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).

• TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

  PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups

  Has reproduction · 89

  TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency

  melanogaster simulated long-read whole-genome genome

• TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

  PMID 17199898 · PMC1774580 · BMC bioinformatics · 2007 · 7 claims · 8 setups

  Full-text index only

  TPRpred detects divergent/remote-homolog TPR repeat units that existing resources (Pfam, SMART, REP) fail to detect

  scop-derived malt nr-70 scop profile-based dali remote

• Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

  PMID 19811662 · PMC2766370 · Molecular cancer · 2009 · 7 claims · 6 setups

  Full-text index only

  LCN-HRM enables detection and sequencing-based characterisation of low-level mutations that are undetectable by direct sequencing alone

  hct116 ffpe genomic tx84 dideoxynucleotide high lcn-hrm

• AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

  PMID 17485433 · PMC5947781 · Bioinformatics (Oxford, England) · 2007 · 7 claims · 2 setups

  Full-text index only

  AutoCSA is an automated algorithm, extended from the CSA protocol, that detects DNA sequence variants in cancer genomes with minimal manual intervention

  training kinase capillary targeted

• High incidence of p53 gene mutation in human ovarian cancer and its association with nuclear accumulation of p53 protein and tumor DNA aneuploidy.

  PMID 1429209 · PMC5918982 · Japanese journal of cancer research : Gann · 1992 · 7 claims · 4 setups

  Full-text index only

  p53 gene mutations occur at high incidence in human ovarian carcinoma, especially common epithelial type

  ovarian pcr-single direct immunohistochemistry

• Alteration of the p53 tumor suppressor gene occurs independently of K-ras activation and more frequently in serous adenocarcinomas than in other common epithelial tumors of the human ovary.

  PMID 7852189 · PMC5919385 · Japanese journal of cancer research : Gann · 1994 · 7 claims · 4 setups

  Full-text index only

  p53 gene mutations occur more frequently in serous adenocarcinomas than in other common epithelial ovarian tumors combined

  common ovarian restriction sscp direct

• 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

  Full-text index only

  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

• p53 mutations in cervical carcinogenesis--low frequency and lack of correlation with human papillomavirus status.

  PMID 8142262 · PMC1968818 · British journal of cancer · 1994 · 7 claims · 6 setups

  Full-text index only

  Somatic mutation in the p53 gene hotspot regions occurs infrequently in cervical carcinomas

  cervical tumour paired hpv-positive immunocytochemistry pcr sequencing

• FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

  PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 65

  FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

  simulated four rna-seq randomly simulated paired-end read-mappability

• High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

  PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

  genomic ecotilling non-synonymous ecotilling sanger universal-primer

• Human spermatozoa contain multiple targets for protein S-nitrosylation: an alternative mechanism of the modulation of sperm function by nitric oxide?

  PMID 17683036 · PMC2777308 · Proteomics · 2007 · 7 claims · 5 setups

  Full-text index only

  Human sperm proteins undergo S-nitrosylation upon exposure to NO donors, detectable by the biotin switch assay

  percoll-washed fixed pooled excised biotin situ streptavidin-agarose

• Using proteomic approach to identify tumor-associated antigens as markers in hepatocellular carcinoma.

  PMID 18672925 · PMC2680441 · Journal of proteome research · 2008 · 8 claims · 6 setups

  Full-text index only

  34 immunoreactive protein spots were detected in 2DE Western blots probed with HCC patient sera but not normal sera

  hepg2 excised identified recombinant two-dimensional western in-gel

• A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise.

  PMID 18615428 · PMC2855839 · Proteomics · 2008 · 6 claims · 4 setups

  Full-text index only

  Noise in SELDI-TOF/MALDI-TOF mass spectrometry data is heteroscedastic across the m/z range, with larger variance at lower m/z values, contrary to the homogeneous noise assumption of existing wavelet denoising methods.

  serum raw denoised simulated seldi-tof wavelet-based peak

• Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

  PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups

  Full-text index only

  eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs

  drosophila caenorhabditis xenopus five pairwise evoprint comparison

• Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions.

  PMID 19900591 · PMC2878865 · Ageing research reviews · 2010 · 8 claims · 8 setups

  Full-text index only

  NGS platforms offer superior performance, specificity, and cost-effectiveness compared to traditional Sanger sequencing

  genome alzheimer's embryonic tissues genome genotyping rna-seq

• Sequence variations of GRM6 in patients with high myopia.

  PMID 19862333 · PMC2765235 · Molecular vision · 2009 · 7 claims · 8 setups

  Full-text index only

  Three novel GRM6 variations with predicted functional consequences (c.67-82delCAGGCGGGCCTGGCGCinsT, c.858-5a>g, c.1537G>A) were found in high myopia patients but absent in 96 controls

  genomic pcr mglur6 grm6 pcr heteroduplex pcr-restriction

• A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data.

  PMID 19681055 · PMC2782493 · Proteomics · 2009 · 8 claims · 2 setups

  Full-text index only

  PDA_stFFT is a novel automatic peak detection method for prOTOF MS data that does not require a priori knowledge of protein masses

  peptide serum maldi-tof

• Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours.

  PMID 11870543 · PMC2375272 · British journal of cancer · 2002 · 8 claims · 5 setups

  Full-text index only

  DFFA is localized within the 1p36.2-3 smallest region of overlap (SRO) of deletions defined in Scandinavian neuroblastoma tumours, distal to marker D1S244

  scandinavian chromosome unfinished neuroblastoma pcr bac-library in-silico

• Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

  PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

  Full-text index only

  A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

  yeast yeast-related interaction random dictionary-based manual graph

• Identification of novel citrullinated autoantigens of synovium in rheumatoid arthritis using a proteomic approach.

  PMID 17125526 · PMC1794520 · Arthritis research & therapy · 2006 · 8 claims · 6 setups

  Full-text index only

  51 citrullinated protein spots were detected in RA synovial tissue, of which 30 (58.8%) were autoantigenic (reactive with RA sera)

  synovial excised coli recombinant two-dimensional maldi-tof recombinant