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 13

System / cell line: random ✕ Assay: association ✕ Clear

Screening large-scale association study data: exploiting interactions using random forests.

PMID 15588316 · PMC545646 · BMC genetics · 2004 · 7 claims · 3 setups

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Random forest importance measure significantly outperforms the Fisher Exact test as a screening tool when risk SNPs interact.

simulated same simulation random fisher
Application of two machine learning algorithms to genetic association studies in the presence of covariates.

PMID 19014573 · PMC2620353 · BMC genetics · 2008 · 8 claims · 3 setups

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The relative performance of RF and MARS for detecting genotype-trait associations depends on both the strategy used to handle covariates and the true underlying model of association (e.g., confounding vs. mediation vs. interaction).

simulated cohort simulation applied
N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

random reference healthy long-term resequencing quantitative sequence
Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

PMID 19924232 · PMC2773120 · PloS one · 2009 · 8 claims · 5 setups

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37 miRNAs are significantly differentially expressed between MYCN-amplified (MNA) and non-MNA neuroblastoma tumors, suggesting direct or indirect regulation by MYCN

neuroblastoma shep-tet21 stem-loop array tlda
Comparative genomics of Drosophila and human core promoters.

PMID 16827941 · PMC1779564 · Genome biology · 2006 · 8 claims · 6 setups

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Drosophila core promoters contain 298 highly significant (p≤1e-16) non-randomly positioned 8-mers within 100 bp of the TSS, grouped into 15 distinct DNA motifs

drosophila core genome-wide mono gene
Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

biomedical refseq training independent text-mining data-mining candidate
Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups

Has reproduction · 100

A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity

n×m common independent viral blood gene random
Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

Has reproduction · 78

A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

colorectal matched combined expression microarray rna-seq consensus
Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups

Has reproduction · 50

BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes

bovine direct amplified synthetic
DNA sequence variants in the LOXL1 gene are associated with pseudoexfoliation glaucoma in a U.S. clinic-based population with broad ethnic diversity.

PMID 18254956 · PMC2270804 · BMC medical genetics · 2008 · 8 claims · 5 setups

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Three LOXL1 SNPs previously associated with pseudoexfoliation in Nordic populations are significantly associated with pseudoexfoliation syndrome and pseudoexfoliation glaucoma in a U.S. ethnically diverse population

patients randomly cohort pxf taqman direct full-gene
Ontological Discovery Environment: a system for integrating gene-phenotype associations.

PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups

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ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems

strains integrated bipartite phish gene differential pairwise
Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups

Has reproduction · 64

Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important

agaricia agaricites coral sites 2brad population hierarchical
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

coriell myeloma duplicate snp targeted genotyping machine

Experiments

Screening large-scale association study data: exploiting interactions using random forests.

Application of two machine learning algorithms to genetic association studies in the presence of covariates.

N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

Comparative genomics of Drosophila and human core promoters.

Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

DNA sequence variants in the LOXL1 gene are associated with pseudoexfoliation glaucoma in a U.S. clinic-based population with broad ethnic diversity.

Ontological Discovery Environment: a system for integrating gene-phenotype associations.

Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.