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 15

System / cell line: proteins ✕ Assay: ppi ✕ Clear

A protein interaction based model for schizophrenia study.

PMID 19091023 · PMC2638163 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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Products of 36 schizophrenia candidate genes cluster together into a single connected component within a PPI sub-network of 831 proteins

proteins clusters brain ppi network gene
Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

PMID 18598366 · PMC2474618 · BMC bioinformatics · 2008 · 7 claims · 6 setups

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Experimentally measured protein-protein interaction sub-networks are not random samples of their parent networks.

yeast drosophila networks dppi reanalysis computer repeated
Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.

PMID 41953002 · PMC13053772 · iScience · 2026 · 7 claims · 8 setups

Has reproduction · 78

An integrated framework of bioinformatics, machine learning, and ΔG clustering can prioritize PAHs for AD-associated neurotoxicity.

proteins microarray ad-associated pahs target differential wgcna
Protein function assignment through mining cross-species protein-protein interactions.

PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups

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CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens

sapiens cross-species majority simple
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

Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs

afb1 breast training candidate computational bulk weighted
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

PMID 15892868 · PMC1175952 · Genome biology · 2005 · 8 claims · 6 setups

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Two quantitative benchmarks (functional-annotation-based and physical-interaction-based log likelihood ratio scores) can measure relative accuracy of human PPI datasets

medline annotated interactions consolidated conditional co-citation bayesian
Analysis of protein sequence and interaction data for candidate disease gene prediction.

PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

ophid biocarta kegg pfam-annotated common benchmarking multiple-interval
Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

PMID 19859549 · PMC2762604 · PloS one · 2009 · 8 claims · 8 setups

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A comprehensive platelet proteome of 1507 unique proteins was identified from ten independent human platelet samples, the most comprehensive platelet proteome assembled to date

platelets platelet anti-coagulated lc-ms phospho-proteomic membrane
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
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
Network properties of complex human disease genes identified through genome-wide association studies.

PMID 19956617 · PMC2779513 · PloS one · 2009 · 7 claims · 6 setups

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Complex disease genes are significantly less central (lower degree/closeness, higher eccentricity) in the human interactome than essential and monogenic disease genes, occupying an intermediate niche between monogenic disease genes and non-disease genes

complex interactome gene disease-sharing gene protein-protein
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 20

AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats

ipf common key rats microarray network protein-protein
Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.

PMID 36015199 · PMC9413912 · Pharmaceutics · 2022 · 8 claims · 8 setups

Has reproduction · 19

Shared differentially expressed genes link glioblastoma with ischemic stroke and with moyamoya disease, revealing molecular associations among the diseases.

glioblastoma ischemic moyamoya shared bulk microarray gene
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
Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies.

PMID 41909810 · PMC13022592 · Frontiers in bioinformatics · 2026 · 8 claims · 4 setups

Has reproduction · 56

ChickpeaOmicsR is the first comprehensive/specialized R package integrating transcriptomic, genomic, and proteomic (RNA-seq, GWAS, PPI) data within a unified, reproducible framework and standardizing fragmented chickpea gene nomenclature.

cicer chickpea icarda bulk gene protein-protein

Experiments

A protein interaction based model for schizophrenia study.

Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

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

Protein function assignment through mining cross-species protein-protein interactions.

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

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

Analysis of protein sequence and interaction data for candidate disease gene prediction.

Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

Ontological visualization of protein-protein interactions.

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

Network properties of complex human disease genes identified through genome-wide association studies.

Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.

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

Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies.