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).

• Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

  PMID 19906700 · PMC2808873 · Nucleic acids research · 2010 · 7 claims · 4 setups

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  NCG is a web database integrating duplicability, orthology, evolutionary appearance, and network topology data for 736 human cancer genes

  cancer proteome pten genome orthology protein-protein

• Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

  PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

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  Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

  proteins cdc candidate yersinia all-against-all computational cross-species

• Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK.

  PMID 34427554 · PMC8549364 · Microbial genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  bla_CTX-M-27 is located on IncFII pKSR100-like plasmids, flanked by IS26 and IS903B

  sonnei same shigella assembled illumina oxford novo

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

  PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

  yeast yeast-related interaction random dictionary-based manual graph

• Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.

  PMID 17335570 · PMC1828162 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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  An initial diversification of bHLHs occurred in the pre-Cambrian, prior to metazoan cladogenesis

  metazoan identified amphimedon nematostella genome sequence gene

• Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

  PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

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  Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

  pooled computational identified additional label-free lspad pathway-associated