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).

• Characteristics of small breast and/or ovarian cancer families with germline mutations in BRCA1 and BRCA2.

  PMID 10188893 · PMC2362698 · British journal of cancer · 1999 · 7 claims · 7 setups

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  Presence of at least one ovarian cancer case in a small family strongly predicts finding a BRCA1 or BRCA2 mutation.

  genomic pcr family truncation pcr multiplex

• High proportion of recurrent germline mutations in the BRCA1 gene in breast and ovarian cancer patients from the Prague area.

  PMID 16168118 · PMC1242140 · Breast cancer research : BCR · 2005 · 8 claims · 4 setups

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  BRCA1 c.5266dupC (5382insC) is the dominant recurrent mutation driving hereditary breast/ovarian cancer in this Czech population

  genomic pcr-amplified cdna truncation direct rt-pcr

• Co-circulation and evolution of polioviruses and species C enteroviruses in a district of Madagascar.

  PMID 18085822 · PMC2134956 · PLoS pathogens · 2007 · 8 claims · 8 setups

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  Madagascar VDPVs are intertypic/interspecies recombinants with Sabin 2-derived sequence in the 5'-half of the genome and HEV-C-derived sequence in the 3'-half

  vdpv mad04 pvr-tg21 hep-2c rt-pcr monoclonal plaque

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• Identification of common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

  PMID 18613968 · PMC2483966 · Virology journal · 2008 · 7 claims · 7 setups

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  Quasispecies complexity and diversity within HVR1 are lower in the SVR group than in the TF group

  serum hvr1 svr rt-pcr shannon hamming

• Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer.

  PMID 18489799 · PMC2413254 · BMC cancer · 2008 · 8 claims · 6 setups

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  Pathogenic BRCA1/BRCA2 mutations were identified in 294 of 1,010 (29.1%) unrelated high-risk Czech probands

  genomic pcr-amplified brca1 pha-stimulated truncation heteroduplex direct

• Molecular analysis of X-linked chronic granulomatous disease in five unrelated Korean patients.

  PMID 15082894 · PMC2822302 · Journal of Korean medical science · 2004 · 8 claims · 4 setups

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  Five unrelated Korean X-linked CGD patients each carry a distinct CYBB gene mutation: c.1663insT, c.1111-1G>T, c.39_40insG, c.927delC, and c.434T>C

  neutrophils genomic splice-site activated pcr-single sequencing

• Expression profiling of drug response--from genes to pathways.

  PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups

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  Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.

  blastocyst skin specified cortex pathway two-color microarray

• EGASP: the human ENCODE Genome Annotation Assessment Project.

  PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

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  Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

  encode computational manual rt-pcr

• Clinical characterization and the mutation spectrum in Swedish adenomatous polyposis families.

  PMID 18433509 · PMC2386495 · BMC medicine · 2008 · 8 claims · 8 setups

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  A combination of mutation-screening techniques (PTT, SSCP/HD, D-HPLC, sequencing, MLPA, mosaicism analysis, expression analysis) achieved a 100% mutation detection frequency in classical FAP

  peripheral genomic cdna truncation sscp d-hplc

• Influenza A (H3N2) outbreak, Nepal.

  PMID 16102305 · PMC3320503 · Emerging infectious diseases · 2005 · 7 claims · 6 setups

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  Nepal H3N2 outbreak isolates show antigenic drift, with ~40% antigenically distinct from the A/Wyoming/3/03 vaccine strain by hemagglutination inhibition

  influenza throat ha1 amino hemagglutination rt-pcr rapid

• Insights into the physiology of childbirth using transcriptomics.

  PMID 16752954 · PMC1475648 · PLoS medicine · 2006 · 7 claims · 4 setups

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  Labor results in a change in the transcriptome in each component of the uterus studied

  uterine lower microarray quantitative re-analysis

• Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

  PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

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  Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

  peripheral blood pooled trio gene quantitative promoter

• Therapy effect of either paclitaxel or cyclophosphamide combination treatment in patients with epithelial ovarian cancer and relation to TP53 gene status.

  PMID 9703286 · PMC2063030 · British journal of cancer · 1998 · 6 claims · 4 setups

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  Paclitaxel/cisplatin therapy produces a higher positive response rate than cyclophosphamide/cisplatin therapy in advanced ovarian cancer

  patients frozen genomic clinically randomized rt-pcr temporal

• Germline truncating mutations in both MSH2 and BRCA2 in a single kindred.

  PMID 14735197 · PMC2409581 · British journal of cancer · 2004 · 8 claims · 8 setups

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  Kindred MON1080 carries germline truncating mutations in both MSH2 and BRCA2, with two family members being double heterozygotes

  colonic astrocytoma breast microdissected immunohistochemistry microsatellite truncation

• Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

  PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

  presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous

• MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene.

  PMID 18154640 · PMC2233610 · BMC medical genetics · 2007 · 8 claims · 6 setups

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  Chromosome 8p23.1 has previously been proposed as a nuclear modifier locus for A1555G-associated hearing loss phenotype

  blood a1555g lymphoblastoid nuclear pcr-rflp direct rt-pcr

• Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

  PMID 29783948 · PMC5963079 · BMC genomics · 2018 · 8 claims · 8 setups

  Has reproduction · 85

  Whole transcriptome sequencing with extensive TSS mapping identified 3078 transcription start sites and 629 ncRNAs in V. cholerae N16961

  cholerae lexa identified directional end rt-pcr

• APC mutation analysis by chemical cleavage of mismatch and a protein truncation assay in familial adenomatous polyposis.

  PMID 7524601 · PMC2033526 · British journal of cancer · 1994 · 7 claims · 8 setups

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  Chemical cleavage of mismatch (HOT) analysis combined with sequencing identified inactivating constitutional APC mutations in 9 of 10 (90%) linkage-confirmed FAP patients, far exceeding the ~30% detection rate reported in the literature.

  blood pcr pcr-amplified cdna chemical sequencing single-strand