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).

Publications 1.3k Datasets 392.5k Experiments 14

System / cell line: hapmap ✕ Assay: score ✕ Clear

Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups

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Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.

pools individual same parental pooled individual test-retest
A modified T-test feature selection method and its application on the HapMap genotype data.

PMID 18267305 · PMC5054219 · Genomics, proteomics & bioinformatics · 2007 · 7 claims · 4 setups

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A modified t-test ranking measure, extended to handle nominal SNP genotype data via vector transformation, can effectively rank SNPs by their discriminative capability for population classification.

hapmap modified f-statistics informativeness
HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

white same hapmap snp haplotype tagging
Mutations in the UBIAD1 gene, encoding a potential prenyltransferase, are causal for Schnyder crystalline corneal dystrophy.

PMID 17668063 · PMC1925147 · PloS one · 2007 · 8 claims · 7 setups

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Mutations in UBIAD1 are causal for Schnyder crystalline corneal dystrophy

pedigrees pedigree genomic ubiad1 microsatellite fine direct
A human genome-wide library of local phylogeny predictions for whole-genome inference problems.

PMID 18710563 · PMC2556685 · BMC genomics · 2008 · 7 claims · 5 setups

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A genome-wide library of nearly 16 million local maximum parsimony phylogenies was constructed from HapMap CEU and YRI SNP data across all human autosomes

hapmap 5-snp genome-wide first maximum mutual pearson
Gene-centric characteristics of genome-wide association studies.

PMID 18060058 · PMC2092383 · PloS one · 2007 · 8 claims · 5 setups

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High-density SNP chips using either direct or indirect selection approaches provide very high coverage in genic regions and capture most known common disease variants under the HapMap framework.

phase omim snps snp disease genomic
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

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

hapmap genotype genotype raw case-control
Patterns of evolutionary constraints on genes in humans.

PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

mammalian hapmap panther significant comparative population chi-square
SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

PMID 18366708 · PMC2289803 · BMC medical genetics · 2008 · 7 claims · 6 setups

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Illumina validation/design scores above 0.6 are not strongly correlated with actual SNP genotyping performance (Gentrain score)

randomly heirs seattlesnps african resequencing genome-wide tag
Whole genome association mapping by incompatibilities and local perfect phylogenies.

PMID 17042942 · PMC1624851 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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Blossoc scores the perfect phylogenetic tree spanning the largest compatible region around each marker as a decision tree for case/control status to detect association

coalescent-simulated artificial empirical same perfect-phylogeny hapminer haplotype
Variation resources at UC Santa Cruz.

PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

chimpanzee affymetrix hapmap perlegen snp fixed linkage
MutDB: update on development of tools for the biochemical analysis of genetic variation.

PMID 17827212 · PMC2238958 · Nucleic acids research · 2008 · 7 claims · 5 setups

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MutDB integrates dbSNP and Swiss-Prot genetic variation data with protein structural information, functional disruption prediction scores, and clinical phenotype links (OMIM, dbGAP)

proteins mutdb nonsynonymous genes sequence web functional
Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

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CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

missense same synthetic tp53 random support principal
A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

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SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

teds diagnosed ceph snp individual transmission

Experiments

Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

A modified T-test feature selection method and its application on the HapMap genotype data.

HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

Mutations in the UBIAD1 gene, encoding a potential prenyltransferase, are causal for Schnyder crystalline corneal dystrophy.

A human genome-wide library of local phylogeny predictions for whole-genome inference problems.

Gene-centric characteristics of genome-wide association studies.

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

Patterns of evolutionary constraints on genes in humans.

SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

Whole genome association mapping by incompatibilities and local perfect phylogenies.

Variation resources at UC Santa Cruz.

MutDB: update on development of tools for the biochemical analysis of genetic variation.

Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.