Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.

  PMID 41547856 · PMC12917120 · Nature communications · 2026 · 8 claims · 8 setups

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  GARDEN identifies and characterizes rare pathogenic cell populations/regions in spatial omics by embedding graph-based dynamic attention into a spatially-aware graph fusion contrastive model

  breast anterior brain olfactory 10x starmap slide-seqv2

• 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

• Targeting the Lipid Metabolism Proteins FASN and GPAM in Alveolar Type II Cells Decreases Lung Metastasis.

  PMID 41778850 · PMC7619144 · Cancer discovery · 2026 · 7 claims · 8 setups

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  AT2 cells and surfactant lipids (e.g., PC, PE, PI, PG) are enriched in the vicinity of breast cancer lung metastases in both patients and mice

  postmortem lungs lung at2 immunohistochemistry maldi-msi longitudinal

• Vγ1 γδ T cells steer airway macrophages toward a profibrotic response in an autochthonous lung cancer mouse model.

  PMID 41779856 · PMC12959402 · Science advances · 2026 · 7 claims · 6 setups

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  Lung tumors drive expansion of both CD27+ and CD27- pulmonary γδ T cells, which acquire distinct spatial and phenotypic changes in the tumor microenvironment

  spc-cre+ microdissected sorted merged flow confocal single-cell

• SMART: spatial multi-omic aggregation using graph neural networks and metric learning.

  PMID 41896208 · PMC13031631 · Nature communications · 2026 · 8 claims · 5 setups

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  SMART accurately identifies spatial regions of anatomical structures and is compatible with spatial datasets of any type and number of omics layers

  simulated lymph brain spleen simulated spatial multi-section

• iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.

  PMID 42108258 · PMC13158306 · Signal transduction and targeted therapy · 2026 · 8 claims · 5 setups

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  iS2C2 integrates the S2C2 cell-cell communication algorithm with LLMs to generate biologically interpretable hypotheses from scRNA-seq and spatial transcriptomics data

  single-cell algorithm domain scrna-seq single-cell perturbation llm-based

• 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

• Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

  PMID 41542331 · PMC12802566 · Health science reports · 2026 · 7 claims · 8 setups

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  BPC differentiation is significantly altered in UC, driven by a FABP1-led functional gene matrix

  colorectal colon patients bulk single-cell spatial bulk

• Ectopic CD11c Drives SMAD3-Mediated Aberrant Antigen Presentation and Epithelial-Mesenchymal Transition in Esophageal Squamous Cell Carcinoma.

  PMID 41799568 · PMC12963642 · Cancer communications (London, England) · 2026 · 8 claims · 13 setups

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  An ESCC epithelial cell subcluster with ectopic CD11c (ITGAX) expression, found in both mice and humans, exhibits concurrent impaired antigen presentation and EMT phenotypes

  4-nqo-induced escc esophageal lung multiplex flow whole-genome