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).

• Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

  PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

  Full-text index only

  Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

  normalized individuals subset same affymetrix fluorescent snp

• Telomerase-Associated Genes as Prognostic Markers in High-Grade Serous Ovarian Cancer.

  PMID 42050900 · PMC13137916 · Medical science monitor : international medical journal of experimental and clinical research · 2026 · 8 claims · 8 setups

  Full-text index only

  TAGs are linked to HGSOC progression and yield a candidate prognostic model

  hgsoc tcga-ov scrna-seq-derived single-cell bulk cellchat

• Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.

  PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups

  Has reproduction · 100

  Exploratory adaptation (stochastic gene-regulatory network perturbation) explains how GBM cells adapt phenotypically across spatially distinct tumor regions

  patient-derived low-grade tf-gene single-sample bulk differential gene

• Pseudotimecascade Visualizes Gene Expression Cascade in Pseudotime Analysis.

  PMID 41939293 · PMC13047748 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups

  Full-text index only

  Pseudotimecascade jointly analyzes multiple genes to uncover their relative temporal ordering and stage-specific activation patterns along pseudotime.

  bone genes same scrna-seq single-sample gene

• Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.

  PMID 33253153 · PMC7728210 · PLoS computational biology · 2020 · 7 claims · 5 setups

  Has reproduction · 90

  A systematic clustering algorithm for ATAC-seq data can be built by binarizing the genome into open/closed chromatin (1/0) strings and computing Hamming distances between samples for hierarchical clustering.

  monocytes natural hematopoietic leukemia atac-seq hierarchical

• Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

  PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 8 setups

  Has reproduction

  Metabolic status is closely tied to tumor differentiation state, with distinct metabolic reprogramming occurring during thyroid cancer dedifferentiation

  thyroid fuscc gse193581 aggregated untargeted whole-exome transcriptomics

• QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

  PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

  genomic same pseudo-normal artificially snp fish molecular

• Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

  PMID 39074091 · PMC11285958 · PloS one · 2024 · 7 claims · 8 setups

  Full-text index only

  JAG, DLL, and NOTCH family gene/protein expression varies diversely across 15 cancer types relative to normal tissue, sometimes discordant between mRNA and protein levels.

  tumor degs cancer jag bulk proteomics gene

• The Molecular and Functional Landscape of Resistance to FOLFIRI Chemotherapy in Metastatic Colorectal Cancer.

  PMID 40981426 · PMC12877753 · Cancer discovery · 2026 · 8 claims · 7 setups

  Full-text index only

  FOLFIRI-resistant PDX tumors show transcriptional upregulation of innate immunity and mitochondrial metabolism genes and reduced expression of DNA polymerase POLD1

  mcrc pdx patients patient-derived drug whole-exome bulk