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).

• Ontological Discovery Environment: a system for integrating gene-phenotype associations.

  PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups

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  ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems

  strains integrated bipartite phish gene differential pairwise

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

  PMID 18654633 · PMC2464715 · PLoS genetics · 2008 · 8 claims · 5 setups

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  A Bayesian-inspired penalised maximum likelihood stochastic search method can simultaneously analyse all SNPs (up to 500K) from a GWA study in a few hours on a desktop workstation

  fregene-simulated 80k-snp 480k 192k simulated null whole-genome

• Indirect genomic effects on survival from gene expression data.

  PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups

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  A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.

  dutch uppsala dlbcl gene gene literature permutation

• An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

  PMID 18302794 · PMC2292209 · BMC genetics · 2008 · 7 claims · 5 setups

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  Among the four HapMap populations, CHB shows the best correlation with the Shanghai population on allele frequencies, LD, and haplotype frequencies

  unrelated shanghai tsnps snp allele linkage