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).

• Bayesian transcriptome assembly.

  PMID 25367074 · PMC4397945 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  Bayesembler, a probabilistic transcriptome assembler built on a Bayesian model of the RNA sequencing process with Gibbs sampling over expressed candidates, abundances and read assignments, is introduced.

  k562 embryonic dendritic rna-seq simulated paired-end long-read

• Genetic variation in an individual human exome.

  PMID 18704161 · PMC2493042 · PLoS genetics · 2008 · 8 claims · 7 setups

  Full-text index only

  The ~12,500 nonsilent coding variants in the HuRef exome can be reduced ~8-fold to a set of ~1,600 variants most likely to affect protein function.

  huref genes subset whole-genome allele functional

• Assessing the gene space in draft genomes.

  PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

  Full-text index only

  The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

  caenorhabditis toxoplasma homo briggsae cegma blast tblastn

• Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

  PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

  Full-text index only

  The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

  monocytogenes additional food j774 whole-genome comparative pcr

• Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

  PMID 27092297 · PMC4820441 · Frontiers in cellular and infection microbiology · 2016 · 7 claims · 7 setups

  Has reproduction · 89

  STEC are prevalent in surface waters of four Lower Mainland BC watersheds, recovered from 21.6, 23.2, 19.5, and 9.2% of samples across sites, with seasonal variation (13.3% in fall to 34.3% in winter).

  surface coli presumptive confirmed hydrophobic sandwich monoplex

• 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

  Full-text index only

  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

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative