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).

• Sex differences in cancer risk among germline p53 mutation carriers.

  PMID 15280910 · PMC2409855 · British journal of cancer · 2004 · 6 claims · 3 setups

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  Cancer risk in germline p53 mutation carriers differs by sex, with females at higher risk than males in adulthood, was first reported by Chompret et al 2000, three years before a confirmatory study by Hwang et al 2003 claimed similar findings without citing the earlier work.

  children first-degree p53 germline family-based

• Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

  PMID 16319823 · PMC1477589 · European journal of human genetics : EJHG · 2006 · 7 claims · 8 setups

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  ALX4 and MSX2 mutations contribute approximately equally to PFM/CB and cause skull defects that are usually clinically indistinguishable

  pfm selected point-mutation-negative family dhplc bidirectional multiplex

• Mutation analysis in a German family identified a new cataract-causing allele in the CRYBB2 gene.

  PMID 17653036 · PMC2774456 · Molecular vision · 2007 · 8 claims · 4 setups

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  A novel heterozygous mutation (383A>T; D128V) in exon 5 of CRYBB2 cosegregates with congenital cataract in all three affected family members and is absent in unaffected relatives.

  genomic pcr-amplified computational pcr restriction pcr-rflp

• Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

  PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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  Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

  serous same lmp braf-mutant gene hotspot erbb2

• 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

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  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

• 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

• Extraction of human kinase mutations from literature, databases and genotyping studies.

  PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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  A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

  pubmed large labeled swissprot literature supervised comparative

• Evaluation of models to predict BRCA germline mutations.

  PMID 17016486 · PMC2360540 · British journal of cancer · 2006 · 7 claims · 7 setups

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  Four commonly used BRCA risk prediction models (BRCAPRO, Manchester, Penn, Myriad-Frank) have only modest ability to rule in or rule out BRCA1/2 germline mutation carrier status at a 10% probability threshold.

  proband pedigrees randomly brca1 brcapro manchester

• A common missense variant in BRCA2 predisposes to early onset breast cancer.

  PMID 16280055 · PMC1410744 · Breast cancer research : BCR · 2005 · 7 claims · 4 setups

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  BRCA2 C5972T homozygosity (TT genotype) is rare but confers a roughly five-fold increased risk of breast cancer.

  peripheral blood-derived blood case-control genotyping sequencing mutation

• A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm.

  PMID 16002787 · PMC1174901 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  An evolution-mimicking algorithm (EMA) that shuffles and mutates loop sequences while keeping the G-quartet intact can screen DNA aptamers based on inhibitory activity rather than binding affinity.

  plasma bovine clot-inhibition binding

• 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

• Iterative class discovery and feature selection using Minimal Spanning Trees.

  PMID 15355552 · PMC520744 · BMC bioinformatics · 2004 · 7 claims · 5 setups

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  Iterating between MST-based clustering and t-statistic feature selection removes noise genes step-wise while sharpening the sample clustering

  simulated breast acute diffuse synthetic cdna microarray

• Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

  PMID 16327884 · PMC1298935 · PLoS genetics · 2005 · 8 claims · 8 setups

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  Point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated CL/P

  family additional unrelated mutant direct linkage targeted

• An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

  PMID 18445289 · PMC2386494 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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  Using RNAsubopt suboptimal solutions computed once for the wild-type sequence, specific multiple-point mutations likely to cause conformational rearrangement can be selected without brute-force enumeration.

  example hepatitis minimum suboptimal multiple-point

• Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations.

  PMID 35186917 · PMC8851031 · Frontiers in cell and developmental biology · 2022 · 8 claims · 3 setups

  Has reproduction · 56

  SARS-CoV-2 viral preparations show selective enrichment of specific host tRNAs, tRNA fragments, and SRP RNA compared to uninfected VeroE6 cells

  veroe6 cell-free small large trna

• In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

  PMID 16995940 · PMC1590028 · BMC genomics · 2006 · 8 claims · 6 setups

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  In silico ESE-prediction algorithms (ESEfinder, RescueESE, PESX) do not reliably predict actual in vivo splicing behavior of missense mutations

  hmlh1 same cos-7 hela ese splice minigene

• 1p36 is a preferential target of chromosome 1 deletions in astrocytic tumours and homozygously deleted in a subset of glioblastomas.

  PMID 17934521 · PMC2650419 · Oncogene · 2008 · 8 claims · 8 setups

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  Total 1p deletion is rare (2%) in astrocytic tumours, whereas partial deletions involving 1p36 are common and increase with malignancy grade (22% in anaplastic astrocytomas, 34% in glioblastomas)

  astrocytic glioblastomas array-cgh microsatellite quantitative

• Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE).

  PMID 17697348 · PMC2042502 · BMC genetics · 2007 · 8 claims · 5 setups

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  CTCE eliminates the need for laboratory optimization of separation conditions for each exonic target sequence.

  pcr-amplified target exonic cycling ctce

• 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

• Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

  PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

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  PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

  hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag