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).

• ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

  PMID 12493080 · PMC139979 · BMC bioinformatics · 2002 · 6 claims · 6 setups

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  ORFer retrieves protein and nucleic acid sequences and annotations from NCBI GenBank using the XML sequence format

  sequences parsed bacillus anopheles large-scale sequence orf

• Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

  PMID 18588693 · PMC2446391 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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  A decision tree built on 10 selected sequence-derived features classifies SAPs as Disease or Polymorphism with 82.6% accuracy and 0.607 MCC in cross-validation.

  sap sequence-derived humvar same decision independent greedy

• FGF: a web tool for Fishing Gene Family in a whole genome database.

  PMID 17584790 · PMC1933194 · Nucleic acids research · 2007 · 6 claims · 3 setups

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  FGF efficiently searches and identifies gene families in whole-genome databases and outputs visual phylogenetic trees annotated with gene structure, chromosome position, duplication fate, and selective pressure (Ka/Ks)

  genome rice gene large-scale

• Discovery and hypothesis generation through bioinformatics.

  PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

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  Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

  genome chemokine gene-expression proteins genome-wide phylogenetic microarray