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).

• Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.

  PMID 15784611 · PMC1069129 · Nucleic acids research · 2005 · 7 claims · 8 setups

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  Position-specific phylogenetic features describing evolutionary conservation at a site (e.g. SIFT score, normalized site entropy, residue frequency change) are the best individual discriminators of disease-causing versus neutral GPCR mutations.

  dbsnp gpcr transmembrane sequence six-frame sift logistic

• Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

  PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups

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  A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.

  pooled genome est novel tandem whole-genome est

• Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer.

  PMID 36140751 · PMC9498802 · Genes · 2022 · 7 claims · 6 setups

  Has reproduction · 51

  Clair3 and Human-SNP-wf (which incorporates Clair3) achieved the highest performance among the six variant callers tested.

  giab hg001 brca1 filtered long-read read bam

• Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

  PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

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  Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

  genbank hiv-1 protease integrase blastp phylogenetic amino

• A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation.

  PMID 19958498 · PMC2788387 · BMC genomics · 2009 · 8 claims · 4 setups

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  Comparative homology modeling of wild-type and mutant α-mannosidase across human, cow, cat and guinea pig reveals a significant correlation between genotype severity and phenotype severity in α-mannosidosis

  lysosomal full-length pro-peptide bovine homology sequence weblogo

• Empirical codon substitution matrix.

  PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

  orthologous million codon same pairwise empirical comparative