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).

• Genome-wide identification of human functional DNA using a neutral indel model.

  PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

  chromosome human-mouse genome individual whole-genome probabilistic comparative

• Evolutionary distance estimation and fidelity of pair wise sequence alignment.

  PMID 15840174 · PMC1087827 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  Evolutionary distance estimation is relatively unaffected by alignment error as long as 50% or more of homologous sites remain identical between sequences

  simulated simulated sequence indel

• Decoding of superimposed traces produced by direct sequencing of heterozygous indels.

  PMID 18654614 · PMC2429969 · PLoS computational biology · 2008 · 7 claims · 3 setups

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  A dynamic programming method (implemented as web app Indelligent) can decode superimposed allelic sequences from a single mixed trace, using only the observed string of ambiguous peak calls, without a reference sequence or reverse trace.

  genomic artificial simulated direct computational comparative