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).

• Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources.

  PMID 42045691 · PMC13175893 · Nature genetics · 2026 · 6 claims · 7 setups

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  INSPIRE is a deep-learning method that unifies adversarial learning with a GNN-based encoder and integrated NMF to interpretably integrate multiple spatial transcriptomics datasets

  synthetic dorsolateral brain cortex simulated visium spatial

• Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.

  PMID 42062553 · PMC13259927 · Nature methods · 2026 · 8 claims · 6 setups

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  Xenium data show strong consistency across patients and technical replicates, with little technical variation between platforms

  ffpe matched xenium xenium single-nucleus immunohistochemistry

• Dissecting the immunosuppressive microenvironment of LAMA3 + malignant cells and SPP1 + macrophages in esophageal squamous cell carcinoma using single-cell and spatial transcriptomics.

  PMID 41845425 · PMC13104401 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  A LAMA3+ epithelial subpopulation (C3) enriched at the invasive tumor front shows strong EMT signatures and is associated with poor prognosis

  escc epithelial scrna-seq tcga-escc scrna-seq spatial infercnv

• Parasitic connections: a patescibacterial epibiont, its methylotrophic gammaproteobacterial host, and their phages.

  PMID 41805398 · PMC13059738 · mBio · 2026 · 8 claims · 7 setups

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  Strigamonas methylophilicida sp. nov. is a new patescibacterial genus and species within the family Absconditicoccaceae

  freshwater fixed rsa individual phase transmission fluorescence-activated

• MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments.

  PMID 41917425 · PMC13201759 · Communications biology · 2026 · 7 claims · 6 setups

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  MIMIC is a reproducible, semi-automated workflow that co-registers and jointly analyzes MALDI-MSI and IMC data using a chain of before/after microscopy images.

  liver regions artificial maldi-msi imaging multi-step

• Dysregulation of alternative splicing patterns in the ovaries of reproductively aged mice.

  PMID 41630016 · PMC13046076 · Reproduction (Cambridge, England) · 2026 · 8 claims · 5 setups

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  Reproductive aging in mouse ovaries is associated with widespread alternative splicing changes, including shifts in exon usage, splice site selection, and transcript boundaries.

  ovary computational direct cryosectioning translation

• Spatial transcriptomics unveils immune cellular ecosystems associated with patient survival in diffuse large B-cell lymphoma.

  PMID 42010788 · PMC13102037 · Oncoimmunology · 2026 · 7 claims · 7 setups

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  DLBCL tissues are organized into six recurrent, spatially defined cellular ecosystems (Cell-Eco) with distinct immune compositions, transcriptional programs, and neighborhood architectures.

  dlbcl cd45+ spots scrna-seq spatial scrna-seq cell-type

• Single-cell spatial analysis stratifies lung adenocarcinoma with rare actionable mutations and reveals immune-modulatory cellular crosstalk.

  PMID 42013848 · PMC13198233 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Consensus meta-program (MP) expression patterns stratify LUAD patients with rare and reference oncogenic mutations into ICI-MP-H and ICI-MP-L subgroups reflecting differential predicted ICI benefit

  luad matched tcga epithelial single-cell multiplex bulk

• 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

• Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

  PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 8 setups

  Has reproduction · 78

  INVADE-seq (single-cell RNA-seq combined with 16S rRNA targeting) detects a sparse but widespread bacterial presence across diverse testicular cell types

  testis young testicular invade-seq histology sperm

• An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

  PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

  oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor

• Comprehensive analysis of metastatic gastric cancer tumour cells using single-cell RNA-seq.

  PMID 33441952 · PMC7806779 · Scientific reports · 2021 · 8 claims · 6 setups

  Has reproduction · 47

  Carcinoma cell profiles are distinct for each patient, while diverse microenvironmental (nonmalignant) subsets are shared across different patients.

  tumour single differentially seurat-identified single-cell differential gene

• Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

  PMID 41526381 · PMC12902073 · Nature communications · 2026 · 8 claims · 8 setups

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  BioCRE, a novel bi-orientation regression algorithm, more accurately links genes to candidate cis-regulatory elements (CREs) than existing tools Signac and ArchR

  gastrulating gastrula gold-standard embryo single-cell computational promoter

• Single-cell spatial transcriptomic analysis of human skin anatomy.

  PMID 41872488 · PMC13083264 · Nature genetics · 2026 · 8 claims · 6 setups

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  MERFISH-based spatial atlas of ~1.2 million cells resolves 45 cell types across 114 samples and 15 anatomic sites in normal human skin

  normal skin gtex matched merfish scrna-seq bulk

• Spatial multi-omics unveils the monoclonal origin, neuroendocrine plasticity, and microenvironment niches in combined small-cell lung cancer.

  PMID 41966692 · PMC13130634 · Cell reports. Medicine · 2026 · 8 claims · 6 setups

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  Different histologic components within cSCLC tumors share a monoclonal origin

  ffpe sections tumor luad multi-region spatial single-nucleus

• Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

  PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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  EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

  crc epcam+ aggregated cancer scrna-seq copy pseudobulk

• Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.

  PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts

  tcga-brca triple-negative ffpe bulk univariate kaplan-meier

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell

• A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

  PMID 36333777 · PMC9636832 · Microbiome · 2022 · 8 claims · 7 setups

  Has reproduction · 64

  Reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut-associated) and Deferribacteres (midgut-associated)

  rimicaris quality-filtered dereplicated deferribacteres shotgun ssu differential

• A DNA microarray survey of gene expression in normal human tissues.

  PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups

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  Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.

  normal common computational each two-color comparative unsupervised