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).

• Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

  PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database

  epithelial-based tcga gdsc muscle-invasive differential co-expression signature

• 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

• Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.

  PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups

  Has reproduction · 71

  Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.

  breast colorectal brca representative gene comparative multi-omic

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• Therapy effect of either paclitaxel or cyclophosphamide combination treatment in patients with epithelial ovarian cancer and relation to TP53 gene status.

  PMID 9703286 · PMC2063030 · British journal of cancer · 1998 · 6 claims · 4 setups

  Full-text index only

  Paclitaxel/cisplatin therapy produces a higher positive response rate than cyclophosphamide/cisplatin therapy in advanced ovarian cancer

  patients frozen genomic clinically randomized rt-pcr temporal

• Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

  PMID 17868458 · PMC2375029 · Genome biology · 2007 · 8 claims · 8 setups

  Full-text index only

  Co-culture of certain breast cancer cell lines with stromal fibroblasts induces interferon-response genes (IRGs) in a subset of cancer cells

  mda-mb231 epithelial breast early-stage cdna quantitative facs

• Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD.

  PMID 36762572 · PMC10104628 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023 · 7 claims · 7 setups

  Has reproduction · 81

  SCAD, a transfer learning framework integrating adversarial discriminative domain adaptation (ADDA), can infer single-cell drug sensitivities by transferring knowledge from bulk RNA-seq pharmacogenomic data (GDSC) to scRNA-seq target domains

  pan-cancer pc9 451lu a375 bulk scrna-seq computational

• 25th Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, USA, 10-14 December 2002 Update on preclinical and translational research.

  PMID 12631391 · PMC154153 · Breast cancer research : BCR · 2003 · 8 claims · 8 setups

  Full-text index only

  Growth factor signalling (EGF/HER-2/MAPK, AKT) phosphorylates the oestrogen receptor and drives development of endocrine-resistant breast cancer

  xenograft serum frozen tumour xenograft mass cdna

• A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

  PMID 19861443 · PMC2783430 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

  Full-text index only

  A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease

  duke nci-60 mayo spanish gene cdna igvh

• Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients.

  PMID 17626639 · PMC1952070 · BMC cancer · 2007 · 7 claims · 4 setups

  Full-text index only

  EGFR mutations (exon 19 deletions, exon 21 L858R) did not correlate with gefitinib response in this cohort

  microdissected formalin-fixed archival clinical pcr fluorescence laser

• Social and ethical implications of genomics, race, ethnicity, and health inequities.

  PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups

  Full-text index only

  Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.

  population prostate non-small-cell breast genome-wide gene somatic

• PIK3CA-activating mutations and chemotherapy sensitivity in stage II-III breast cancer.

  PMID 18371219 · PMC2397526 · Breast cancer research : BCR · 2008 · 7 claims · 4 setups

  Full-text index only

  PIK3CA mutations are not associated with altered sensitivity to preoperative anthracycline-based or taxane-based chemotherapy in ER-positive and ER-negative breast tumors

  tumor breast stage direct immunohistochemistry fluorescence

• scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

  PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups

  Has reproduction · 62

  scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer

  panglaodb cancer geo gse137829 single-cell bulk

• Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.

  PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 51

  A 15-gene immune infiltration-related signature (IRS) predicts overall survival in breast cancer, with higher IRS indicating worse prognosis

  tcga metabric geo breast immune bulk microarray

• No significant role for beta tubulin mutations and mismatch repair defects in ovarian cancer resistance to paclitaxel/cisplatin.

  PMID 16095531 · PMC1199587 · BMC cancer · 2005 · 6 claims · 4 setups

  Full-text index only

  TUBB exon 4 mutations are not found in primary ovarian carcinomas treated with paclitaxel/cisplatin

  ovarian same pcr agarose microsatellite

• A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.

  PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups

  Has reproduction · 51

  An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73

  bladder tcga bulk univariate integrative

• Machine learning developed an intratumor heterogeneity signature for predicting clinical outcome and immunotherapy benefit in bladder cancer.

  PMID 39100839 · PMC11291408 · Translational andrology and urology · 2024 · 8 claims · 8 setups

  Has reproduction · 40

  An integrative machine learning procedure (10 methods, 101 algorithm combinations) identified an Enet (alpha=0.2)-based intratumor heterogeneity-related signature (IRS) with the highest average C-index (0.69) across TCGA and GEO cohorts

  bladder skin bulk integrative immune

• Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.

  PMID 15686596 · PMC549029 · Molecular cancer · 2005 · 8 claims · 5 setups

  Full-text index only

  A chromatin library coupled with experimental validation can productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin.

  t-47d agarose chromatin cloning

• Pharmacogenomics of gemcitabine: can genetic studies lead to tailor-made therapy?

  PMID 17595663 · PMC2360307 · British journal of cancer · 2007 · 8 claims · 14 setups

  Full-text index only

  A SNP in the cytidine deaminase (CDA) gene (208G>A, haplotype *3) decreases gemcitabine clearance, increases Cmax/AUC, and increases neutropenia risk when gemcitabine is combined with platinum drugs or 5-FU

  japanese paraffin-embedded tumour recombinant prospective immunohistochemistry pcr

• Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

  PMID 17397520 · PMC1868923 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

  Full-text index only

  Genome-wide expression microarray studies reveal transcriptional networks/signatures that explain breast cancer biological and clinical heterogeneity

  breast early-stage diffuse dlbcl gene