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).
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Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.
PMID 39775580 · PMC11684664 · PloS one · 2024 · 7 claims · 8 setups
MitoDEGs in MI are mainly involved in mitochondrial function and ATP synthesis pathways
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Identification of gene interactions associated with disease from gene expression data using synergy networks.
PMID 18234101 · PMC2258206 · BMC systems biology · 2008 · 8 claims · 4 setups
Synergy of a gene pair with respect to disease, defined as I(G1,G2;C) - [I(G1;C)+I(G2;C)], identifies gene pairs that interact cooperatively with respect to a phenotype rather than independently.
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Adaptive history of single copy genes highly expressed in the term human placenta.
PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups
222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta
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Cardiovascular genetic medicine: genomic assessment of prognosis and diagnosis in patients with cardiomyopathy and heart failure.
PMID 20559924 · PMC4745893 · Journal of cardiovascular translational research · 2008 · 8 claims · 6 setups
Molecular signature analysis (MSA) uses machine-learning/classification methods (e.g., PAM/nearest shrunken centroids) on gene expression patterns to classify samples by phenotype for diagnosis, prognosis, or therapy response.
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Has reproduction · 80
Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.
PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups
Combining WGCNA hub genes and VAE 10-dimensional representation as features for an SVM classifier achieves high accuracy in predicting CRC
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Has reproduction · 84
An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.
PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups
A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference
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Functional analysis of human hematopoietic stem cell gene expression using zebrafish.
PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups
277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow
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Genomic expression during human myelopoiesis.
PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups
An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.
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Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.
PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups
Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions
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A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.
PMID 18194558 · PMC2248205 · BMC genetics · 2008 · 8 claims · 5 setups
A hierarchical/modular approach integrating quality control, LD, physical distance, and gene ontology identifies authentic associations among those found by statistical tests in pooled DNA GWAS
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Solute exchange through gap junctions lessens the adverse effects of inactivating mutations in metabolite-handling genes.
PMID 36107487 · PMC9534548 · eLife · 2022 · 8 claims · 8 setups
Colorectal cancer (CRC) cells are coupled by gap junctions assembled predominantly from Cx26 (GJB2)
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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
90 interacting genes were identified at the intersection of AAA DEGs and periodontitis WGCNA module genes
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Has reproduction · 70
GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses.
PMID 33758032 · PMC8547006 · mSystems · 2021 · 8 claims · 7 setups
GAUGE automatically annotates GEO microbial transcriptomic data sets (microarray and RNA-seq), increasing the proportion of annotatable studies from 4% to 33%
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Assembling a jigsaw puzzle with 20,000 parts.
PMID 12801408 · PMC193613 · Genome biology · 2003 · 8 claims · 8 setups
Re-routing the intracellular interaction domains of receptor tyrosine kinases can redirect their signaling output, e.g. converting a growth signal into an apoptosis signal.
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Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.
PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups
Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.
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Ontological Discovery Environment: a system for integrating gene-phenotype associations.
PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups
ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems
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Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.
PMID 16989739 · PMC3933161 · Journal of cellular and molecular medicine · 2006 · 6 claims · 8 setups
Mutations in APP, PS1 and PS2 genes and polymorphisms in the APOE gene are implicated in AD pathogenesis
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Has reproduction · 55
Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.
PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 7 claims · 8 setups
131 robust DEGs (89 upregulated, 42 downregulated) were identified by RRA integration of three vitiligo datasets and are closely associated with melanogenesis and vitiligo development
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Has reproduction · 62
A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.
PMID 31290545 · PMC6616200 · Database : the journal of biological databases and curation · 2019 · 7 claims · 8 setups
A curated collection of 33 GEO transcriptome datasets (1860 profiles) relevant to IgE-mediated atopic disease was assembled and made available on the Gene Expression Browser (GXB) platform
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Has reproduction
Using random walks to identify cancer-associated modules in expression data.
PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups
Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.