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).

• POSTN(+) fibroblast‑secreted small extracellular vesicles drive macrophage M2 polarization through BMP4/BMPR2/Smad signaling.

  PMID 41645751 · PMC12891935 · Oncology reports · 2026 · 8 claims · 8 setups

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  Integration of two HNSCC scRNA-seq datasets reveals two distinct fibroblast subtypes: POSTN- and POSTN+ fibroblasts

  hnscc tcga-hnscc oscc oscc-derived single-cell bulk immunohistochemistry

• Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline.

  PMID 41850291 · PMC13030954 · Cell reports methods · 2026 · 8 claims · 7 setups

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  Metapipeline-DNA automates germline and somatic DNA sequencing analysis end-to-end, from raw reads through preprocessing, feature detection, QC, and visualization.

  pcawg giab pcawg-5 tumor-normal whole-genome germline somatic

• Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

  PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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  A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

  larc scrna-seq scissor+ single-cell bulk pseudotime

• Notch3 regulates pericyte phenotypic plasticity in colorectal cancer.

  PMID 41618002 · PMC12960917 · Communications biology · 2026 · 8 claims · 8 setups

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  Murine tumor pericytes originate from normal tissue-resident pericytes that proliferate inside tumors

  aom crc pdgfrβ-creert2 notch3-creert2 scrna-seq facs lineage

• Single-cell RNA sequencing of adenoid cystic carcinoma of the breast reveals cellular heterogeneity and tumor microenvironment features.

  PMID 41761191 · PMC13041279 · BMC medical genomics · 2026 · 8 claims · 7 setups

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  H19+ myoepithelial cells (H19+myoEpC) represent the dominant malignant subpopulation in ACCB, characterized by the majority of large-scale CNVs and high expression of oncogenic pathway genes and ligands (e.g., LAMB1, WNT6)

  tumor hnacc epithelial accb single-cell scrna-seq copy

• 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

• 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

• A global database for modeling tumor-immune cell communication.

  PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

  Has reproduction · 66

  TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

  pubmed scrna-seq tcga basal manual scrna-seq bulk

• Protocol for quantifying interaction patterns among genomic alterations in cancer.

  PMID 41686643 · PMC12915222 · STAR protocols · 2026 · 6 claims · 5 setups

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  Background-aware permutation strategies that constrain permutation per gene and per sample enable robust, scalable inference of condition-specific (context-aware) genetic interactions across cancer cohorts

  msk-met somatic copy-number binary

• Deep-Learning Tool ScVital Enables Species-Agnostic Integration of Cancer Cell States.

  PMID 41223329 · PMC13053053 · Cancer research · 2026 · 7 claims · 7 setups

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  scVital is a variational autoencoder with an adversarially trained discriminator that embeds scRNA-seq data from different species into a species-agnostic latent space to overcome batch effect.

  pbmc normal pancreatic lung scrna-seq

• A human tumor-immune organoid model of glioblastoma.

  PMID 41505256 · PMC12969483 · Cell reports · 2026 · 8 claims · 8 setups

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  iHOTT is an autologous co-culture platform integrating patient-derived tumor cells and matched PBMCs within human cortical organoids

  ihott sorted recurrent flow immunostaining multiplex

• 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

• 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

• Probing the cancer genome.

  PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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  Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

  mcf-7 tumor lung oral sanger solexa gistic

• Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

  PMID 42074110 · PMC13115843 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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  25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

  kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide

• DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.

  PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 8 claims · 7 setups

  Has reproduction · 84

  DeepProg is a novel ensemble framework of deep-learning and machine-learning approaches that robustly predicts patient survival subtypes using multi-omics data

  cancer breast hepatocarcinoma tcga multi-omics gene rna-seq

• 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

• A Soft Matrix Microenvironment Promotes Laterally Spreading Tumors via Oxidative Phosphorylation-Dependent Cell Adhesion.

  PMID 41833005 · PMC13248847 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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  LSTs exhibit a more malignant phenotype than PAs, with higher inferred CNV scores, stronger genetic correlation with colorectal cancer, and downregulation of adhesion molecules

  patients bulk colorectal epithelial clinical bulk single-cell

• SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

  PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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  SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

  single hcc2218 nsclc array gene multi-omics

• 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