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).

• Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

  PMID 19946270 · PMC4002225 · Nature genetics · 2010 · 8 claims · 8 setups

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  PARK2 is a frequently and specifically targeted gene within recurrent 6q25.2-q27 copy number losses in glioblastoma and colon cancer

  colon gbm cancer dbtrg array pcr colony

• Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

  PMID 16244706 · PMC1262189 · PLoS genetics · 2005 · 7 claims · 5 setups

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  Putative pathogenic RMRP mutations are located in highly conserved nucleotides across mammals, whereas polymorphisms are located in non-conserved positions.

  genomic rmrp family non-finnish sequencing comparative microsatellite

• Gene losses during human origins.

  PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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  A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

  pseudogene chimpanzee human-specific population comparative phylogenetic fisher's

• Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

  PMID 19005564 · PMC2579325 · PloS one · 2008 · 8 claims · 7 setups

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  Doublet mutations are significantly more frequent in EGFR (6.0%) and TP53 (2.3%) in human lung cancer than spontaneous doublets in mouse lacI (0.7%), about 8-fold and 3-fold higher respectively.

  egfr tp53 laci lung literature comparative statistical

• CanPredict: a computational tool for predicting cancer-associated missense mutations.

  PMID 17537827 · PMC1933186 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  CanPredict is a web application providing public access to a random forest classifier that combines SIFT, LogR.E-value, and GOSS scores to predict whether a missense mutation is cancer-associated

  missense observed sjoblom refseq cross-validation recurrence comparative

• Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

  PMID 19861435 · PMC2783876 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 7 claims · 7 setups

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  Comprehensive genomic analysis shows thymic carcinomas are molecularly distinct from thymomas

  resected thymic previously mass dideoxynucleotide array

• A genome-wide screen for copy number alterations in Aicardi syndrome.

  PMID 19760649 · PMC3640635 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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  Aicardi syndrome is thought to result from heterozygous defects in an essential X-linked gene, or from a sex-limited autosomal gene defect, due to its occurrence almost exclusively in females and in 47,XXY males.

  genomic subject array quantitative fluorescence

• Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

  PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups

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  Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.

  fresh-frozen same banked resected array mutational pcr

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

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  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage

• Gefitinib for non-small-cell lung cancer patients with epidermal growth factor receptor gene mutations screened by peptide nucleic acid-locked nucleic acid PCR clamp.

  PMID 17106442 · PMC2360739 · British journal of cancer · 2006 · 5 claims · 4 setups

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  NSCLC patients with EGFR mutations detected by PNA-LNA PCR clamp show significantly higher response rates and longer survival with gefitinib than EGFR wild-type patients.

  clinical nsclc pna-lna direct phase

• DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

  PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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  Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

  aml tumor novo additional genome snp comparative

• Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

  PMID 19949810 · PMC2865568 · Journal of neurology · 2010 · 7 claims · 4 setups

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  CNVs are a rare cause of non-CMT1A Charcot-Marie-Tooth disease

  unrelated genomic mtmr2 array quantitative sanger

• Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa.

  PMID 19890396 · PMC2767505 · PloS one · 2009 · 8 claims · 4 setups

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  Rifampicin resistance (rpoB) and pyrazinamide resistance (pncA) mutations occur at different nucleotide positions in the MDR and XDR strains, showing they were acquired independently and that the XDR strain did not evolve directly from this MDR strain.

  tuberculosis additional whole-genome spoligotyping comparative

• Ethnic differences and functional analysis of MET mutations in lung cancer.

  PMID 19723643 · PMC2767337 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 7 setups

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  MET mutations identified in lung tumors are predominantly germline rather than somatic

  tumor established recombinant cos-7 pcr elisa-based apoptosis

• High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.

  PMID 19648524 · PMC4648268 · The European respiratory journal · 2009 · 8 claims · 8 setups

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  High-throughput -omics technologies have revolutionised understanding of lung cancer biology and hold promise for personalised management of lung cancer

  tumour serum nsclc comparative snp methylation

• MutScreener: primer design tool for PCR-direct sequencing.

  PMID 16845093 · PMC1538803 · Nucleic acids research · 2006 · 8 claims · 4 setups

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  MutScreener is a web-based application that automates PCR-direct sequencing assay design by annotating gene structure and designing PCR and sequencing primers.

  sim4 cdna gene comparative sequence pcr

• p53 gene mutations associated with anaplastic transformation of human thyroid carcinomas.

  PMID 1483945 · PMC5918745 · Japanese journal of cancer research : Gann · 1992 · 6 claims · 4 setups

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  p53 gene mutations were found in 2 of 9 anaplastic thyroid carcinomas by RNase protection analysis and confirmed by DNA sequencing

  anaplastic genomic coexisting rnase pcr sequencing

• Adapting to a changing world: RAG genomics and evolution.

  PMID 16004728 · PMC3525258 · Human genomics · 2005 · 8 claims · 7 setups

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  RAG-1/RAG-2 origin is a foundational hallmark of adaptive immunity, enabling V(D)J recombination of antigen receptor genes.

  rag-1 patients zebrafish vertebrate comparative site-directed clinical

• Comparative genomics search for losses of long-established genes on the human lineage.

  PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

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  A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

  dog genome chimp gorilla comparative overlap visual

• Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

  PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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  Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

  hgmd refseq aligned svm svm reciprocal inter-species