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).

• beta- Catenin mutations and aberrant nuclear expression during endometrial tumorigenesis.

  PMID 11161379 · PMC2363713 · British journal of cancer · 2001 · 7 claims · 4 setups

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  Cell membrane β-catenin immunoreactivity shows a stepwise decrease from normal endometrium, through atypical hyperplasia, to grade 3 carcinoma.

  endometrial immunohistochemistry rt-pcr pcr

• Frequent loss of the AXIN1 locus but absence of AXIN1 gene mutations in adenocarcinomas of the gastro-oesophageal junction with nuclear beta-catenin expression.

  PMID 14970870 · PMC3215949 · British journal of cancer · 2004 · 8 claims · 7 setups

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  Nuclear β-catenin expression in GEJ adenocarcinoma cell lines correlates with enhanced TCF-mediated reporter gene transcription

  gej paired showing tumours tcf pcr-sscp bidirectional

• The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

  PMID 16859552 · PMC1538596 · BMC genomics · 2006 · 7 claims · 7 setups

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  Numts co-amplified with mtDNA during PCR generate false heteroplasmic signals at specific nucleotide positions.

  143b ffpe blood cloned southern pcr rt-pcr

• Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

  PMID 19912651 · PMC2784748 · BMC cell biology · 2009 · 7 claims · 7 setups

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  hnRNP L is a novel Sam68-interacting protein partner identified by proteomics and confirmed by co-immunoprecipitation

  lncap hek293 nih3t3 co-immunoprecipitation sucrose indirect

• An SVM-based system for predicting protein subnuclear localizations.

  PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.

  single-localization multi-localization same svm sequence

• Rapid preparation of nuclei-depleted detergent-resistant membrane fractions suitable for proteomics analysis.

  PMID 18534013 · PMC2440737 · BMC cell biology · 2008 · 6 claims · 4 setups

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  A modified differential detergent extraction method (pelleting nuclei/intact cells at low speed before detergent solubilization) yields DRM fractions with markedly reduced nuclear protein contamination compared to the conventional method.

  lncap fractions immunofluorescence differential concentration

• No evidence of a Neanderthal contribution to modern human diversity.

  PMID 18304371 · PMC2374707 · Genome biology · 2008 · 8 claims · 7 setups

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  There is no evidence of any Neanderthal contribution to modern human genetic diversity

  neanderthal culture modern genomic mitochondrial nuclear gene-specific

• Genetic polymorphisms of Echinococcus tapeworms in China as determined by mitochondrial and nuclear DNA sequences.

  PMID 19800346 · PMC2823955 · International journal for parasitology · 2010 · 8 claims · 7 setups

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  Species identification by mitochondrial (cox1) and nuclear (ef1a) markers was identical across isolates, indicating introgressive hybridization among sympatric Echinococcus species is infrequent.

  granulosus multilocularis shiquicus echinococcus mitochondrial nuclear statistical

• Benchmarking ortholog identification methods using functional genomics data.

  PMID 16613613 · PMC1557999 · Genome biology · 2006 · 8 claims · 7 setups

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  InParanoid is the best overall ortholog identification method for identifying functionally equivalent proteins when sensitivity and selectivity are combined into an overall score.

  known human-mouse expression interpro co-expression

• Somatic mutations in mitochondria: the chicken or the egg?

  PMID 16207343 · PMC1257449 · Arthritis research & therapy · 2005 · 6 claims · 6 setups

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  Patients with RA have a higher incidence of somatic mtDNA mutations (in MT-ND1 transcripts) in synoviocytes and synovial tissue compared with OA patients

  mutated synovial sequencing mhc expression

• The use of urine proteomic and metabonomic patterns for the diagnosis of interstitial cystitis and bacterial cystitis.

  PMID 15258332 · PMC3850593 · Disease markers · 2003 · 6 claims · 2 setups

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  Urine MS and 1H-NMR spectral patterns can be used to discriminate IC-affected, BC-affected, and unaffected individuals with approximately 84% success rate.

  urine surface-binding high-resolution

• Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.

  PMID 34103501 · PMC8187371 · Nature communications · 2021 · 7 claims · 4 setups

  Has reproduction · 99

  Nanopore methylation detection tools exhibit a tradeoff between false positives and false negatives and high dispersion relative to expected per-site methylation frequencies.

  coli lymphoblastoid na12878 mixture nanopore cas9-targeted whole-genome

• TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.

  PMID 34197621 · PMC8464036 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 60

  TRAPID 2.0 is a web application performing global characterization of de novo transcriptomes via structural, functional, and taxonomic annotation in an initial processing phase, followed by an exploratory phase of downstream analyses.

  mmetsp query putative ciliate taxonomic similarity non-coding

• The gentle art of gene arrangement: the meaning of gene clusters.

  PMID 11897017 · PMC139018 · Genome biology · 2002 · 8 claims · 7 setups

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  Gene order in eukaryotic genomes is likely optimized by natural selection rather than arising purely by chance reshuffling.

  populations mhc interphase cartilaginous sequence codon comparative

• Dark matter in a deep-sea vent and in human mouth.

  PMID 17803764 · PMC2040194 · Environmental microbiology · 2007 · 7 claims · 8 setups

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  The first genome sequence from the uncultured TM7 phylum was obtained by capturing and sequencing DNA from a single cell using a microfluidic device, yielding a 2.86 Mb assembly with 3245 predicted genes.

  uncultured mycoplasma cyanidioschyzon kineococcus single-cell genome whole-genome

• Evolution of organelle-associated protein profiling.

  PMID 19110081 · PMC2680700 · Journal of proteomics · 2009 · 8 claims · 8 setups

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  Traditional biochemical organelle isolation followed by MS cataloguing suffers high false-positive rates because organelles cannot be purified to homogeneity and are structurally heterogeneous

  golgi nuclear lipid clathrin-coated density qualitative silac

• Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

  PMID 18841935 · PMC2716176 · Analytical chemistry · 2008 · 7 claims · 6 setups

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  An integrated hardware/software online-offline platform (TriVersa NanoMate + 12T LTQ FT Ultra + AUTOMATION WAREHOUSE) automates collection of high-resolution MS/MS data for polypeptides >3 kDa that cannot be acquired online on a chromatographic timescale

  acid-extracted hela online offline

• A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

  PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

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  Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

  genes hela proteins worm co-expression quantitative functional

• PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

  PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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  PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing

  simulated gaw12 breast monte pedigree-based genetic

• Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.

  PMID 34875090 · PMC8887463 · Nucleic acids research · 2022 · 6 claims · 8 setups

  Has reproduction · 56

  Halo-seq pairs a light-activatable Halo-DBF ligand with Click chemistry to label and purify spatially defined RNA populations in living cells with high spatial specificity (~100 nm radius)

  hela apex-seq proximity dot comparative