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).

• Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource.

  PMID 16507150 · PMC1413975 · Breast cancer research : BCR · 2006 · 6 claims · 7 setups

  Full-text index only

  kConFab is a collaborative resource providing epidemiological, clinical, and biospecimen data from high-risk familial breast/ovarian cancer families, available to researchers worldwide for ethically approved, peer-reviewed projects.

  germline unaffected index randomly brca1 tyrer-cuzick strp

• Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.

  PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 7 claims · 5 setups

  Has reproduction · 62

  A DNN model using the top 34 betweenness-centrality-ranked hub genes predicts bone metastasis with AUC of 92.11% on the GEO validation data.

  breast degs geo tcga gene protein-protein machine

• Evaluation of BRCA1 and BRCA2 mutations and risk-prediction models in a typical Asian country (Malaysia) with a relatively low incidence of breast cancer.

  PMID 18627636 · PMC2575532 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

  Full-text index only

  27 deleterious BRCA1/BRCA2 mutations were detected in 28 breast cancer patients (14 in BRCA1, 13 in BRCA2) among 187 tested

  blood-derived family brca1 direct multiplex boadicea

• 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

  170 unique human AFB1 targets were identified by merging ChEMBL, SwissTargetPrediction, and PharmMapper predictions

  afb1 breast training candidate computational bulk weighted

• Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.

  PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 51

  A 15-gene immune infiltration-related signature (IRS) predicts overall survival in breast cancer, with higher IRS indicating worse prognosis

  tcga metabric geo breast immune bulk microarray

• BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

  PMID 16417652 · PMC1413985 · Breast cancer research : BCR · 2006 · 8 claims · 7 setups

  Full-text index only

  BOADICEA predicts accurately the number of BRCA1 and BRCA2 mutations across family groups and discriminates well between carriers and noncarriers

  french-canadian families brca1-positive same targeted full-length multiplex

• Mutation analysis of the ATR gene in breast and ovarian cancer families.

  PMID 15987455 · PMC1175065 · Breast cancer research : BCR · 2005 · 8 claims · 5 setups

  Full-text index only

  ATR mediates the DNA damage response by phosphorylating tumor suppressors such as p53, BRCA1 and CHK1, making it a plausible candidate breast/ovarian cancer susceptibility gene

  index atr variant mutation direct variant

• Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

  PMID 17945002 · PMC2242669 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

  Full-text index only

  -26G>A polymorphism in the BRCA2 5' UTR is functional: the A allele drives roughly twice the reporter gene expression of the G allele in MCF-7 and HeLa cells

  mcf-7 hela brca2 peripheral luciferase transcription genotyping

• Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

  PMID 17397520 · PMC1868923 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

  Full-text index only

  Genome-wide expression microarray studies reveal transcriptional networks/signatures that explain breast cancer biological and clinical heterogeneity

  breast early-stage diffuse dlbcl gene

• Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor beta on mRNA stability and translatability.

  PMID 19754929 · PMC2759954 · BMC genetics · 2009 · 8 claims · 4 setups

  Full-text index only

  Breast tumor heterozygotes show a significant difference in relative mRNA levels between the two alleles of rs4986938

  breast hek293 erβ1 allelic luciferase stability

• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

  PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

  Full-text index only

  CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

  missense same synthetic tp53 random support principal

• CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

  PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups

  Full-text index only

  Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.

  breast commercial vertebrate genes cdna activity computational

• Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

  PMID 17054774 · PMC1636663 · Molecular cancer · 2006 · 7 claims · 7 setups

  Full-text index only

  The alternative splice isoform Δp53 mRNA is co-expressed with full-length p53 mRNA in breast tumors and cell lines

  breast universal p53 subset qrt-pcr bioinformatic structure

• Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

  PMID 16595073 · PMC3500178 · Human genomics · 2006 · 7 claims · 5 setups

  Full-text index only

  A bioinformatics strategy cross-referencing carcinogenesis-related gene lists with breast-tissue expression data can identify candidate breast cancer risk nsSNPs.

  breast carcinogenesis-related nssnp-containing african gene snp functional

• Mutation analysis of the AATF gene in breast cancer families.

  PMID 20025740 · PMC2806411 · BMC cancer · 2009 · 6 claims · 6 setups

  Full-text index only

  No AATF sequence alteration identified was predicted to be pathogenic or showed significant association with breast cancer risk

  genomic showing aatf case conformation direct pathogenicity

• Re-evaluating early breast neoplasia.

  PMID 18279539 · PMC2374963 · Breast cancer research : BCR · 2008 · 8 claims · 7 setups

  Full-text index only

  The classic single linear model of breast cancer progression requires revision based on high-throughput molecular genetic and gene expression data.

  dcis breast patient-matched premalignant comparative combined cdna

• SEMdag: Fast learning of Directed Acyclic Graphs via node or layer ordering.

  PMID 39775401 · PMC11709272 · PloS one · 2025 · 8 claims · 5 setups

  Has reproduction · 81

  SEMdag() is a two-step order-based algorithm for fast learning of high-dimensional linear SEMs, using knowledge-based (KB) or data-driven bottom-up (BU) node/layer ordering followed by penalized (L1) DAG estimation

  amyotrophic breast coronavirus st-elevation rna-seq comparative

• DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.

  PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 6 claims · 7 setups

  Has reproduction · 84

  DeepProg, an ensemble of deep-learning and machine-learning models, robustly predicts patient survival subtypes from multi-omics data and explicitly models survival as the objective while predicting new patient risks

  tcga breast metabric brca bulk mirna methylation

• ATM variants and cancer risk in breast cancer patients from Southern Finland.

  PMID 16914028 · PMC1592307 · BMC cancer · 2006 · 8 claims · 6 setups

  Full-text index only

  Neither 5557G>A nor ivs38-8T>C, nor any haplotype containing them, was significantly associated with breast cancer risk in any patient group

  familial brca1 same genotype genotyping denaturing direct

• Mutation analysis of the MDM4 gene in German breast cancer patients.

  PMID 18279506 · PMC2259322 · BMC cancer · 2008 · 8 claims · 8 setups

  Full-text index only

  Resequencing of the whole MDM4 coding region in 40 German familial breast cancer patients uncovered two coding variants (V74V and D153G) in 4/40 patients

  german bilateral mdm4 lymphoid direct rflp-based splice