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).

• The HuRef Browser: a web resource for individual human genomics.

  PMID 19036787 · PMC2686481 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  The HuRef Browser is a unified web application integrating assembly, annotation, and assembly-to-assembly comparison (ATAC) views for the diploid HuRef individual human genome.

  individual huref whole-genome assembly-to-assembly variant

• 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

• siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.

  PMID 17640392 · PMC2323231 · Genome biology · 2007 · 8 claims · 8 setups

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  The PtdIns(3,4,5)P3-mTOR signaling pathway is a primary positive regulator of transferrin uptake.

  hela sirna secondary synthetic

• A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

  PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

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  A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

  domestic red same white partial comparative pcr

• Competitive enzymatic reaction to control allele-specific extensions.

  PMID 15767273 · PMC1065263 · Nucleic acids research · 2005 · 6 claims · 7 setups

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  Protease-mediated allele-specific extension (PrASE) uses competition between polymerase activity and Proteinase K-mediated polymerase degradation to allow extension of perfectly matched primers while eliminating slower mismatched primer extension.

  genomic immobilized four individuals multiplex protease-mediated effect

• Statistical challenges in preprocessing in microarray experiments in cancer.

  PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups

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  Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset

  lung beer individual outlier expression rank-covariance quality-control

• Evolutionarily conserved human targets of adenosine to inosine RNA editing.

  PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

  panel brain chicken flna comparative rt-pcr homology

• Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling.

  PMID 17634103 · PMC1947971 · BMC genomics · 2007 · 8 claims · 4 setups

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  A closed-form approximation to the F-test non-centrality parameter (NCP) incorporating genetic model parameters (disease allele frequency, marker allele frequency, prevalence, genotype relative risk, sample size, genetic model, number of pools/replicates, machine variability) can be used to compute power for DNA pooling association studies

  modeled analytic factorial power

• Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

  PMID 18692127 · PMC3341170 · Genomics · 2008 · 8 claims · 7 setups

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  Autozygosity mapping identified a highly significant homozygous region on chromosome 13q14.11-q14.3 (Z/LOD=10.41)

  family p2ry5 affected snp microsatellite sanger

• A conversation with John Sulston.

  PMID 14580111 · PMC2588810 · The Yale journal of biology and medicine · 2002 · 8 claims · 5 setups

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  C. elegans, with about 1,000 cells, is an ideal model for studying how cells divide, communicate, differentiate, and undergo programmed death, bridging single-celled organisms and complex animals

  elegans genomic survey lineage ablation physical

• SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis.

  PMID 15980517 · PMC1160189 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  SNPAnalyzer is an integrated web-based workbench that performs four statistical SNP analyses (Hardy-Weinberg equilibrium, haplotype estimation, linkage disequilibrium, and QTL analysis) in one common computational environment.

  african simulated hardy-weinberg haplotype linkage

• High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

  PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

  genomic ecotilling non-synonymous ecotilling sanger universal-primer

• Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP.

  PMID 19784376 · PMC2747018 · PloS one · 2009 · 8 claims · 8 setups

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  Native human U1 snRNP shows differential incorporation of four protein isoforms (U1-70k isoforms 1/2, Sm-B/B')

  native snrna intact denatured proteomic denaturing nucleic