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 18

System / cell line: square ✕ Assay: disease ✕ Clear

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
Analysis of protein sequence and interaction data for candidate disease gene prediction.

PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

ophid biocarta kegg pfam-annotated common benchmarking multiple-interval
PDA: Pooled DNA analyzer.

PMID 16643673 · PMC1539032 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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No software existed prior to PDA for complete pooled-DNA analysis including data standardization, allele frequency estimation, and single/multipoint association tests

heterozygous pools ordered peak pooled single-point
Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

PMID 16824219 · PMC1534050 · BMC neurology · 2006 · 7 claims · 5 setups

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The C282Y variant allele of HFE is significantly overrepresented in PD patients compared to controls, suggesting it confers higher risk for PD

genomic same pooled pcr-rflp pcr-based cross-tabulation
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
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
Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation.

PMID 12194772 · PMC2732546 · Emerging infectious diseases · 2002 · 8 claims · 5 setups

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Clonal complex, as defined by MLST, is an epidemiologically relevant unit for long- and short-term investigation of C. jejuni epidemiology.

jejuni same clonal mlst multilocus heat-stable flaa
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
Phenotype, genotype, and worldwide genetic penetrance of LRRK2-associated Parkinson's disease: a case-control study.

PMID 18539534 · PMC2832754 · The Lancet. Neurology · 2008 · 8 claims · 7 setups

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LRRK2-associated PD can be distinguished from idiopathic PD by a more benign motor and non-motor phenotype

unrelated patients people homozygous genetic standardized olfaction
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
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
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
Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

PMID 19844207 · PMC2797562 · Molecular psychiatry · 2010 · 8 claims · 7 setups

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rs1344706 in ZNF804A is associated with schizophrenia in the Irish ICCSS sample, replicating the original Cardiff finding

irish iccss postmortem genomic snp haplotype logistic
Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

PMID 17700570 · PMC2360390 · British journal of cancer · 2007 · 8 claims · 3 setups

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Germline protein-truncating BRCA2 mutations confer an elevated relative risk (~7.8-fold) of early-onset prostate cancer in Caucasian men

peripheral population-based same germline epidemiological genotype-phenotype
Coxiella burnetii genotyping.

PMID 16102309 · PMC3320512 · Emerging infectious diseases · 2005 · 8 claims · 5 setups

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Multispacer sequence typing (MST) is the first reliable method for typing Coxiella burnetii isolates

coxiella burnetii matrix sequence pcr molecular pcr-based
An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

PMID 16872505 · PMC1550395 · BMC medical genetics · 2006 · 7 claims · 7 setups

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Marginally significant (uncorrected) transmission distortion was found for four SNPs after stratification by HLA-DRB1*1501 status, disease course, or gender.

pooled australian independent trio pool snapshot snplex
Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups

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Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.

perfused lung microarray principal wilcoxon
Phenotypic features and genetic characterization of male breast cancer families: identification of two recurrent BRCA2 mutations in north-east of Italy.

PMID 16764716 · PMC1586026 · BMC cancer · 2006 · 8 claims · 6 setups

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The 9106C>T (Q2960X) and IVS16-2A>G BRCA2 mutations are recurrent in MBC families from North-East Italy and may reflect a founder effect.

blood germline tumor family mutation mlpa microsatellite

Experiments

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

Analysis of protein sequence and interaction data for candidate disease gene prediction.

PDA: Pooled DNA analyzer.

Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

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

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

Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation.

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

Phenotype, genotype, and worldwide genetic penetrance of LRRK2-associated Parkinson's disease: a case-control study.

Gene-centric characteristics of genome-wide association studies.

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

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

Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

Coxiella burnetii genotyping.

An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

Phenotypic features and genetic characterization of male breast cancer families: identification of two recurrent BRCA2 mutations in north-east of Italy.