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 30

System / cell line: patients ✕ Assay: effect ✕ Clear

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
Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

PMID 41685349 · PMC12891912 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

Has reproduction

An integrated RNA-guided variant interpretation workflow combining OUTRIDER, FRASER, MOLGENIS VIP, and Borzoi enhances clinical variant interpretation and reclassification of VUS in rare disease cases.

udn blood skin snvs whole-genome bulk splice-altering
Exome sequencing identifies the cause of a mendelian disorder.

PMID 19915526 · PMC2847889 · Nature genetics · 2010 · 8 claims · 7 setups

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Exome sequencing of a small number of unrelated affected individuals, combined with filtering against public SNP databases and HapMap exomes, is sufficient to identify the causal gene for a monogenic disorder of unknown etiology.

patients chromosomes dhodh utero exome directed sanger
25th Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, USA, 10-14 December 2002 Update on preclinical and translational research.

PMID 12631391 · PMC154153 · Breast cancer research : BCR · 2003 · 8 claims · 8 setups

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Growth factor signalling (EGF/HER-2/MAPK, AKT) phosphorylates the oestrogen receptor and drives development of endocrine-resistant breast cancer

xenograft serum frozen tumour xenograft mass cdna
RADAR: differential analysis of MeRIP-seq data with a random effect model.

PMID 31870409 · PMC6927177 · Genome biology · 2019 · 8 claims · 6 setups

Has reproduction · 10

RADAR is a novel analytical tool for differential methylation analysis of MeRIP-seq data combining gene-level INPUT normalization with a Poisson random effect model.

simulated fallopian pancreatic liver merip-seq m6a-merip-seq pca
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

PMID 35012625 · PMC8743438 · Genome biology · 2022 · 7 claims · 8 setups

Has reproduction · 68

GENEVA is a semi-automated, study-design-agnostic framework that mines large-scale public RNA-seq data to identify conditions modulating a gene of interest's expression

gtex lncap heart breast bulk rna-seq meta-analysis
Positive Relationships between Intraocular Pressure and Thyroid Function in Graves' Ophthalmopathy: A Three-Aspect Evidence Analysis.

PMID 40992768 · PMC12479196 · Yonsei medical journal · 2025 · 6 claims · 4 setups

Has reproduction · 68

Increased thyroid function is a risk factor for elevated IOP in patients with Graves' ophthalmopathy.

patients nhanes gtex geo retrospective cross-sectional summary-data-based
Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood.

PMID 18162506 · PMC7611804 · Diabetes · 2008 · 8 claims · 8 setups

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Heterozygous INS mutations are a common cause of permanent neonatal diabetes (PNDM) diagnosed before 6 months of age

peripheral patients mody young-onset pcr microsatellite variant
Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

PMID 18927607 · PMC2559870 · PloS one · 2008 · 8 claims · 5 setups

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No pathogenic mutations were found in LRRK2, PRKN, or ATXN3 in a Nigerian cohort of apparently sporadic PD patients.

nigerian same novel sanger targeted repeat
Mutation analysis of the MDM4 gene in German breast cancer patients.

PMID 18279506 · PMC2259322 · BMC cancer · 2008 · 8 claims · 8 setups

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Resequencing of the whole MDM4 coding region in 40 German familial breast cancer patients uncovered two coding variants (V74V and D153G) in 4/40 patients

german bilateral mdm4 lymphoid direct rflp-based splice
Genetic association study and meta-analysis of the HTR2C Cys23Ser polymorphism and migraine.

PMID 17901921 · PMC3451673 · The journal of headache and pain · 2007 · 8 claims · 3 setups

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The HTR2C Cys23Ser polymorphism is not significantly associated with migraine or migraine with aura in the case-control study

blood-derived migraine pooled allelic case-control meta-analysis
Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

Has reproduction · 54

Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9
Molecular epidemiology of measles viruses in the United States, 1997-2001.

PMID 12194764 · PMC2732556 · Emerging infectious diseases · 2002 · 8 claims · 6 setups

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The diversity of measles virus genotypes observed in the US from 1997–2001 reflects multiple imported sources of virus, indicating no strain of measles is endemic in the United States.

b95a clinical pcr measles viral extraction rt-pcr
MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

sporadic mitochondrial reported ataxia mitochondrial functional compensatory
Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.

PMID 35143511 · PMC8830616 · PloS one · 2022 · 8 claims · 6 setups

Has reproduction · 48

A hybrid signature combining the Nottingham Prognostic Index with SIS-selected gene expressions can be built in a data-driven fashion (NPI treated as a gene expression during feature selection).

metabric scan-b gene rna-seq feature
Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

PMID 16934001 · PMC1550284 · PLoS genetics · 2006 · 7 claims · 6 setups

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The E320Q, Q463H, and L706S STAT1 alleles are intrinsically deleterious for both IFNG/GAF-mediated and IFNA/ISGF3-mediated immunity when tested in STAT1-deficient transfected cells

ebv-transformed sv40-transformed nuclear stat1-deficient cdna western immunofluorescence
Molecular and clinical genetics of mitochondrial diseases due to POLG mutations.

PMID 18546365 · PMC2891192 · Human mutation · 2008 · 8 claims · 4 setups

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POLG mutations cause at least 6 major heterogeneous phenotypes of neurodegenerative mitochondrial disease (MCHS, Alpers syndrome, ANS, MEMSA, arPEO, adPEO)

blood parental model sanger parental microsatellite
Critical care: applying genomics to inflammation outcomes.

PMID 16330338 · PMC1314943 · Environmental health perspectives · 2005 · 8 claims · 6 setups

Full-text index only

Genetic factors drive key aspects of an individual's inflammatory outcome after trauma, burns, or sepsis

leukocytes whole-blood healthy peripheral genomewide whole-genome microarray
Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India.

PMID 18552984 · PMC2426732 · Molecular vision · 2008 · 8 claims · 4 setups

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Coding/flanking regions of RHO, PRPF31, and IMPDH1, plus exons 4F/4G/4H of RP1, were PCR-amplified and directly sequenced in 48 isolated and 53 adRP Indian patients and 75 controls

genomic peripheral probands identified pcr reverse clinical
Coexistence of two different pseudohypoparathyroidism subtypes (Ia and Ib) in the same kindred with independent Gs{alpha} coding mutations and GNAS imprinting defects.

PMID 19858129 · PMC3030964 · Journal of medical genetics · 2010 · 7 claims · 5 setups

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Two unrelated PHP-I families each include at least one patient with a Gsα coding mutation (PHP-Ia) and another with GNAS imprinting defects (PHP-Ib)

genomic erythrocyte gnas sanger methylation-specific microsatellite

Experiments

Indirect genomic effects on survival from gene expression data.

Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

Exome sequencing identifies the cause of a mendelian disorder.

25th Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, USA, 10-14 December 2002 Update on preclinical and translational research.

RADAR: differential analysis of MeRIP-seq data with a random effect model.

Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

Positive Relationships between Intraocular Pressure and Thyroid Function in Graves' Ophthalmopathy: A Three-Aspect Evidence Analysis.

Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood.

Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

Mutation analysis of the MDM4 gene in German breast cancer patients.

Genetic association study and meta-analysis of the HTR2C Cys23Ser polymorphism and migraine.

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

Molecular epidemiology of measles viruses in the United States, 1997-2001.

MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.

Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

Molecular and clinical genetics of mitochondrial diseases due to POLG mutations.

Critical care: applying genomics to inflammation outcomes.

Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India.

Coexistence of two different pseudohypoparathyroidism subtypes (Ia and Ib) in the same kindred with independent Gs{alpha} coding mutations and GNAS imprinting defects.