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).

• A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

  PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

  orthologous randomized high-score promoters pssm-based comparative motif

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• In silico analysis of missense substitutions using sequence-alignment based methods.

  PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

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  Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

  clinically sequence curated deep blosum62 sift align-gvgd

• The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

  PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

  putative nonredundant homo genes computational pssm semantic

• Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

  PMID 20008508 · PMC2836564 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Most TEs insert within specific 'hotspots' along the targeted TE rather than uniformly.

  genome sequences unique nested chi-square position-specific