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).

• Loss of long-range co-expression is a common feature in cancer.

  PMID 41935098 · PMC13247121 · NPJ systems biology and applications · 2026 · 8 claims · 7 setups

  Full-text index only

  In cancer, the strongest co-expressed gene pairs (top MI values) are predominantly intra-chromosomal, unlike in normal tissue.

  tissues same bladder cancer bulk differential bootstrap

• Determination of complete chromosomal haplotypes by bulk DNA sequencing.

  PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups

  Has reproduction · 97

  A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts

  rpe-1 na12878 aneuploid linked-read hi-c bulk

• Gli3R-mediated inhibition of hedgehog signaling alters the embryonic transcriptome in zebrafish.

  PMID 41546624 · PMC12958812 · G3 (Bethesda, Md.) · 2026 · 8 claims · 5 setups

  Full-text index only

  Ubiquitous overexpression of zGli3R (Tg(ubb:zGli3R)) causes widespread changes to the 30 hpf zebrafish embryonic transcriptome

  hpf dpf bulk gene bright-field

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.

  PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups

  Has reproduction · 77

  457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis

  tcga-oc tcga-oc-gse26193 ov_gse154600 iose-80 bulk univariate copy

• Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.

  PMID 42074115 · PMC13116134 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Has reproduction · 67

  Combined 125I radiation and carfilzomib treatment causes structured, non-random remodeling of the TE transcriptome in KYSE150 ESCC cells.

  kyse150 bulk rna-seq-based differential

• Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

  PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

  crc epcam+ aggregated cancer scrna-seq copy pseudobulk

• Development of a split-toxin CRISPR screening platform to systematically identify regulators of human myoblast fusion.

  PMID 41540035 · PMC12808753 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  A CRISPR screening platform combining human myoblast models, a custom muscle-targeted gRNA library (MyoCRISPR-KO Lib), and a split-toxin selection system enables quantitative enrichment of fusion-defective myocytes.

  myoblasts myoblast time-course immunostaining gene

• YAP1 Dysfunction Promotes Molecular Properties Linked to Breast Cancer Susceptibility.

  PMID 41431390 · PMC13040214 · Cancer prevention research (Philadelphia, Pa.) · 2026 · 7 claims · 8 setups

  Full-text index only

  YAP1 nuclear localization and mRNA expression significantly increase in luminal epithelial cells (LEp) with increased age and with genetic risk for breast cancer (e.g., BRCA1/2 mutation carriers)

  breast hmec post-stasis 184d-p16sh ihc bulk odds

• Microglia-containing cerebral organoids derived from induced pluripotent stem cells for the study of neurological diseases.

  PMID 36936782 · PMC10014280 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 74

  A novel protocol using FGF/EGF/heparin growth factor supplementation and 10% CO2 culture generates cerebral organoids containing neurons, astrocytes, and microglia from iPSCs/hESCs

  hesc-derived hesc als-pdc-affected cerebral microarray immunostaining bulk

• Redefinition of the toll-like receptor repertoire in Ciona robusta through genomic, structural, and expression analyses.

  PMID 41568004 · PMC12816324 · Frontiers in cellular and infection microbiology · 2025 · 8 claims · 8 setups

  Full-text index only

  CiTLR13 is a redundant annotation of CiTLR1 (same genomic locus, >94% sequence identity), so it is not a distinct TLR gene

  ciona six lrr tlr blastp domain nucleotide

• Polyploidy-driven expansion and regulatory diversification of the Kelch repeat F-box gene family in sweetpotato.

  PMID 42050392 · PMC13262408 · BMC genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  KFB family size does not scale linearly with ploidy, reflecting lineage-specific gene retention and loss rather than genome multiplication alone

  proteomes kfb four pairwise blastp physicochemical chromosomal

• Decoding the Mechanisms of Hepatocellular Carcinoma Cancer Stem Cells and Identifying Potential Therapeutic Strategies Based on Single-cell Omics.

  PMID 41771574 · PMC12951371 · Cancer genomics & proteomics · 2026 · 7 claims · 8 setups

  Full-text index only

  Malignant cells from HCC tumors resolve into six transcriptionally distinct subpopulations, including a progenitor-like CSC subset expressing EPCAM, SOX9, and SOX4

  malignant tumor csc six single-cell spatial copy

• Have microarrays failed to deliver for developmental biology?

  PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

  Full-text index only

  Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

  drosophila caenorhabditis developing xenopus cdna genome-wide microarray