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).

• AGPAT3 reshapes tumor cell vulnerability to IFNγ-mediated ferroptosis and enhances immunotherapy efficacy through lipid remodeling.

  PMID 41807033 · PMC12983827 · Journal for immunotherapy of cancer · 2026 · 8 claims · 8 setups

  Full-text index only

  A ferroptosis-driver gene signature (FD.sig) and machine learning model (FD.model) can predict ICI response

  pan-cancer tcga a375 machine single-cell bulk

• Single duplex DNA sequencing with CODEC detects mutations with high sensitivity.

  PMID 37106072 · PMC10181940 · Nature genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 78

  CODEC concatenates both strands of an original DNA duplex into a single NGS read pair via an adapter quadruplex and strand-displacing extension, enabling single-duplex resolution

  cfdna na12878 genomic sperm targeted whole-genome whole-exome

• Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

  PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

  Full-text index only

  TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

  myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental

• DAGFormer: A graph-based domain adaptation approach for single-cell cancer drug response prediction.

  PMID 41417875 · PMC12795466 · PLoS computational biology · 2025 · 7 claims · 5 setups

  Has reproduction

  DAGFormer constructs cellular neighbor graphs using diverse topological strategies to represent intercellular interactions for drug response prediction

  pan-cancer jhu006 scc47 pc9 bulk scrna-seq

• Wx: a neural network-based feature selection algorithm for transcriptomic data.

  PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.

  tcga gse72056 gse40419 gse103322 bulk single-cell rna-seq

• Comprehensive analysis of the causal risk factor from hypertension associated with prognosis and therapeutic response in renal cell carcinoma by multi-omics analysis and validation.

  PMID 41680825 · PMC12998095 · Biology direct · 2026 · 8 claims · 8 setups

  Full-text index only

  A 48-gene cross-species hypertension (HTN) gene module identified from human and SHR rat scRNA-seq can classify ccRCC patients into two molecular subgroups with distinct survival and targeted therapy response

  aortic spontaneously tcga icgc single-cell bulk summary-data-based

• Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

  PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

  Full-text index only

  RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

  tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic

• Atlas-guided discovery of transcription factors for T cell programming.

  PMID 41639465 · PMC13017511 · Nature · 2026 · 8 claims · 8 setups

  Full-text index only

  A multi-omics atlas (Taiji pipeline) integrating RNA-seq and ATAC-seq across nine CD8+ T cell states can predict TF activity and identify state-selective versus multi-state TFs

  cd8+ lcmv p14 c57bl rna-seq pearson crispr

• iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

  PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

  nsclc coad brca tcga scrna-seq bulk rna-seq

• Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy.

  PMID 41820396 · PMC13121706 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  TRIM, a conditional multi-modal variational autoencoder integrating paired scRNAseq and scTCRseq data, predicts T cell clonality and transcriptional states at unmeasured tissue sites/timepoints.

  hnscc colorectal pan-cancer tcr paired umap convolutional

• Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies.

  PMID 35680918 · PMC9184574 · Scientific data · 2022 · 8 claims · 8 setups

  Has reproduction · 82

  Four reference samples (Sample A, Sample B, Sample C, Sample Spike-in/AC5) were developed with large numbers of high-confidence positive and negative small variant positions to serve as known content for oncopanel performance assessment.

  agilent burning integrated igenetech targeted

• Colorectal microenvironment determines the prognosis of colorectal cancer.

  PMID 41495419 · PMC12868731 · Experimental & molecular medicine · 2026 · 8 claims · 7 setups

  Full-text index only

  The colorectal microenvironment (classified via NBT gene expression as tumor-supportive vs healthy) can serve as a prognostic biomarker predicting cancer invasiveness and recurrence

  paired nbt slide bulk bulk 16s single-cell

• Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.

  PMID 35053177 · PMC8773604 · Biomolecules · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  The 76GS, KS, and MLR EMT scoring metrics show concordant trends in quantifying EMP across bulk RNA-seq datasets spanning multiple cancer types

  bulk py2t mcf10a airway transcriptomic rna-seq single-cell

• Systematic elucidation of genetic mechanisms underlying cholesterol uptake.

  PMID 37228746 · PMC10203276 · Cell genomics · 2023 · 8 claims · 8 setups

  Full-text index only

  Genome-scale CRISPR-Cas9 knockout screening in HepG2 cells identifies 490 genes whose disruption alters LDL-C uptake

  hepg2 depmap flow genome-scale individual

• Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

  PMID 41564862 · PMC12866174 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  A 19-factor cancer-immunoinstructive secretory signature (CISS) is present across multiple human cancers and correlates with pro-tumorigenic tumor microenvironments and poor patient survival.

  pancreatic kpc pdac tcga-paad rna-seq bulk proteomics

• Identification and Validation of an Autophagy-Related Gene Signature for Prognostic Prediction and Immunotherapy Response in Esophageal Squamous Cell Carcinoma.

  PMID 41681864 · PMC12897147 · Cancers · 2026 · 8 claims · 8 setups

  Full-text index only

  A 4-ARG prognostic model (NBEA, CLOCK, NLRX1, MAGEA3) built via stepwise multivariate Cox regression stratifies ESCC patients into high- and low-risk groups with significantly different survival.

  escc gse53625 gse160269 imvigor210 microarray univariate single-cell

• CLK1 Promotes Myeloid-Derived Suppressor Cell Trafficking and Reprograms the Tumor Microenvironment by Activating Hippo/YAP Signaling in Colorectal Cancer.

  PMID 41686262 · PMC13136879 · Cancer immunology research · 2026 · 8 claims · 8 setups

  Full-text index only

  CLK1 is markedly upregulated in immune-cold colorectal tumors and correlates with increased MDSC infiltration and CD8+ T-cell exclusion

  colorectal tcga-coad ct26 tumor scrna-seq bulk multiplex

• DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.

  PMID 41761000 · PMC13043845 · Discover oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  Neuroactive ligand–receptor signaling is among the most significantly upregulated pathways in LUAD relative to normal lung tissue.

  tcga-luad tcga luad dendritic-cell bulk survival pan-cancer