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).

• The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

  PMID 19654113 · PMC2759552 · Bioinformatics (Oxford, England) · 2009 · 7 claims · 2 setups

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  IGB is an open-source, Java-based desktop genome browser supporting real-time zooming/panning, moveable tiered feature layout, incremental or genome-scale data loading, and dynamic genome graphs

  arabidopsis pyrosequencing expression

• Large-scale discovery and validation of functional elements in the human genome.

  PMID 15774039 · PMC1088940 · Genome biology · 2005 · 8 claims · 8 setups

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  Genome-wide tiling microarray hybridization reveals large, diverse sets of transcripts, many of which lack existing gene annotations

  liver genome yeast lines tiling computational dnase

• 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

• Genome Network and FANTOM3: assessing the complexity of the transcriptome.

  PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

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  63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

  fantom3 genome large-scale mammalian cage full-length genome

• Shaken not stirred: a global research cocktail served in Hinxton.

  PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

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  Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

  budding caenorhabditis drosophila escherichia two-color double chip-chip

• Epigenetics and phenotypic variation in mammals.

  PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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  Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

  mammalian mhc chromosomes embryonic methylation high-throughput chip