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 3.2k

Assay: gene ✕ Clear

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

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Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

anopheles mtdna microsatellite population
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

PMID 19919682 · PMC3091323 · Genome biology · 2009 · 8 claims · 4 setups

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BioGPS aggregates distributed, third-party gene annotation resources into a single customizable portal for human, mouse, and rat genes.

biogps diverse tissues specified web reference exon
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
Toward the use of genomics to study microevolutionary change in bacteria.

PMID 19855823 · PMC2756242 · PLoS genetics · 2009 · 7 claims · 5 setups

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The clonal population structure of bacteria, combined with occasional DNA import, provides a powerful context for identifying genetic bases of adaptive phenotypes via association studies.

neisseria campylobacter helicobacter sequence multilocus phylogeny-based
Magnetization transfer imaging in 'premanifest' Huntington's disease.

PMID 19823894 · PMC2837878 · Journal of neurology · 2010 · 8 claims · 4 setups

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MTI parameters (mean MTR and normalized peak height) of whole brain, grey matter and white matter did not differ significantly between premanifest HD carriers and non-carriers

premanifest magnetization 3d-t1-weighted clinical
Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

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Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

lung gene differentially significantly laser histology principal
Improved mutation tagging with gene identifiers applied to membrane protein stability prediction.

PMID 19758467 · PMC2745585 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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MutationTagger achieves 87% F-measure for the mutation retrieval task on a benchmark dataset

pubmed uniprot five mutation gene sequence
A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

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Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

serum plasmids coli pcr oligonucleotide chip
Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.

PMID 19744994 · PMC2773259 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 5 setups

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560 genetic skin diseases can be decomposed into 71 elementary phenotypic features (42 dermatologic, 29 systemic) that combine to represent each disease as a point in a multidimensional phenotype space

genodermatoses phenotype disease gene-phenotype manual correlation principal
Delineation of a gene network underlying the pulmonary response to oxidative stress in asthma.

PMID 19730131 · PMC3328512 · Journal of investigative medicine : the official publication of the American Federation for Clinical Research · 2009 · 8 claims · 6 setups

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Integration of multiple public microarray datasets via a four-way Venn diagram identifies genes commonly expressed in asthma- and cigarette smoke-exposed lung

respiratory lung a549 gene affymetrix network
Helicobacter Pylori's plasticity zones are novel transposable elements.

PMID 19727398 · PMC2731543 · PloS one · 2009 · 8 claims · 8 setups

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Plasticity zones are a novel class of transposable elements (named TnPZs), flanked by direct repeats of 5'AAGAATG and inserted at multiple discrete chromosomal sites

pylori shimaa model mammalian pcr-based genome pcr
Utilization of genomic signatures to identify phenotype-specific drugs.

PMID 19714244 · PMC2729377 · PloS one · 2009 · 8 claims · 8 setups

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A RAS pathway gene expression signature applied to NCI-60 cells identifies compounds selectively active against RAS-activated cells, including the MEK inhibitor Hypothemycin

nci-60 breast mda-mb-231 signature-drug gene signature
The origins of lactase persistence in Europe.

PMID 19714206 · PMC2722739 · PLoS computational biology · 2009 · 8 claims · 5 setups

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The −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly linked to the Linearbandkeramik culture.

simulated simulation 910*t farming demic approximate comparison
Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

PMID 19706770 · PMC2745517 · Cancer research · 2009 · 8 claims · 8 setups

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Genome-wide DNA copy number analysis of 161 primary breast tumors identified six novel focally amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4

breast mcf10a mcf10ca1h snp quantitative rt-qpcr
Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing.

PMID 19682357 · PMC2782262 · BMC microbiology · 2009 · 8 claims · 5 setups

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The RCA assay correctly identified all ERG11 mutations in eight 'reference' azole-resistant C. albicans isolates with known mutations.

clinical pcr template padlock sequencing antifungal
Exploration of effective biomarkers for venous thrombosis embolism in Behçet's disease based on comprehensive bioinformatics analysis.

PMID 38987624 · PMC11236978 · Scientific reports · 2024 · 6 claims · 8 setups

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Four hub genes (E2F1, GATA3, HDAC5, MSH2) serve as diagnostic biomarkers for VTE in BD with high accuracy (AUC 0.816)

peripheral degs candidate microarray weighted protein–protein
Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

tcga-luad best brain advanced bulk kaplan-meier pearson
Elevated phenylacetylglutamine caused by gut dysbiosis associated with type 2 diabetes increases neutrophil extracellular traps formation and exacerbates brain infarction.

PMID 40471587 · PMC12599254 · Clinical science (London, England : 1979) · 2025 · 7 claims · 8 setups

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Plasma PAGln levels are significantly higher in ischemic stroke patients with T2D than in those without T2D

fecal plasma sprague-dawley cerebral 16s metagenome targeted
Ecotype diversity and conversion in Photobacterium profundum strains.

PMID 24824441 · PMC4019646 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 77

No single gene restricts the environmental niche of each bathytype; instead a set of strain-specific genetic features confers depth-specific stress tolerance (temperature, pressure, nutrients).

photobacterium profundum predicted orthologous whole-genome pulsed-field comparative
Identification of a pediatric acute hypoxemic respiratory failure signature in peripheral blood leukocytes at 24 hours post-ICU admission with machine learning.

PMID 37009294 · PMC10063855 · Frontiers in pediatrics · 2023 · 7 claims · 5 setups

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A machine learning stability selection approach (bootstrapped logistic regression, 100 simulations) can identify genes associated with PaO2/FiO2 < 200 vs ≥200 when standard differential expression with FDR correction shows no overlap between cohorts.

pediatric combined top-ranked whole-blood machine pathway

Experiments

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

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

Toward the use of genomics to study microevolutionary change in bacteria.

Magnetization transfer imaging in 'premanifest' Huntington's disease.

Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

Improved mutation tagging with gene identifiers applied to membrane protein stability prediction.

A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.

Delineation of a gene network underlying the pulmonary response to oxidative stress in asthma.

Helicobacter Pylori's plasticity zones are novel transposable elements.

Utilization of genomic signatures to identify phenotype-specific drugs.

The origins of lactase persistence in Europe.

Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing.

Exploration of effective biomarkers for venous thrombosis embolism in Behçet's disease based on comprehensive bioinformatics analysis.

Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

Elevated phenylacetylglutamine caused by gut dysbiosis associated with type 2 diabetes increases neutrophil extracellular traps formation and exacerbates brain infarction.

Ecotype diversity and conversion in Photobacterium profundum strains.

Identification of a pediatric acute hypoxemic respiratory failure signature in peripheral blood leukocytes at 24 hours post-ICU admission with machine learning.