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 19

System / cell line: random ✕ Assay: protein-interaction ✕ Clear

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
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
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
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
The use of edge-betweenness clustering to investigate biological function in protein interaction networks.

PMID 15740614 · PMC555937 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Edge-Betweenness clustering separates protein interaction graphs into subgraphs whose GO term distributions show significant correlations, revealing biologically meaningful functional modules.

interaction yeast edge-betweenness chi-squared robustness
Pathway analysis of kidney cancer using proteomics and metabolic profiling.

PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups

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31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue

ccrcc rcc computational random gel immunoblotting immunohistochemistry
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
Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

yeast yeast-related interaction random dictionary-based manual graph
Prioritization of candidate cancer genes--an aid to oncogenomic studies.

PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

genes cancer interpro interactome averaged cross-validation domain
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

PMID 17984082 · PMC2239001 · Nucleic acids research · 2008 · 8 claims · 7 setups

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The Biodefense Proteomics Resource Center (RC) is a public cyberinfrastructure that stores, integrates, and disseminates experimental data from seven Proteomics Research Centers (PRCs) on biodefense pathogens and host interactions

brucella toxoplasma bacillus homo label-free mass genomic
Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups

Has reproduction · 67

Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.

vibrio coli anguillarum transposon-insertion conjugative functional
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
Translating genome sequences into biological understanding.

PMID 12801409 · PMC193614 · Genome biology · 2003 · 8 claims · 7 setups

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Gene-trap insertional mutagenesis in mouse ES cells (BayGenomics) generates a large resource of cell lines and knockout mice for studying gene expression patterns and function.

embryonic transfectable drosophila computational gene-trap pooled cross-species
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups

Has reproduction · 88

COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.

peripheral leukocytes plasma degs bulk single-cell plasma
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 · 7 setups

Has reproduction · 72

edgeR identifies 9 DEGs associated with pCR and 13 DEGs associated with relapse from 579 immune genes in a small TNBC sample set (n=55)

ffpe same nanostring training nanostring immunohistochemistry differential
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
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

Has reproduction · 30

MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

simplified genome-scale cerevisiae coli minspan spearman comparative
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
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

Experiments

Biocomputing enters its adolescence.

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

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

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

The use of edge-betweenness clustering to investigate biological function in protein interaction networks.

Pathway analysis of kidney cancer using proteomics and metabolic profiling.

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

Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

Prioritization of candidate cancer genes--an aid to oncogenomic studies.

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

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

Translating genome sequences into biological understanding.

Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

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

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

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

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

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