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 9

System / cell line: each ✕ Assay: power ✕ Clear

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
Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling.

PMID 17634103 · PMC1947971 · BMC genomics · 2007 · 8 claims · 4 setups

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A closed-form approximation to the F-test non-centrality parameter (NCP) incorporating genetic model parameters (disease allele frequency, marker allele frequency, prevalence, genotype relative risk, sample size, genetic model, number of pools/replicates, machine variability) can be used to compute power for DNA pooling association studies

modeled analytic factorial power
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
DBD--taxonomically broad transcription factor predictions: new content and functionality.

PMID 18073188 · PMC2238844 · Nucleic acids research · 2008 · 8 claims · 3 setups

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DBD is a database of predicted sequence-specific DNA-binding transcription factors covering over 700 publicly available proteomes, up from 150 in the initial version.

proteomes eukaryotic genomes hmm-based comparative heatmap
Identification of genomic regions contributing to etoposide-induced cytotoxicity.

PMID 19089452 · PMC2714550 · Human genetics · 2009 · 7 claims · 6 setups

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Etoposide-induced cytotoxicity in CEPH lymphoblastoid cell lines is heritable, with genetics explaining 17-25% of variation

ceph subset hapmap simulated growth heritability non-parametric
Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

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A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

liver simulated conserved nearly gene simulation kolmogorov-smirnov
Testing groups of genomic locations for enrichment in disease loci using linkage scan data: a method for hypothesis testing.

PMID 16848972 · PMC3525155 · Human genomics · 2006 · 8 claims · 2 setups

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A method testing enrichment of a group of genomic locations for disease loci by comparing the average NPL score of the group to a null distribution from randomly drawn groups of equal size

simulated pedigrees simulated real
Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

PMID 18598366 · PMC2474618 · BMC bioinformatics · 2008 · 7 claims · 6 setups

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Experimentally measured protein-protein interaction sub-networks are not random samples of their parent networks.

yeast drosophila networks dppi reanalysis computer repeated
Association testing of novel type 2 diabetes risk alleles in the JAZF1, CDC123/CAMK1D, TSPAN8, THADA, ADAMTS9, and NOTCH2 loci with insulin release, insulin sensitivity, and obesity in a population-based sample of 4,516 glucose-tolerant middle-aged Danes.

PMID 18567820 · PMC2518507 · Diabetes · 2008 · 8 claims · 5 setups

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CDC123/CAMK1D rs12779790 risk allele (homozygous) is associated with decreased insulinogenic index, corrected insulin response (CIR), and AUC-insulin/AUC-glucose ratio, indicating impaired insulin release

inter99 same taqman oral general

Experiments

Power analysis for genome-wide association studies.

Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling.

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.

DBD--taxonomically broad transcription factor predictions: new content and functionality.

Identification of genomic regions contributing to etoposide-induced cytotoxicity.

Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

Testing groups of genomic locations for enrichment in disease loci using linkage scan data: a method for hypothesis testing.

Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

Association testing of novel type 2 diabetes risk alleles in the JAZF1, CDC123/CAMK1D, TSPAN8, THADA, ADAMTS9, and NOTCH2 loci with insulin release, insulin sensitivity, and obesity in a population-based sample of 4,516 glucose-tolerant middle-aged Danes.