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 20

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

Needles in the haystack: identifying individuals present in pooled genomic data.

PMID 19798441 · PMC2747273 · PLoS genetics · 2009 · 8 claims · 7 setups

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The distribution of T for null samples (individuals not in F or G) deviates strongly from the assumed standard normal, in both location and width.

cgems hapmap genetic-distance within-population snp-count
SNP@Evolution: a hierarchical database of positive selection on the human genome.

PMID 19732458 · PMC2755008 · BMC evolutionary biology · 2009 · 7 claims · 6 setups

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SNP@Evolution is a hierarchical database integrating HET, FST, and iHS from HapMap Phase II and III to identify genome-wide positive selection signals

hapmap autosomes simulated sliding snp sliding haplotype-based
A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

PMID 17996079 · PMC2206057 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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An HMM using paired germline genotype calls and tumour allelic SNP intensities can estimate allele-specific copy-numbers, distinguishing events like uniparental disomy from allelic imbalance.

hapmap bladder prostate simulated affymetrix simulation
What can genome-wide association studies tell us about the genetics of common disease?

PMID 18454206 · PMC2323402 · PLoS genetics · 2008 · 8 claims · 4 setups

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Apparent patterns of common, low-effect disease-associated alleles largely reflect statistical power of studies rather than the true underlying distribution of disease variants

case gwa simulated literature cochran-armitage computer
Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

genome autosomal hapmap chromosome snp chromosomal minor
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
Direct inference of SNP heterozygosity rates and resolution of LOH detection.

PMID 18052545 · PMC2098867 · PLoS computational biology · 2007 · 6 claims · 7 setups

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A large proportion of SNPs in dbSNP have high-variance HET rate estimates, limiting their reliability for LOH study design.

dbsnp theoretical simulated hapmap snp probability sequential
SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

PMID 18847484 · PMC2576268 · BMC bioinformatics · 2008 · 7 claims · 8 setups

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SPSmart is a novel tool for accessing and combining large-scale SNP genotype databases with population information

hapmap perlegen stanford michigan snp cross-database chromosome
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
Sequence polymorphisms cause many false cis eQTLs.

PMID 17637838 · PMC1906859 · PloS one · 2007 · 8 claims · 7 setups

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Many reported local/cis eQTLs are false positives caused by probe-region sequence polymorphisms affecting hybridization rather than true cis-regulatory expression differences.

lymphoblastoid hematopoietic caenorhabditis genome anova-based sanger eqtl
Detecting natural selection by empirical comparison to random regions of the genome.

PMID 19783549 · PMC2778377 · Human molecular genetics · 2009 · 8 claims · 5 setups

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Comparing candidate loci to empirically matched random genomic regions (ENCODE data) avoids the strong demographic/mutation assumptions required by theoretical neutral models and provides a robust test for selection

ceu genomic simulated long-read snp population
Human SNPs resulting in premature stop codons and protein truncation.

PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

genome transcripts validated x-snp-encoded database blast exon-intron
Personalized genomic medicine with a patchwork, partially owned genome.

PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

phenotypically single genome chimpanzee molecular diploid encode
Widespread ultraconservation divergence in primates.

PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups

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The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.

hg18 genome genes computed comparative snp gene
Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups

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Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.

bxd simulated subset populations genome-wide simulation genotype-phenotype
Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES).

PMID 19903357 · PMC3087512 · BMC genetics · 2009 · 7 claims · 6 setups

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LALES Latinos show strong evidence of recent population admixture, primarily from Native American and European ancestries with smaller Asian and African contributions.

lales native genotyping structure hardy-weinberg
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
Fast-evolving noncoding sequences in the human genome.

PMID 17578567 · PMC2394770 · Genome biology · 2007 · 8 claims · 6 setups

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1,356 conserved noncoding sequences show human-specific accelerated substitution rates (ANC sequences) relative to chimpanzee

chimpanzee genome hapmap comparative genomic segmental
A comparative study of techniques for differential expression analysis on RNA-Seq data.

PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 58

edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq
Microsatellites and SNPs linkage analysis in a Sardinian genetic isolate confirms several essential hypertension loci previously identified in different populations.

PMID 19715579 · PMC2741446 · BMC medical genetics · 2009 · 8 claims · 6 setups

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Three loci (2q24, 11q23.1-25, 13q14.11-21.33) were identified by both the microsatellite and SNP genome-wide scans

talana volunteers same ogliastra genome-wide clinical genotype

Experiments

Needles in the haystack: identifying individuals present in pooled genomic data.

SNP@Evolution: a hierarchical database of positive selection on the human genome.

A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

What can genome-wide association studies tell us about the genetics of common disease?

Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

Gene-centric characteristics of genome-wide association studies.

Direct inference of SNP heterozygosity rates and resolution of LOH detection.

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

Patterns of evolutionary constraints on genes in humans.

Sequence polymorphisms cause many false cis eQTLs.

Detecting natural selection by empirical comparison to random regions of the genome.

Human SNPs resulting in premature stop codons and protein truncation.

Personalized genomic medicine with a patchwork, partially owned genome.

Widespread ultraconservation divergence in primates.

Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES).

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

Fast-evolving noncoding sequences in the human genome.

A comparative study of techniques for differential expression analysis on RNA-Seq data.

Microsatellites and SNPs linkage analysis in a Sardinian genetic isolate confirms several essential hypertension loci previously identified in different populations.