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 16

System / cell line: genes ✕ Assay: artificial ✕ Clear

POCUS: mining genomic sequence annotation to predict disease genes.

PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups

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Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance

omim genome disease comparative pocus expression-id
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

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Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

genome gene omim known naïve linkage disease-centric
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
Optimality driven nearest centroid classification from genomic data.

PMID 17912341 · PMC1991588 · PloS one · 2007 · 7 claims · 5 setups

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A theoretical result determines the subset of features of a given size that minimizes the misclassification rate for a nearest-centroid (LDA) classifier, based on equation (4).

artificial simulated previously-published simulated simulation clinical
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

PMID 17784955 · PMC2375021 · Genome biology · 2007 · 8 claims · 6 setups

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Gene-gene functional similarity can be measured using kappa statistics applied to a binary gene-annotation-term matrix built from 14 annotation categories.

genome protein-protein genes artificial kappa clustering gene
In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

PMID 17726045 · PMC2094079 · Nucleic acids research · 2007 · 8 claims · 6 setups

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Two exonic mutations, PINK1 E417G and PARK7 E64D, disrupt binding to U1 snRNA and cause skipping of the mutation-harboring exon

hek293 genome lymphocytes minigene artificial genome-wide
A golden age of brain exploration.

PMID 15660159 · PMC544547 · PLoS biology · 2005 · 8 claims · 3 setups

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Over 99% of neuroscience literature focuses on only 1% of the ~15,000–16,000 genes expressed in the brain, leaving most brain-expressed genes uncharacterized.

brain transgenic situ microarray bacterial
Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets.

PMID 17439973 · PMC1888811 · Nucleic acids research · 2007 · 8 claims · 5 setups

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p53REs are not simple direct repeats of half-sites; the two half-sites couple to form a higher-order 20-bp full-site palindrome

compiled genome artificial sequence computational simulated
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

Has reproduction · 62

H. caudiculatum (lower canopy) exhibits about twice as many differentially expressed genes as H. dentatum (upper canopy), with a higher proportion of both increased and decreased gene abundance during dehydration.

hymenophyllum dark-adapted annotated differentially bulk relative chlorophyll
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups

Has reproduction · 55

352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

endometrial degs hub decidua microarray wgcna machine
Correcting scale distortion in RNA sequencing data.

PMID 39875825 · PMC11776150 · BMC bioinformatics · 2025 · 8 claims · 8 setups

Has reproduction · 76

Local averaging reveals expression-level-dependent biases that differ from sample to sample across all RNA-seq datasets studied, and are not corrected by conventional normalization (TPM/FPKM)

tcga su2c gse47774 gtex bulk computational d'agostino
MatchMiner: a tool for batch navigation among gene and gene product identifiers.

PMID 12702208 · PMC154578 · Genome biology · 2003 · 8 claims · 3 setups

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MatchMiner's LookUp function automates batch translation of an input list of gene identifiers into a matching list of a different identifier type.

nci-60 fish-mapped random batch fish-mapped cross-validation
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

PMID 25122613 · PMC4216921 · Genome research · 2014 · 8 claims · 7 setups

Has reproduction · 87

mRNA codon and amino acid pools are highly stable across mouse development and across tissues, simply reflecting the genomic background distribution of any possible transcriptome.

c57bl strand-specific pol computational
The sequence and de novo assembly of the giant panda genome.

PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

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A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

giant panda whole-genome novo read
A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.

PMID 18194558 · PMC2248205 · BMC genetics · 2008 · 8 claims · 5 setups

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A hierarchical/modular approach integrating quality control, LD, physical distance, and gene ontology identifies authentic associations among those found by statistical tests in pooled DNA GWAS

pooled sickle centenarian snp pooled gene
Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.

PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

Has reproduction · 23

Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations

newly duck southeast chinese whole-genome phylogenetic population

Experiments

POCUS: mining genomic sequence annotation to predict disease genes.

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

Speeding disease gene discovery by sequence based candidate prioritization.

Optimality driven nearest centroid classification from genomic data.

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

A golden age of brain exploration.

Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets.

A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

Correcting scale distortion in RNA sequencing data.

MatchMiner: a tool for batch navigation among gene and gene product identifiers.

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

The sequence and de novo assembly of the giant panda genome.

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.

Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.