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 19

System / cell line: test ✕ Assay: tag ✕ Clear

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups

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3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).

brain hbrr topo-cloned tag microarray quantitative
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
Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

PMID 15720714 · PMC551616 · BMC genetics · 2005 · 7 claims · 5 setups

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None of the six candidate gene regions showed evidence of association with type 1 diabetes (all multi-locus/single-locus test P values > 0.2)

genomic case-control nramp1 type sanger snp microsatellite
Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.

PMID 16504056 · PMC1402321 · BMC genetics · 2006 · 7 claims · 8 setups

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No statistical evidence of a major association between T1D and any of the interferon or interferon-related genes tested (IFNA cluster, IFNB1, IFNW1, IFNG, ICSBP1)

t1d european warren resequencing database tag
Adaptations to climate in candidate genes for common metabolic disorders.

PMID 18282109 · PMC2242814 · PLoS genetics · 2008 · 8 claims · 7 setups

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A network-based bioinformatics approach (Molecular Triangulation) was used to select 82 candidate genes belonging to the core subnetwork of metabolic syndrome phenotypes.

individuals population genic compiled snp spearman bayesian
iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.

PMID 18974167 · PMC2639305 · Bioinformatics (Oxford, England) · 2008 · 6 claims · 3 setups

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iMapper is a web application for automated analysis and mapping of insertional mutagenesis sequence data against vertebrate and invertebrate Ensembl genomes (human, mouse, rat, zebrafish, Drosophila, S. cerevisiae).

piggybac splinkerette-pcr-derived sequence splinkerette genome throughput
A model-based approach to selection of tag SNPs.

PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups

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The Li and Stephens hidden Markov model outperforms other tested models (simple Markov, two-state HMM, HMM-4D, greedy GR-1/GR-2) in description code-length, tag set information content, and prediction of tagged SNPs.

hapmap encode enr112 tag cross-validated entropy tagged
Application of machine learning in SNP discovery.

PMID 16398931 · PMC1955739 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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PolyBayes produces high false-positive SNP predictions even with stringent parameters

diverse soybean candidate same sts polybayes polyphred
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
ECgene: an alternative splicing database update.

PMID 17132829 · PMC1716719 · Nucleic acids research · 2007 · 8 claims · 5 setups

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ECgene provides functional annotation (domain, GO, expression pattern) for alternatively spliced genes

nine genome sage cdna genome-based chi-squared sage
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
Genetic differences between avian and human isolates of Candida dubliniensis.

PMID 19788816 · PMC2819872 · Emerging infectious diseases · 2009 · 7 claims · 6 setups

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13 of 14 avian-associated C. dubliniensis isolates form a genetically distinct subgroup within MLST clade C1, separate from human isolates

candida fecal avian-associated multilocus pcr multiplex
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

Has reproduction · 74

Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

intestinalis same rna-seq strand-specific technical reverse
Polymorphism screening and haplotype analysis of the tryptophan hydroxylase gene (TPH1) and association with bipolar affective disorder in Taiwan.

PMID 15799788 · PMC1079843 · BMC medical genetics · 2005 · 8 claims · 7 setups

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Systematic screening of TPH1 exons and promoter region in Taiwanese Han identified five sequence variants: A-1067G, G-347T, T3804A, C27224T, A27237G.

taiwanese bpd bess arms multiplex
Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

PMID 15640441 · PMC546178 · Nucleic acids research · 2005 · 8 claims · 7 setups

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NCL aggregation of DNA-modified gold nanoparticles shows extraordinary selectivity against terminal mismatches at the free ends of surface-bound duplexes

probe-modified probe-gnp synthetic four uv-vis ssdna pcr
Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

PMID 18086709 · PMC2241899 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Preferred nucleotide sequences around the initiation codon are diverse among eukaryote species, but differences roughly reflect evolutionary relationships between species

eukaryote genes hexanucleotide saccharomyces comparative cluster hexanucleotide
Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

PMID 18036257 · PMC2222243 · BMC medical genetics · 2007 · 8 claims · 5 setups

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Resequencing 81 candidate osteoporosis genes in 24 Koreans identified 942 variants (888 SNPs, 43 indels, 11 microsatellites)

genomic sequenced korean common sanger sequence population
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription

Experiments

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

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

Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.

Adaptations to climate in candidate genes for common metabolic disorders.

iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.

A model-based approach to selection of tag SNPs.

Application of machine learning in SNP discovery.

Power analysis for genome-wide association studies.

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

ECgene: an alternative splicing database update.

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

Genetic differences between avian and human isolates of Candida dubliniensis.

Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

Polymorphism screening and haplotype analysis of the tryptophan hydroxylase gene (TPH1) and association with bipolar affective disorder in Taiwan.

Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.