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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Computational analysis of the synergy among multiple interacting genes.
PMID 17299419 · PMC1828751 · Molecular systems biology · 2007 · 8 claims · 3 setups
Multivariate synergy of a set of factors with respect to a phenotype can be defined via the maximum-information partition, i.e., comparing the mutual information of the full set to the best achievable sum of mutual information over any partition into disjoint subsets.
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Has reproduction · 97
Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.
PMID 37883426 · PMC10602290 · PloS one · 2023 · 6 claims · 7 setups
TAA/TAV pathogenesis is more associated with immune-related gene expression than TAA/BAV, with two WGCNA gene modules (brown and blue) enriched for immune functions.
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Validation of analytic methods for biomarkers used in drug development.
PMID 18829475 · PMC2744124 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups
Analytical method validation (assessing assay performance/reproducibility) is a distinct process from clinical qualification (linking a biomarker to biological processes and clinical endpoints), though the two are intertwined.
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Has reproduction · 55
Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.
PMID 35901050 · PMC9333241 · PloS one · 2022 · 5 claims · 8 setups
Several co-expressed gene modules are significantly associated with left ventricle ejection fraction (LVEF) and the DCM phenotype, enriched in fibrosis-related, small molecule transporting-related, and immune response-related pathways.
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Has reproduction
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.
PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups
Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.
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Has reproduction
Pleiotropic effects of MORC2 derive from its epigenetic signature.
PMID 40302207 · PMC12782172 · Brain : a journal of neurology · 2026 · 8 claims · 8 setups
A MORC2-specific DNA methylation episignature exists that is universal across all MORC2-associated phenotypes and conserved across blood and fibroblast tissue
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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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Has reproduction · 49
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.
PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups
ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC
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SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis.
PMID 15980517 · PMC1160189 · Nucleic acids research · 2005 · 8 claims · 4 setups
SNPAnalyzer is an integrated web-based workbench that performs four statistical SNP analyses (Hardy-Weinberg equilibrium, haplotype estimation, linkage disequilibrium, and QTL analysis) in one common computational environment.
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Gene-centric characteristics of genome-wide association studies.
PMID 18060058 · PMC2092383 · PloS one · 2007 · 8 claims · 5 setups
High-density SNP chips using either direct or indirect selection approaches provide very high coverage in genic regions and capture most known common disease variants under the HapMap framework.
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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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Has reproduction · 57
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.
PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups
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
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Genomics research and malaria control: great expectations.
PMID 14624242 · PMC261879 · PLoS biology · 2003 · 8 claims · 8 setups
Genomics research on humans, P. falciparum, and An. gambiae holds great promise for developing new drugs, vaccines, diagnostics, and vector control tools for malaria.
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The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.
PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups
P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.