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 27

System / cell line: network ✕ Assay: ratio ✕ Clear

Comprehensive comparison of gene expression diversity among a variety of human stem cells.

PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 6 claims · 7 setups

Has reproduction · 71

iPSC gene expression is more strongly influenced by tissue origin than other stem cell types, whereas ESCs and somatic stem cells (MSCs, HSCs) are more strongly impacted by culture condition.

undifferentiated stem batch-corrected bulk microarray batch
Shaken not stirred: a global research cocktail served in Hinxton.

PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

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Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

budding caenorhabditis drosophila escherichia two-color double chip-chip
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

PMID 19906700 · PMC2808873 · Nucleic acids research · 2010 · 7 claims · 4 setups

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NCG is a web database integrating duplicability, orthology, evolutionary appearance, and network topology data for 736 human cancer genes

cancer proteome pten genome orthology protein-protein
Detection of venous thromboembolism by proteomic serum biomarkers.

PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups

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A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays

serum anova-selected citrated depleted direct artificial d-dimer
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
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
Identification and analysis of co-occurrence networks with NetCutter.

PMID 18781200 · PMC2526157 · PloS one · 2008 · 8 claims · 4 setups

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Random sampling from a complete permutation set of the bipartite graph permits co-occurrence analysis with optimal stringency, and the edge-swapping (ES) model closely approximates this and is the preferred null-model among six tested.

publime bipartite randomized co-occurrence null-model signal-to-noise
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
The dystrobrevin-binding protein 1 gene: features and networks.

PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

vertebrate dtnbp1 comparative cross-species molecular
Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

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A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

genome-sequenced trachomatis same concatenated whole-genome multilocus ompa
Allele quantification using molecular inversion probes (MIP).

PMID 16314297 · PMC1301601 · Nucleic acids research · 2005 · 8 claims · 5 setups

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MIP technology at high multiplex (>20,000 SNPs) can provide copy number measurements while simultaneously obtaining allele information

reference ffpe lines na18573 mip restriction quantitative
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
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.

PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups

Has reproduction · 57

t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes

calanus same 11k degs bulk dimensionality differential
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
Characterisation of the genetic diversity of Brucella by multilocus sequencing.

PMID 17448232 · PMC1877810 · BMC microbiology · 2007 · 8 claims · 5 setups

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Brucella isolates show low overall genetic diversity (1.5%) across nine sequenced loci, confirming the genus is genetically conserved.

brucella sequenced concatenated allelic multilocus ratio neighbour-joining
The role of positive selection in determining the molecular cause of species differences in disease.

PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

orthologous omim meta-database panther comparative disease protein-protein
Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

Has reproduction · 50

A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database

epithelial-based tcga gdsc muscle-invasive differential co-expression signature
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 estrogen hypothesis of schizophrenia implicates glucose metabolism: association study in three independent samples.

PMID 18460190 · PMC2391158 · BMC medical genetics · 2008 · 8 claims · 4 setups

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A novel candidate-gene selection strategy combining unbiased schizophrenia expression/linkage data with the estrogen hypothesis as a biological filter identifies glycolysis as a candidate pathway network for schizophrenia

case-control same compilation snp haplotype pairwise
Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 7 claims · 8 setups

Has reproduction · 79

Meta-analysis confirms a positive bidirectional association between DED and DEP (DED patients have increased DEP prevalence and vice versa).

studies taiwan twb ded meta-analysis genome-wide conditional

Experiments

Comprehensive comparison of gene expression diversity among a variety of human stem cells.

Shaken not stirred: a global research cocktail served in Hinxton.

Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

Detection of venous thromboembolism by proteomic serum biomarkers.

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

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

Identification and analysis of co-occurrence networks with NetCutter.

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

The dystrobrevin-binding protein 1 gene: features and networks.

Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

Allele quantification using molecular inversion probes (MIP).

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

Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.

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

Characterisation of the genetic diversity of Brucella by multilocus sequencing.

The role of positive selection in determining the molecular cause of species differences in disease.

Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

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

The estrogen hypothesis of schizophrenia implicates glucose metabolism: association study in three independent samples.

Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.