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).

• CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

  PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 4 setups

  Has reproduction · 87

  CoINcIDE is a novel framework for discovering patient subtypes across multiple datasets that requires no between-dataset transformations (e.g., batch correction)

  breast ovarian simulated gene consensus simulated

• Easy and efficient ensemble gene set testing with EGSEA.

  PMID 29333246 · PMC5747338 · F1000Research · 2017 · 8 claims · 2 setups

  Has reproduction · 97

  EGSEA combines results from up to 12 prominent gene set testing algorithms to obtain a consensus ranking of biologically relevant gene sets

  mammary bulk microarray

• Stromal androgen signaling acts as tumor niches to drive prostatic basal epithelial progenitor-initiated oncogenesis.

  PMID 36323713 · PMC9630272 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  Loss of AR in stromal Gli1-lineage cells diminishes prostate epithelial oncogenesis and tumor development in vivo

  ugm hi-myc prostate hmyctg+ genetically single-cell immunohistochemistry

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 8 claims · 8 setups

  Has reproduction · 59

  Key genes AR, AKT1, UBC, CDH1, SMAD3, ROR1, and ROR2 are associated with chemotherapy resistance and poor prognosis in metastatic breast cancer

  breast tcga-brca geo gse40622 gene pan-cancer differential

• The diagnosis and management of pre-invasive breast disease: promise of new technologies in understanding pre-invasive breast lesions.

  PMID 14580250 · PMC314415 · Breast cancer research : BCR · 2003 · 8 claims · 8 setups

  Full-text index only

  ADH and ductal carcinoma in situ (DCIS) are precursor lesions molecularly similar to adjacent invasive breast cancer

  locally adh brca1 malignant array chromosome-based cdna

• INTERFEROME: the database of interferon regulated genes.

  PMID 18996892 · PMC2686605 · Nucleic acids research · 2009 · 8 claims · 6 setups

  Full-text index only

  INTERFEROME is an open-access database integrating IRG expression data with annotation, orthologue sequences from 37 species, tissue expression, and gene regulatory (TFBS) information

  chimp ifn-treated tissues irg microarray in-house basal

• Molecular tumor profiling: translating genomic insights into clinical advances.

  PMID 15287965 · PMC507868 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Gene-expression profiling can distinguish BRCA1- and BRCA2-linked breast tumors from sporadic breast tumors with similar hormone-receptor status

  breast ovarian panel tumor gene-expression candidate-gene large-scale

• SMAC, a computational system to link literature, biomedical and expression data.

  PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  SMAC is a tool that extracts, prioritises, integrates and analyses biomedical and molecular data according to user-defined terms

  pubmed invasive geo genes semantic computational gene

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

  PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

  Full-text index only

  Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

  chromosome genomic pbmc multi-species phylogenetic bisulphite