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).

• Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

  PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups

  Has reproduction · 93

  Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.

  melanogaster dgrp complete wolbachia-infected whole-genome diagnostic coverage-based

• Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples.

  PMID 18793462 · PMC2537568 · BMC bioinformatics · 2008 · 8 claims · 4 setups

  Full-text index only

  Batch size affects genotype calling results (call rate and concordance) and the resulting lists of significantly associated SNPs.

  hapmap genotype genotype raw case-control

• Allelotyping of pooled DNA with 250 K SNP microarrays.

  PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups

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  The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.

  pool nspi individual snp individual call

• Modeling genetic inheritance of copy number variations.

  PMID 18832372 · PMC2588508 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  A joint HMM framework for parents-offspring trios significantly improves CNV call rates and boundary inference accuracy compared to existing methods.

  simulated parent-offspring hapmap hmm-based snp genotype

• Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

  PMID 16515697 · PMC1448207 · BMC medical genetics · 2006 · 8 claims · 7 setups

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  CMS compares IBS allele/genotype sharing between distantly related (beyond grandparental) affected and unaffected individuals from founder populations to detect disease loci while reducing confounding from population stratification and genetic heterogeneity.

  amish unrelated same overall microsatellite combinatorial permutation