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).
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Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector.
PMID 17317684 · PMC1874629 · Nucleic acids research · 2007 · 7 claims · 7 setups
Gene-Collector is a method for multiplex nucleic acid amplification that specifically circularizes only correctly paired (cognate) PCR primer products on a Collector probe, degrading non-cognate artifacts by exonuclease treatment.
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Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.
PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups
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.
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Designating eukaryotic orthology via processed transcription units.
PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups
Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs
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Computational verification of protein-protein interactions by orthologous co-expression.
PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups
Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.
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Predicting failure rate of PCR in large genomes.
PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups
The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.
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The matrix metalloproteinase-3 (MMP-3) 5A/6A promoter polymorphism is not associated with ischaemic heart disease: analysis employing a family based approach.
PMID 15665388 · PMC3839324 · Disease markers · 2004 · 6 claims · 3 setups
The MMP-3 -1612 5A/6A polymorphism is not associated with ischaemic heart disease in an Irish population.
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Has reproduction · 90
Inferring a spatial code of cell-cell interactions across a whole animal body.
PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups
cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells
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Has reproduction · 95
Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.
PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups
Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns
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Has reproduction · 69
Discovery and characterization of Alu repeat sequences via precise local read assembly.
PMID 26503250 · PMC4666360 · Nucleic acids research · 2015 · 7 claims · 8 setups
Combining Alu-supporting read detection (RetroSeq) with local de novo assembly (CAP3) reconstructs the full sequence of non-reference Alu insertions from Illumina paired-end WGS reads
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Genome comparison without alignment using shortest unique substrings.
PMID 15910684 · PMC1166540 · BMC bioinformatics · 2005 · 8 claims · 8 setups
A number of sequence comparison tasks, including detection of unique genomic regions, can be accomplished efficiently without an alignment step using shortest unique substrings.
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Addressing the obesity epidemic: a genomics perspective.
PMID 17362622 · PMC1893129 · Preventing chronic disease · 2007 · 8 claims · 8 setups
Obesity is a multifactorial disorder reflecting complex interactions of genes, environment, and lifestyle
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Polymorphism screening and haplotype analysis of the tryptophan hydroxylase gene (TPH1) and association with bipolar affective disorder in Taiwan.
PMID 15799788 · PMC1079843 · BMC medical genetics · 2005 · 8 claims · 7 setups
Systematic screening of TPH1 exons and promoter region in Taiwanese Han identified five sequence variants: A-1067G, G-347T, T3804A, C27224T, A27237G.
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A human genome-wide library of local phylogeny predictions for whole-genome inference problems.
PMID 18710563 · PMC2556685 · BMC genomics · 2008 · 7 claims · 5 setups
A genome-wide library of nearly 16 million local maximum parsimony phylogenies was constructed from HapMap CEU and YRI SNP data across all human autosomes
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Biocomputing enters its adolescence.
PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups
A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins
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Competitive enzymatic reaction to control allele-specific extensions.
PMID 15767273 · PMC1065263 · Nucleic acids research · 2005 · 6 claims · 7 setups
Protease-mediated allele-specific extension (PrASE) uses competition between polymerase activity and Proteinase K-mediated polymerase degradation to allow extension of perfectly matched primers while eliminating slower mismatched primer extension.