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: protein-protein ✕ Assay: correlated ✕ Clear

Protein co-evolution, co-adaptation and interactions.

PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

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The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

nuoe intra-protein coli interacting phylogenetic correlated domain-restricted
Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

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Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

saccharomyces correlated chip-chip gene
Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

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Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

postmortem genes gene proteins microarray protein-protein hierarchical
Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.

PMID 39775580 · PMC11684664 · PloS one · 2024 · 7 claims · 8 setups

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MitoDEGs in MI are mainly involved in mitochondrial function and ATP synthesis pathways

left mus combined heart microarray weighted bulk
Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.

PMID 18257909 · PMC2374702 · Genome biology · 2008 · 8 claims · 3 setups

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Compiled a list of 120 core presynaptic gene prototypes (PS120) and catalogued their conservation across insect proteomes.

insect vamp2 ps120 comparative sequence protein-protein
Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.

PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 6 claims · 8 setups

Has reproduction · 71

109 shared genes were identified between HIV-1- and PAH-associated WGCNA modules

pbmc shared hub pbmcs weighted kegg differential
Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.

PMID 41953002 · PMC13053772 · iScience · 2026 · 8 claims · 8 setups

Has reproduction · 78

PARP1, PTPN1, and ITGA4 are core PAH protein targets identified via PPI network analysis and XGBoost feature selection from AD-associated DEGs

brain geo predicted gse44771 wgcna differential protein-protein
Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.

PMID 37883426 · PMC10602290 · PloS one · 2023 · 6 claims · 8 setups

Has reproduction · 97

TAA/TAV pathogenesis is more strongly associated with immune-related gene expression than TAA/BAV.

aortic genes wgcna gene cibersort
Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

PMID 40857330 · PMC12380325 · PloS one · 2025 · 6 claims · 8 setups

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90 interacting genes were identified at the intersection of AAA DEGs and periodontitis WGCNA module genes

abdominal gingival overlapping interacting microarray weighted kegg
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups

Has reproduction · 80

A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence

peripheral genes overlapping neutrophil-related microarray weighted kegg
Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.

PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups

Has reproduction · 58

EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD

pbmc intersected candidate wgcna differential kegg
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

Has reproduction · 83

170 unique human AFB1 targets were identified by merging ChEMBL, SwissTargetPrediction, and PharmMapper predictions

afb1 breast training candidate computational bulk weighted
The Proteomic Code: a molecular recognition code for proteins.

PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

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The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide
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
Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 8 setups

Has reproduction · 72

edgeR-based DEG selection is more appropriate for feature selection than Elastic Net when sample sizes are small.

ffpe same nanostring tnbc nanostring immunohistochemistry differential
Whither genomics?

PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

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Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

mammalian budding yeast general expression genome-wide synthetic

Experiments

Protein co-evolution, co-adaptation and interactions.

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.

Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.

Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.

Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.

Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.

Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.

Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

The Proteomic Code: a molecular recognition code for proteins.

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

Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

Whither genomics?