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 242

Assay: selected ✕ Clear

GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

PMID 16698959 · PMC3303178 · Nucleic acids research · 2006 · 7 claims · 5 setups

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GREM enables genome-wide isolation and quantitative analysis of transcriptionally active (promoter-active) repetitive elements while excluding read-through transcript background

testicular genomic coli grem rt-pcr race
Relationship between cyclooxygenase 8473T>C polymorphism and the risk of lung cancer: a case-control study.

PMID 16542464 · PMC1468421 · BMC cancer · 2006 · 8 claims · 4 setups

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The COX-2 8473T>C genotype distribution did not differ significantly between overall lung cancer cases and controls.

peripheral selected lung pcr-based sequencing questionnaire-based
Rbfox2 controls autoregulation in RNA-binding protein networks.

PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

Has reproduction · 48

Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

v6.5 fhfox2 top introns iclip sequencing rt-pcr
Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

PMID 16319823 · PMC1477589 · European journal of human genetics : EJHG · 2006 · 7 claims · 8 setups

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ALX4 and MSX2 mutations contribute approximately equally to PFM/CB and cause skull defects that are usually clinically indistinguishable

pfm selected point-mutation-negative family dhplc bidirectional multiplex
On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve.

PMID 18076765 · PMC2211327 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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The TGDR-AUC algorithm regularizes the empirical AUC by replacing the non-differentiable 0-1 loss with a smooth sigmoid surrogate function and applies constrained threshold gradient descent regularization

simulated serum preprocessed simulation mass high-resolution
Mutation analysis in a German family identified a new cataract-causing allele in the CRYBB2 gene.

PMID 17653036 · PMC2774456 · Molecular vision · 2007 · 8 claims · 4 setups

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A novel heterozygous mutation (383A>T; D128V) in exon 5 of CRYBB2 cosegregates with congenital cataract in all three affected family members and is absent in unaffected relatives.

genomic pcr-amplified computational pcr restriction pcr-rflp
Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

PMID 19025632 · PMC2630941 · Virology journal · 2008 · 8 claims · 4 setups

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Twelve gp41 sites (outside the overlapping rev exon2 reading frame) show positive selection conserved across multiple HIV-1 M subtypes/CRFs, making them candidate targets for broadly protective vaccines.

gp41 hiv-1 recombination site-specific comparative
Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

serous same lmp braf-mutant gene hotspot erbb2
Adaptive history of single copy genes highly expressed in the term human placenta.

PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

term single same lists microarray comparative site
Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

PMID 18842779 · PMC3014055 · The American journal of clinical nutrition · 2008 · 8 claims · 4 setups

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A significant gene x diet interaction exists between 5-LO promoter short alleles (3,4 repeats) and dietary AA intake in determining MI risk

costa buffy genetic real-time allele-specific
Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system.

PMID 18664269 · PMC2515158 · BMC microbiology · 2008 · 8 claims · 7 setups

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18 STR loci (1-5 base repeat units, copy number 4-26) were identified in the M. genitalium G37 genome via bioinformatics analysis.

genitalium clinical selected 246-bp bioinformatics pcr plasmid
The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS.

PMID 18522722 · PMC2447851 · BMC genomics · 2008 · 8 claims · 4 setups

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A consensus Reference Human NumtS compilation (RHNumtS) was produced by comparing Blastn, MegaBlast and BLAT results with previously published compilations.

genome genomic blastn megablast blat
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
Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.

PMID 18509521 · PMC2396875 · PloS one · 2008 · 7 claims · 6 setups

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wKIERA combines a weighted-kernel discriminant (kernel perceptron) with an iterative stochastic probability estimation-of-distribution algorithm to estimate a relevance distribution over variables

serum colon glioblastoma synthetic seldi-tof gene computational
Inferring human colonization history using a copying model.

PMID 18497854 · PMC2367454 · PLoS genetics · 2008 · 8 claims · 6 setups

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A copying-model approach using SNP haplotype sharing can infer both the order of population founding and the donor populations contributing ancestry to each new population.

simulated populations coalescent snp ascertainment
An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

PMID 18445289 · PMC2386494 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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Using RNAsubopt suboptimal solutions computed once for the wild-type sequence, specific multiple-point mutations likely to cause conformational rearrangement can be selected without brute-force enumeration.

example hepatitis minimum suboptimal multiple-point
Identification of PSEN1 and APP gene mutations in Korean patients with early-onset Alzheimer's disease.

PMID 18437002 · PMC2526428 · Journal of Korean medical science · 2008 · 6 claims · 6 setups

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Two different PSEN1 mutations (G206S and M233T) were identified in Korean EOAD patients

genomic blood korean patients direct pcr apoe
Comparative analysis of the tear protein profile in mycotic keratitis patients.

PMID 18385783 · PMC2268856 · Molecular vision · 2008 · 8 claims · 5 setups

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A glutaredoxin-related protein is expressed only in the tears of fungal keratitis patients and is absent in control tears.

pooled in-gel peptide 2de two-dimensional maldi-tof post
Indirect genomic effects on survival from gene expression data.

PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups

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A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.

dutch uppsala dlbcl gene gene literature permutation
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

Experiments

GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

Relationship between cyclooxygenase 8473T>C polymorphism and the risk of lung cancer: a case-control study.

Rbfox2 controls autoregulation in RNA-binding protein networks.

Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve.

Mutation analysis in a German family identified a new cataract-causing allele in the CRYBB2 gene.

Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

Adaptive history of single copy genes highly expressed in the term human placenta.

Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system.

The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS.

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

Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.

Inferring human colonization history using a copying model.

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

Identification of PSEN1 and APP gene mutations in Korean patients with early-onset Alzheimer's disease.

Comparative analysis of the tear protein profile in mycotic keratitis patients.

Indirect genomic effects on survival from gene expression data.

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.