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).

• CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

  PMID 11556834 · PMC2375081 · British journal of cancer · 2001 · 7 claims · 6 setups

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  Germ line CDKN2A mutations were found in 5 of 15 (33.3%) Italian melanoma-prone families, including one novel mutation (P48T) and three known pathogenic mutations (R24P, G101W, N71S)

  genomic radiolabelled tig-er u2os sscp protein-protein retroviral

• Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

  PMID 18632602 · PMC2586155 · Cancer research · 2008 · 8 claims · 7 setups

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  A novel somatic MEK1 K57N mutation was identified in 2 of 207 primary lung adenocarcinomas

  nsclc 293t il-3-independent mutational site-directed cytokine-independence

• A novel breast cancer-associated BRIP1 (FANCJ/BACH1) germ-line mutation impairs protein stability and function.

  PMID 18628483 · PMC2561321 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 6 claims · 7 setups

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  A novel heterozygous BRIP1 germline mutation (c.2992-2995delAAGA) was identified in a breast cancer patient, causing a frameshift and premature stop codon in exon 20.

  genomic laser-capture cell-free hela sscp loss transcription

• Personalized medicine: the future is not what it used to be.

  PMID 19958922 · PMC2844719 · Surgery · 2009 · 8 claims · 8 setups

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  Many rare tumors harbor a genomic Achilles heel that can be exploited for targeted therapy

  sw13 h295r drosophila acc drug synthetic gene

• Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

  PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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  At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

  breast same selected hct116 expression methylation-specific rt-pcr

• Characterization of mutations and loss of heterozygosity of p53 and K-ras2 in pancreatic cancer cell lines by immobilized polymerase chain reaction.

  PMID 12877750 · PMC183853 · BMC biotechnology · 2003 · 6 claims · 5 setups

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  Polony technology can detect intragenic mutations in well-defined hotspots of p53 (codons 175, 245, 248, 249, 273, 282) and K-ras2 (codons 12, 13, 61)

  panc-1 aspc-1 capan-1 immobilized polony-based

• Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

  PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

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  Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

  tumors cancer tumor lung direct database quantitative

• Backseat drivers take the wheel.

  PMID 18068625 · PMC2705833 · Cancer cell · 2007 · 8 claims · 8 setups

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  Systematic resequencing combined with functional validation can distinguish rare driver FLT3 mutations from passenger mutations in AML patients negative for known activating mutations

  pretreatment baf3 additional normal targeted baf3 immunoprecipitation

• High resolution melting for mutation scanning of TP53 exons 5-8.

  PMID 17764544 · PMC2025602 · BMC cancer · 2007 · 7 claims · 5 setups

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  HRM is an effective technique for rapid scanning of TP53 mutations that can markedly reduce required sequencing

  tp53-mutant ovarian breast high hrm dideoxy

• Increased cyclin D1 expression can mediate BRAF inhibitor resistance in BRAF V600E-mutated melanomas.

  PMID 18790768 · PMC2651569 · Molecular cancer therapeutics · 2008 · 8 claims · 6 setups

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  CDK4 mutations (K22Q, R24C, R24L) alone do not confer resistance to the BRAF inhibitor SB590885

  melanoma metastatic wm39 451lu mtt pcr array

• Localization studies of rare missense mutations in cystic fibrosis transmembrane conductance regulator (CFTR) facilitate interpretation of genotype-phenotype relationships.

  PMID 18951463 · PMC2785447 · Human mutation · 2008 · 5 claims · 5 setups

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  R1070P and R1070W CFTR mutants show apical membrane localization/insertion defects consistent with their associated disease severity

  polarized mdck mdck-cftr patients confocal surface western

• A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.

  PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity

  coad consensus cibersort mcp-counter

• Genomic variability within an organism exposes its cell lineage tree.

  PMID 16261192 · PMC1274291 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  Somatic mutations accumulated during normal development implicitly encode an organism's entire cell lineage tree with very high precision.

  robinia arabidopsis randomly genotyping multiplex computer

• Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

  PMID 17359525 · PMC1838427 · BMC molecular biology · 2007 · 8 claims · 8 setups

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  OPTC is a candidate gene involved in POAG pathogenesis

  genomic pcr optc retinal pcr-sscp dhplc sequencing

• A comprehensive catalogue of somatic mutations from a human cancer genome.

  PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

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  Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

  colo-829 additional whole-genome conventional pcr

• An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

  PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups

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  A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.

  lung known leukemia tumor paired-end computational snp

• With the finished human genome in hand, what next?

  PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

  domestic saccharomyces systemic schistosoma comparative functional genetic

• Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel.

  PMID 31913291 · PMC6949293 · Scientific data · 2020 · 6 claims · 7 setups

  Has reproduction · 89

  The Accel-Amplicon CFTR panel generates sequencing data with high coverage depth and near 100% on-target reads.

  genomic adapted aligned pcr amplicon multiplex qpcr

• 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

• Contributions from molecular/biochemical approaches in epidemiology to cancer risk assessment and prevention.

  PMID 1486845 · PMC1519598 · Environmental health perspectives · 1992 · 8 claims · 8 setups

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  Genotoxicity of chemicals is a continuous, graded property (agent score) rather than a simple dichotomy of mutagenic vs. nonmutagenic chemicals

  chemical drosophila normal uv-sensitive short-term drosophila excision