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 682

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Identification of novel markers for liver fibrosis in HIV/hepatitis C virus coinfected individuals using genomics-based approach.

PMID 18614866 · PMC2654216 · AIDS (London, England) · 2008 · 8 claims · 6 setups

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An 8-marker model combining six serum markers, age, and ART experience predicts liver fibrosis stage with an AUROC of 0.904.

pbmcs liver serum blood microarray liver serum
Seeded Bayesian Networks: constructing genetic networks from microarray data.

PMID 18601736 · PMC2474592 · BMC systems biology · 2008 · 8 claims · 4 setups

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Seeding Bayesian Network analysis with prior networks derived from literature and/or PPI data improves recovery of known gene-gene interactions compared to BN analysis without a seed

leukemia interactome pubmed-indexed computational microarray yeast literature
Proteomic surveillance of retinal autoantigens in endogenous uveitis: implication of esterase D and brain-type creatine kinase as novel autoantigens.

PMID 18552983 · PMC2426731 · Molecular vision · 2008 · 7 claims · 6 setups

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Six novel candidate retinal autoantigens (β-actin, esterase D, tubulin β-2, brain-type creatine kinase, VDAC, aspartate aminotransferase) were identified by 2D-WB and mass spectrometry in EAU mice

c57bl retinal recombinant eau two-dimensional maldi-tof one-dimensional
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
Cellular proteins in influenza virus particles.

PMID 18535660 · PMC2390764 · PLoS pathogens · 2008 · 8 claims · 6 setups

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Purified influenza virions contain 36 host-encoded cellular proteins in addition to the 9 previously known viral proteins.

influenza deglycosylated sucrose lc-ms mudpit electron
A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

PMID 18518950 · PMC2464610 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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A new method for building reference gene-expression profiles and scoring/testing connections improves on the original Connectivity Map by enabling statistical significance testing of connections.

lines random gene-expression connectivity
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
Mapping proteins to disease terminologies: from UniProt to MeSH.

PMID 18460185 · PMC2367626 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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Developed a three-step procedure (disease name extraction, exact matching, partial/similarity-based matching) to map UniProtKB/Swiss-Prot disease names to MeSH terms

randomly swiss-prot uniprotkb mesh manual exact partial
Comparative genomic analysis of clinical strains of Campylobacter jejuni from South Africa.

PMID 18431496 · PMC2292242 · PloS one · 2008 · 8 claims · 4 setups

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South African HS:41 strains are clearly distinct from the other South African strains by comparative genomic analysis

clinical genomic jejuni multilocus microarray phylogenetic
PIK3CA-activating mutations and chemotherapy sensitivity in stage II-III breast cancer.

PMID 18371219 · PMC2397526 · Breast cancer research : BCR · 2008 · 7 claims · 4 setups

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PIK3CA mutations are not associated with altered sensitivity to preoperative anthracycline-based or taxane-based chemotherapy in ER-positive and ER-negative breast tumors

tumor breast stage direct immunohistochemistry fluorescence
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

putative nonredundant homo genes computational pssm semantic
Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

PMID 18334959 · PMC2268850 · Molecular vision · 2008 · 7 claims · 5 setups

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A homozygous c.955G>A mutation at the last base of exon 6 of LCA5 disrupts the normal splice donor site.

genomic lca5 lymphocyte affected snp sanger splice
Genome-wide analysis of antisense transcription with Affymetrix exon array.

PMID 18211689 · PMC2257944 · BMC genomics · 2008 · 8 claims · 4 setups

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A modified cDNA synthesis protocol (ATE: Antisense Transcriptome analysis using Exon array), which skips the first-cycle cDNA synthesis and IVT amplification step, labels cDNA in reverse orientation, enabling Exon arrays to detect antisense transcripts

jurkat exon orientation-specific
Discovery and validation of new molecular targets in treating dyslipidemia: the role of human genetics.

PMID 20211435 · PMC3328807 · Trends in cardiovascular medicine · 2009 · 8 claims · 8 setups

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Mendelian randomization uses genetic variants as a 'randomized trial of nature' to assess causal relationships between lipid biomarkers and CHD, overcoming confounding and reverse causality limitations of observational epidemiology.

population myocardial individuals animal genome-wide case-control gene
Identification of four novel cytochrome P4501B1 mutations (p.I94X, p.H279D, p.Q340H, and p.K433K) in primary congenital glaucoma patients.

PMID 20057908 · PMC2802296 · Molecular vision · 2009 · 8 claims · 4 setups

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Mutations in CYP1B1 are a major cause of PCG in the studied patient cohort

genomic cyp1b1 pcg pcr missense clinical
RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

PMID 19958502 · PMC2788391 · BMC genomics · 2009 · 7 claims · 4 setups

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RExPrimer integrates local SNP, indel, pseudogene, and CNV/structural variation databases with the Primer3 core algorithm to avoid mis-priming and SNP-in-Primer effects.

genomic cyp2d6 genome pcr penta-plex sequence
Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

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BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

genomic unrelated best1 best1-4 direct chromosome pathogenicity
Skittle: a 2-dimensional genome visualization tool.

PMID 20042093 · PMC2817707 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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Skittle is a 2D genome visualization tool combining a color-coded Nucleotide Display, a Repeat Map, a Repeat Overview, and an Alignment Cylinder to reveal genomic patterns at multiple scales

chromosome random alpha genome nucleotide repeat alignment
A global view of protein expression in human cells, tissues, and organs.

PMID 20029370 · PMC2824494 · Molecular systems biology · 2009 · 7 claims · 6 setups

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A high fraction (>65%) of proteins is expressed in most human cells and tissues, while very few proteins (<2%) are detected in any single cell type.

normal computational hepatocytes same immunohistochemistry immunofluorescence unsupervised
A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

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SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

teds diagnosed ceph snp individual transmission

Experiments

Identification of novel markers for liver fibrosis in HIV/hepatitis C virus coinfected individuals using genomics-based approach.

Seeded Bayesian Networks: constructing genetic networks from microarray data.

Proteomic surveillance of retinal autoantigens in endogenous uveitis: implication of esterase D and brain-type creatine kinase as novel autoantigens.

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

Cellular proteins in influenza virus particles.

A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

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

Mapping proteins to disease terminologies: from UniProt to MeSH.

Comparative genomic analysis of clinical strains of Campylobacter jejuni from South Africa.

PIK3CA-activating mutations and chemotherapy sensitivity in stage II-III breast cancer.

The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

Genome-wide analysis of antisense transcription with Affymetrix exon array.

Discovery and validation of new molecular targets in treating dyslipidemia: the role of human genetics.

Identification of four novel cytochrome P4501B1 mutations (p.I94X, p.H279D, p.Q340H, and p.K433K) in primary congenital glaucoma patients.

RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

Skittle: a 2-dimensional genome visualization tool.

A global view of protein expression in human cells, tissues, and organs.

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.