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).

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

  PMID 18616806 · PMC2530870 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Lake Malawi cichlids are phenotypically and behaviorally diverse but appear genetically like a single subdivided population rather than distinct species

  five cichlid pairwise lake low-coverage blastx multi-species

• De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.

  PMID 29451882 · PMC5815590 · PloS one · 2018 · 7 claims · 7 setups

  Has reproduction · 45

  This is the first de novo transcriptomic analysis of Cornus officinalis, providing fundamental gene and biosynthetic pathway information.

  cornus frozen high-quality officinalis bulk extraction novo

• Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

  PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups

  Full-text index only

  Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes

  pubmed genes same randomly geneseeker evoc disease

• Update of the G2D tool for prioritization of gene candidates to inherited diseases.

  PMID 17478516 · PMC1933178 · Nucleic acids research · 2007 · 8 claims · 4 setups

  Full-text index only

  G2D is a web server that prioritizes candidate genes for inherited diseases using three distinct algorithms based on different input information.

  genome genomic etrb computational literature go-similarity

• A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

  PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

  tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided

• Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.

  PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 74

  RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).

  pericarp green cuiguan illumina bulk qrt-pcr light