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

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups

  Has reproduction · 67

  A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.

  mammary five singlecellexperiment individual droplet-based quality doublet

• The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progression.

  PMID 16573809 · PMC1450280 · BMC genomics · 2006 · 7 claims · 8 setups

  Full-text index only

  MDA-amplified DNA does not introduce major distortion of copy number imbalance assignments compared to unamplified DNA in control CGH experiments.

  laser-capture-microdissected normal cancer fresh-frozen array gacgh laser

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 8 setups

  Has reproduction · 71

  Liver metastatic potential in RCC is marked by stem-like tumor states, metabolic plasticity, and microenvironmental remodeling.

  right-sided single integrated malignant single-cell copy dimensionality

• "Sequencing-grade" screening for BRCA1 variants by oligo-arrays.

  PMID 18973698 · PMC2583995 · Journal of translational medicine · 2008 · 7 claims · 6 setups

  Full-text index only

  An oligo-array platform can detect BRCA1 SNPs, insertions, and deletions of known and unknown variants, including in heterozygous conditions, with accuracy comparable to direct sequencing

  genomic pcr mcf-10a brca1 oligo-nucleotide direct pcr

• miRge 2.0 for comprehensive analysis of microRNA sequencing data.

  PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups

  Has reproduction · 89

  miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification

  pooled colon datasets small a-to-i novel