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).

• Identifying the important HIV-1 recombination breakpoints.

  PMID 18787691 · PMC2522274 · PLoS computational biology · 2008 · 8 claims · 3 setups

  Full-text index only

  Local sequence identity between co-packaged parental RNAs strongly influences the probability of strand-transfer/breakpoint location, with fewer breakpoints occurring near mismatches

  inter-subtype parental copy-choice probabilistic comparative

• Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

  PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 83

  Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs

  afb1 breast training candidate computational bulk weighted

• Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

  PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 5 setups

  Has reproduction · 75

  Stage-stratified molecular subclassification of Ta and T1 tumors provides greater biological understanding and more clinically meaningful information than subtypes derived from all NMIBCs combined.

  stage tumors copy genome-wide whole-exome

• Innate immune modulation by RNA viruses: emerging insights from functional genomics.

  PMID 18654572 · PMC7097543 · Nature reviews. Immunology · 2008 · 8 claims · 7 setups

  Full-text index only

  Influenza virus signals primarily through RIG-I to induce ISG expression, while West Nile virus signals through both RIG-I and MDA5 cooperatively.

  embryonic liver brain serial gene-expression computational

• Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

  PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups

  Full-text index only

  Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.

  perfused lung microarray principal wilcoxon

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

  PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 49

  B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).

  dlbcl normal same lymphoma help errbs massarray

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential