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).

• RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.

  PMID 31978147 · PMC6980424 · PloS one · 2020 · 7 claims · 6 setups

  Has reproduction · 71

  RNAmountAlign performs pairwise local, global, and semiglobal (query search) alignment and progressive multiple alignment (global and local) using incremental ensemble mountain height, running in O(n^3) time and O(n^2) space for two sequences of length n

  sequences sets target single secondary pairwise sequence

• Ontological visualization of protein-protein interactions.

  PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups

  Full-text index only

  Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks

  gene interacting interaction annotation yeast co-immunoprecipitation

• Ab initio identification of human microRNAs based on structure motifs.

  PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

  Full-text index only

  MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

  genome mirna hairpins chromosome secondary linear five-fold

• Predicting failure rate of PCR in large genomes.

  PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

  Full-text index only

  The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

  genomic genome pcr combined large-scale exact-match mismatch-tolerant