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).

• CoMoDis: composite motif discovery in mammalian genomes.

  PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif

  ncbi35 gata-1 gene imr90 computational microarray seed-motif-anchored

• Inconsistencies in Neanderthal genomic DNA sequences.

  PMID 17937503 · PMC2014787 · PLoS genetics · 2007 · 8 claims · 6 setups

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  The Noonan et al. and Green et al. Neanderthal nuclear DNA datasets yield mutually inconsistent estimates of population split time and Neanderthal admixture proportion when analyzed with the same method

  neanderthal green neanderthal-specific population-genetic fragment-length-stratified hapmap

• Identifying repeat domains in large genomes.

  PMID 16507140 · PMC1431705 · Genome biology · 2006 · 7 claims · 5 setups

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  A repeat domain graph, built using a modified A-Bruijn graph framework, decomposes a repeat library into shared repeat domains and reveals the mosaic structure of repeat families.

  repbase elegans concatenated repeat comparative dot

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand

• Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

  PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups

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  eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs

  drosophila caenorhabditis xenopus five pairwise evoprint comparison

• Organization and evolution of the Cyp2 gene cluster on mouse chromosome 7, and comparison with the syntenic human cluster.

  PMID 14630516 · PMC1241748 · Environmental health perspectives · 2003 · 8 claims · 6 setups

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  The mouse Cyp2a-t cluster on chromosome 7 contains 22 loci from the same six CYP2 subfamilies (Cyp2a, Cyp2b, Cyp2f, Cyp2g, Cyp2s, Cyp2t) found in the human cluster

  genomic bac nine restriction bac pcr southern