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 38

System / cell line: comparison ✕ Assay: chi-square ✕ Clear

Phenotypic characteristics of colo-rectal cancer in I1307K APC germline mutation carriers compared with sporadic cases.

PMID 11720476 · PMC2375261 · British journal of cancer · 2001 · 8 claims · 5 setups

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I1307K APC germline mutation carriers were identified in 28 of 307 (9.1%) unselected Israeli CRC patients

genomic pcr unselected i1307k mutation sequencing clinical
Molecular and clinical analyses of 84 patients with tuberous sclerosis complex.

PMID 16981987 · PMC1592085 · BMC medical genetics · 2006 · 8 claims · 6 setups

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Mutations were identified in 64 of 84 (76%) TSC probands, comprising 9 TSC1 and 55 TSC2 mutations

genomic pcr-amplified tsc healthy dhplc direct pcr
PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing

simulated gaw12 breast monte pedigree-based genetic
A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

individuals sequence resequencing snps targeted sequence genotype
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
Screening of the transcriptional regulatory regions of vascular endothelial growth factor receptor 2 (VEGFR2) in amyotrophic lateral sclerosis.

PMID 17456229 · PMC1868706 · BMC medical genetics · 2007 · 7 claims · 4 setups

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No mutations were identified in the VEGFR2 gene (exons 7, 18, 21, 27, promoter, or 5' UTR) in ALS patients

genomic pcr als direct restriction allele
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis

faecal rsr 16s sargasso shotgun blastn-based 16s
Power analysis for genome-wide association studies.

PMID 17725844 · PMC2042984 · BMC genetics · 2007 · 8 claims · 6 setups

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Developed a method to compute genome-wide association study power using tag SNPs and representative population genotype data (HapMap), equivalent to the cumulative r2-adjusted power of Jorgenson and Witte.

hapmap power pairwise tag
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

PMID 17166280 · PMC1764022 · BMC genomics · 2006 · 8 claims · 6 setups

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C→T (G→A) changes occur most frequently among nucleotide substitutions in the chimpanzee genome

chimpanzee intergenic genome-wide chi-square nucleotide-content
Prevalence of variations in melanoma susceptibility genes among Slovenian melanoma families.

PMID 18803811 · PMC2556318 · BMC medical genetics · 2008 · 8 claims · 7 setups

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CDKN2A germline mutations were found in 7 of 25 (28.0%) Slovenian melanoma families

genomic relative p16ink4a pcr pearson student's
An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

PMID 18302794 · PMC2292209 · BMC genetics · 2008 · 7 claims · 5 setups

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Among the four HapMap populations, CHB shows the best correlation with the Shanghai population on allele frequencies, LD, and haplotype frequencies

unrelated shanghai tsnps snp allele linkage
A comparative analysis of blastoid models through single-cell transcriptomics.

PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups

Has reproduction · 60

EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.

blastoid natural combined integrated scrnaseq lineage kolmogorov-smirnov
p53 mutations in urinary bladder cancer.

PMID 11384101 · PMC2363660 · British journal of cancer · 2001 · 6 claims · 5 setups

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p53 mutations are strongly associated with high-grade/high-stage bladder tumors and are nearly absent in lowly malignant tumors (Ta, G1-G2a)

urinary tumor patients single multiplex-pcr dyedeoxy loss
Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).

PMID 15339345 · PMC517707 · BMC bioinformatics · 2004 · 7 claims · 5 setups

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A Bayesian mixture model is proposed to account for within-class biological variability in SAGE/Digital-Northern/MPSS tag counting data.

astrocytoma same sage classical beta-binomial
Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

orthologous random cattle aligned three-way pairwise bac
Single nucleotide polymorphisms of the APC gene and colorectal cancer risk: a case-control study in Taiwan.

PMID 16569251 · PMC1488868 · BMC cancer · 2006 · 7 claims · 4 setups

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Three novel APC germline mutations were identified in Taiwanese subjects: a frameshift deletion at codon 460 (g.1378delG), and two missense substitutions p.V1125A and p.S1126R

genomic taiwanese dhplc pcr sanger
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

genomic normalized simulated tiling-resolution snp oligonucleotide
Genome screen to detect linkage to common susceptibility genes for intracranial and aortic aneurysms.

PMID 18948608 · PMC2629798 · Stroke · 2009 · 8 claims · 4 setups

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Genomewide linkage analysis in 26 multiplex IA families with AA-affected members identified LOD peaks on chromosome 11 (LOD=3.0) and chromosome 6 (LOD=2.3) using a broad IA/AA-combined phenotype

multiplex individuals fia subjects genomewide snp medical
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

Experiments

Phenotypic characteristics of colo-rectal cancer in I1307K APC germline mutation carriers compared with sporadic cases.

Molecular and clinical analyses of 84 patients with tuberous sclerosis complex.

PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

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

Screening of the transcriptional regulatory regions of vascular endothelial growth factor receptor 2 (VEGFR2) in amyotrophic lateral sclerosis.

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

Power analysis for genome-wide association studies.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

Prevalence of variations in melanoma susceptibility genes among Slovenian melanoma families.

An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

A comparative analysis of blastoid models through single-cell transcriptomics.

p53 mutations in urinary bladder cancer.

Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

Single nucleotide polymorphisms of the APC gene and colorectal cancer risk: a case-control study in Taiwan.

Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

Genome screen to detect linkage to common susceptibility genes for intracranial and aortic aneurysms.

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