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 18

System / cell line: cohort ✕ Assay: prior ✕ Clear

Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

PMID 19862842 · PMC2830005 · Human mutation · 2009 · 8 claims · 6 setups

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Mutations in HGD, which encodes homogentisate dioxygenase, cause AKU by blocking conversion of homogentisic acid to maleylacetoacetic acid in the tyrosine catabolic pathway

aku hgd recombinant hgd missense splice
Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

PMID 16417627 · PMC1382246 · BMC genetics · 2006 · 8 claims · 7 setups

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Heterozygous truncating BRCA2 mutations occur in 47% (7/15) of gastrointestinal MSI cancer cell lines/xenografts, a higher rate than previously reported

gastrointestinal ls174t pl3 msi gene rt-pcr rad51
Population carrier frequency of hMSH2 and hMLH1 mutations.

PMID 11104559 · PMC2363440 · British journal of cancer · 2000 · 6 claims · 6 setups

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Population carrier frequency of hMSH2/hMLH1 mutations in people aged 15-74 years is estimated at 1:3139 (95% CI 1:1247-1:7626)

peripheral scottish finnish baltimore cdna pedigree systematic
Function2Gene: a gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge.

PMID 18631403 · PMC2500032 · BMC bioinformatics · 2008 · 6 claims · 5 setups

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Function2Gene is a set of Perl programs that queries public databases (NCBI, GeneCards, Harvester, with Uniprot/Ensembl also supported) using expert-selected keywords to rank genes by prior probability of disease association.

gene nuclear sle tdt keyword-based snp transmission
A four-gene signature from blood to exclude bacterial etiology of lower respiratory tract infection in adults.

PMID 41285807 · PMC12644739 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 94

A 4-gene signature (ITGB4, ITGA7, IFI27, FAM20A) derived from whole blood RNA-seq discriminates any bacterial from nonbacterial ARI with cross-validated AUC = 0.90

hospitalized adults pediatric blood bulk rna-seq microarray
Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.

PMID 39418301 · PMC11521246 · PLoS computational biology · 2024 · 7 claims · 4 setups

Has reproduction · 23

COPD GWAS loci are more spatially clustered across the genome than expected by chance, with significant enrichment on chromosome 4q.

lung sakornsakolpat string bulk microarray gwas
Causal models in epidemiology: past inheritance and genetic future.

PMID 16859537 · PMC1557493 · Environmental health : a global access science source · 2006 · 8 claims · 3 setups

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Interaction is a fundamental characteristic of any causal process involving probabilistic steps, not a second-order phenomenon identified after accounting for main effects

smokers population cohort observational biomarker pulmonary
Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.

PMID 34654806 · PMC8519947 · Nature communications · 2021 · 7 claims · 4 setups

Has reproduction · 100

Pathway-based signatures derived from on-treatment tumor specimens (PASS-ON) are highly predictive of response to anti-PD1 blockade in metastatic melanoma, achieving validation AUCs of 0.85–0.89.

metastatic bulk
Clinical and genotypic findings in HIV-infected patients with the K65R mutation failing first-line antiretroviral therapy in Nigeria.

PMID 19644383 · PMC2815152 · Journal of acquired immune deficiency syndromes (1999) · 2009 · 8 claims · 3 setups

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K65R mutation is present in a substantial proportion (10.9%) of Nigerian patients failing first-line ART, including many with no prior tenofovir exposure

plasma k65r-positive hiv-1 comparative clinical
Genetic analysis of the GLUT10 glucose transporter (SLC2A10) polymorphisms in Caucasian American type 2 diabetes.

PMID 16336637 · PMC1325051 · BMC medical genetics · 2005 · 7 claims · 5 setups

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GLUT10 (SLC2A10) is a facilitative glucose transporter gene mapped within the T2DM-linked chromosome 20q12-13.1 region

caucasian same subjects xenopus snp linkage haplotype
Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.

PMID 18616825 · PMC2492849 · BMC medical informatics and decision making · 2008 · 7 claims · 5 setups

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An LAD classification model built from a support-set of 3 peptide peaks can distinguish stroke patients from controls with 75% accuracy on an independent validation set

plasma discretized seldi-tof serum logical
Most microsatellite unstable sporadic colorectal carcinomas carry MBD4 mutations.

PMID 11104560 · PMC2363466 · British journal of cancer · 2000 · 8 claims · 2 setups

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MBD4 mutations occur in 89% (17/19) of RER+ sporadic colorectal carcinomas when microdissected tumor sites are analyzed

microdissected frozen pcr comparison
In B-CLL, the codon 72 polymorphic variants of p53 are not related to drug resistance and disease prognosis.

PMID 16109171 · PMC1208864 · BMC cancer · 2005 · 7 claims · 5 setups

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The p53 codon 72 polymorphism is not associated with drug resistance or overall survival in B-CLL

peripheral fresh b-cll sscp-pcr disc kaplan-meier
Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.

PMID 16670016 · PMC1513378 · Lipids in health and disease · 2006 · 8 claims · 6 setups

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A -987C>T polymorphism located 4bp from the 3' end of the MseI RFLP forward primer causes allelic drop-out, producing incorrect -1131T>C genotypes.

asian random subjects unrelated arms-pcr msei sanger
Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

PMID 16824219 · PMC1534050 · BMC neurology · 2006 · 7 claims · 5 setups

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The C282Y variant allele of HFE is significantly overrepresented in PD patients compared to controls, suggesting it confers higher risk for PD

genomic same pooled pcr-rflp pcr-based cross-tabulation
A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion
The RYR2-encoded ryanodine receptor/calcium release channel in patients diagnosed previously with either catecholaminergic polymorphic ventricular tachycardia or genotype negative, exercise-induced long QT syndrome: a comprehensive open reading frame mutational analysis.

PMID 19926015 · PMC2880864 · Journal of the American College of Cardiology · 2009 · 8 claims · 6 setups

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Comprehensive open-reading-frame RYR2 mutational analysis reveals possible CPVT1 mutations located outside the three canonical hot-spot domains

genomic hair-root reference patients pcr screening multi-tissue
Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.

PMID 16542425 · PMC1431555 · BMC cancer · 2006 · 8 claims · 5 setups

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ICAT tandem MS can identify and quantify differences in specific protein expression between NAF from tumor-bearing and disease-free breasts

paired icat-labeled spectra naf icat sds-page liquid

Experiments

Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

Population carrier frequency of hMSH2 and hMLH1 mutations.

Function2Gene: a gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge.

A four-gene signature from blood to exclude bacterial etiology of lower respiratory tract infection in adults.

Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.

Causal models in epidemiology: past inheritance and genetic future.

Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.

Clinical and genotypic findings in HIV-infected patients with the K65R mutation failing first-line antiretroviral therapy in Nigeria.

Genetic analysis of the GLUT10 glucose transporter (SLC2A10) polymorphisms in Caucasian American type 2 diabetes.

Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.

Most microsatellite unstable sporadic colorectal carcinomas carry MBD4 mutations.

In B-CLL, the codon 72 polymorphic variants of p53 are not related to drug resistance and disease prognosis.

Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.

Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

The RYR2-encoded ryanodine receptor/calcium release channel in patients diagnosed previously with either catecholaminergic polymorphic ventricular tachycardia or genotype negative, exercise-induced long QT syndrome: a comprehensive open reading frame mutational analysis.

Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.