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 57

Assay: permutation ✕ Clear

PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

case-control same wtccc genome-wide benchmark stratified
Visualization-based discovery and analysis of genomic aberrations in microarray data.

PMID 15953389 · PMC1181623 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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ChARMView integrates dynamic visualization with automated statistical analysis (EM-based breakpoint detection, one-sample sign test, permutation mean test) to discover chromosomal aberrations from array CGH and gene expression data

saccharomyces breast yeast array gene
Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)

simulated same snp type two-locus 2lomb benchmark
Bias of selection on human copy-number variants.

PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

genome human-mouse cnv-encompassed inbred comparative randomization molecular
Genetical genomics: spotlight on QTL hotspots.

PMID 18949031 · PMC2563687 · PLoS genetics · 2008 · 8 claims · 4 setups

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Distant eQTL hotspots are rare and difficult to reliably verify across published genetical genomics studies

adipose saccharomyces genome-wide permutation gene
The FAS gene, brain volume, and disease progression in Alzheimer's disease.

PMID 19766542 · PMC3100774 · Alzheimer's & dementia : the journal of the Alzheimer's Association · 2010 · 8 claims · 4 setups

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The minor (T) allele of rs1468063 in FAS is significantly associated with faster AD progression after permutation-based multiple-testing correction

peripheral longitudinally same subset snp survival permutation
Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

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Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

genome genomic chromosome randomization
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.

PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups

Has reproduction · 100

WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.

cervical als top yeast bulk stratified protein-protein
Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

PMID 16197552 · PMC1262713 · BMC genomics · 2005 · 8 claims · 5 setups

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Pooling genomic DNA and genotyping on SNP microarrays accurately predicts allelic frequencies relative to individual genotyping

genomic pools training siddt individual pooled k-correction
Protein length in eukaryotic and prokaryotic proteomes.

PMID 15951512 · PMC1150220 · Nucleic acids research · 2005 · 7 claims · 5 setups

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Eukaryotic proteins are significantly longer than prokaryotic proteins across virtually all functional categories and the majority of protein families

eukaryotic proteins genomic cog comparative orthology domain
Inferring combinatorial regulation of transcription in silico.

PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

upstream monocytes same tfbs microarray permutation
Phylogenetic analysis of RhoGAP domain-containing proteins.

PMID 17127216 · PMC5054073 · Genomics, proteomics & bioinformatics · 2006 · 7 claims · 6 setups

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RhoGAP domain-containing proteins, sharing the conserved arginine residue, form a monophyletic group with a common ancestor.

rhogap aligned bayesian domain sequence maximum bayesian
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

orthologous randomized high-score promoters pssm-based comparative motif
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
On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

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Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation
Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

PMID 17663790 · PMC2323240 · Genome biology · 2007 · 8 claims · 6 setups

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A sheep BAC library (CHORI-243) with ~13.5-fold genome coverage was constructed and end-sequenced.

sheep genome bac sequence randomization
Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

PMID 19116668 · PMC2605564 · PloS one · 2008 · 7 claims · 6 setups

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ASE is more robust than total gene expression approaches to environmental variation and trans-acting genetic factors, giving a cleaner representation of cis-acting effects.

hapmap combined coriell ceu allele-specific linear one-sample
Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

PMID 18769673 · PMC2518838 · PloS one · 2008 · 8 claims · 6 setups

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The protein sequence-structure map behaves as a noisy digital communication channel whose capacity C exceeds the transmission rate R for native structures, satisfying Shannon's noisy channel theorem

chains pdbselect25 same single-domain statistical channel negative
Association between the catechol-O-methyltransferase Val158Met polymorphism and cocaine dependence.

PMID 18704099 · PMC2583214 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2008 · 8 claims · 4 setups

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The COMT Val158Met polymorphism is significantly associated with cocaine dependence in individuals of African descent.

cocaine-dependent duplicate genotype study snp genotype haplotype
The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

genome sds chimpanzee colinear comparative interspecific genomic

Experiments

PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

Visualization-based discovery and analysis of genomic aberrations in microarray data.

Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

Bias of selection on human copy-number variants.

Genetical genomics: spotlight on QTL hotspots.

The FAS gene, brain volume, and disease progression in Alzheimer's disease.

Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.

Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

Protein length in eukaryotic and prokaryotic proteomes.

Inferring combinatorial regulation of transcription in silico.

Phylogenetic analysis of RhoGAP domain-containing proteins.

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

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

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

Association between the catechol-O-methyltransferase Val158Met polymorphism and cocaine dependence.

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.