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 24

System / cell line: interacting ✕ Assay: protein-protein ✕ Clear

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

saccharomyces bank caenorhabditis homo yeast mass naive
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
Computational verification of protein-protein interactions by orthologous co-expression.

PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.

cerevisiae orthologs cdc28 yeast co-expression ortholog orthologous
Biocomputing enters its adolescence.

PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

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A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

bank antibody-antigen yeast genome protein-protein empirical integrative
MODBASE, a database of annotated comparative protein structure models and associated resources.

PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

sequences chains template chain comparative pairwise ligand
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
The cohesin complex: sequence homologies, interaction networks and shared motifs.

PMID 11276426 · PMC30708 · Genome biology · 2001 · 8 claims · 8 setups

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Mouse Mmip1 and Smc3 (SMCD) share 99% sequence identity and are products of the same gene

smc1 smc3 mmip1 smc psi-blast phylogenetic sequence
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
Proteomics identification of nuclear Ran GTPase as an inhibitor of human VRK1 and VRK2 (vaccinia-related kinase) activities.

PMID 18617507 · PMC2577208 · Molecular & cellular proteomics : MCP · 2008 · 8 claims · 8 setups

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Nuclear Ran GTPase was identified by mass spectrometry as a novel interacting partner of VRK1 and VRK2B

hek293t recombinant hela gst western co-immunoprecipitation
Ontological visualization of protein-protein interactions.

PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks

gene interacting interaction annotation yeast co-immunoprecipitation
Predicting candidate genes for human deafness disorders: a bioinformatics approach.

PMID 16854223 · PMC1564145 · BMC genomics · 2006 · 8 claims · 4 setups

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A bioinformatic approach combining expression databases and protein interaction data narrows ~2400 candidate genes across deafness loci to a manageable set of candidates.

genomic developing proteins positional expression protein-protein
Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.

PMID 19779549 · PMC2739292 · PLoS computational biology · 2009 · 8 claims · 8 setups

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Human disease genes are much closer to aging genes in the PPI network than expected by chance

protein-protein randomized dan aging network degree-conserved closeness
Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.

PMID 37563310 · PMC10457199 · Nature immunology · 2023 · 8 claims · 8 setups

Has reproduction · 93

Genome-wide pQTL mapping of 91 inflammation-related plasma proteins in 14,824 participants identified 180 significant pQTLs (59 cis, 121 trans) across 108 genomic regions and 70 proteins

plasma blood tissues gut genome-wide pqtl cis-eqtl
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

PMID 16630345 · PMC1489951 · BMC bioinformatics · 2006 · 8 claims · 7 setups

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Sequence conservation (PSIC score difference) at the nsSNP position is the single most useful attribute for predicting deleterious vs neutral status.

swissprot nssnp-containing nssnps machine single-attribute sequence
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
Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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Current syndromic disease classification lacks specificity despite historically serving clinicians well

prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene
Improvements to cardiovascular gene ontology.

PMID 19046747 · PMC2706316 · Atherosclerosis · 2009 · 8 claims · 8 setups

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Gene Ontology (GO) provides a controlled vocabulary that links current functional knowledge of genes to high-throughput genomic and proteomic datasets, aiding data interpretation.

coronary phospholamban mammalian lines gene expression large-scale
GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups

Has reproduction · 76

GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place

user-assembled archs4 generif-derived aggregated gene gene-gene literature
Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

Has reproduction · 64

Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

heart degs dgat2 mitodegs microarray kegg protein-protein
Transcriptomic analysis unravels the molecular response of Lonicera japonica leaves to chilling stress.

PMID 36618608 · PMC9815118 · Frontiers in plant science · 2022 · 8 claims · 8 setups

Has reproduction · 75

Chilling stress significantly alters the ratio of anthocyanins, chlorophylls, and carotenoids, causing leaf color to change from green to purple

japonica arabidopsis pigment bulk functional

Experiments

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

Protein co-evolution, co-adaptation and interactions.

Computational verification of protein-protein interactions by orthologous co-expression.

Biocomputing enters its adolescence.

MODBASE, a database of annotated comparative protein structure models and associated resources.

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

The cohesin complex: sequence homologies, interaction networks and shared motifs.

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

Proteomics identification of nuclear Ran GTPase as an inhibitor of human VRK1 and VRK2 (vaccinia-related kinase) activities.

Ontological visualization of protein-protein interactions.

Predicting candidate genes for human deafness disorders: a bioinformatics approach.

Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.

Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

The Proteomic Code: a molecular recognition code for proteins.

Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

Improvements to cardiovascular gene ontology.

GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

Transcriptomic analysis unravels the molecular response of Lonicera japonica leaves to chilling stress.