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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Has reproduction · 38
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.
PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups
A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).
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Has reproduction · 100
Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.
PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups
Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.
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Has reproduction · 71
Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.
PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups
Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments
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Has reproduction · 93
Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract.
PMID 31608047 · PMC6769089 · Frontiers in microbiology · 2019 · 7 claims · 5 setups
Five amplicon sequence variants (unclassified Flavobacteriales, Fusibacter, Planktotalea, Algicola, and Vibrio) were consistently enriched in disease lesions across three coral species (M. cavernosa, D. labyrinthiformis, D. stokesii)
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Has reproduction · 78
Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.
PMID 41953002 · PMC13053772 · iScience · 2026 · 7 claims · 8 setups
An integrated framework of bioinformatics, machine learning, and ΔG clustering can prioritize PAHs for AD-associated neurotoxicity.
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Has reproduction · 63
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups
RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO
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Full-text index only
A taxonomy of epithelial human cancer and their metastases.
PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups
Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters
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Has reproduction · 77
Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.
PMID 41676443 · PMC12806058 · iMetaOmics · 2025 · 6 claims · 7 setups
Electroacupuncture reshapes microbial co-occurrence network topology and drives keystone species in AD-related BPSD, with R. gnavus emerging as a likely keystone species post-intervention.
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Has reproduction · 66
Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.
PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups
Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient
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Has reproduction · 49
Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.
PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups
B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).
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Has reproduction · 51
Polyploidy and the petal transcriptome of Gossypium.
PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups
Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.
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Full-text index only
BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression.
PMID 18497862 · PMC2375115 · PLoS genetics · 2008 · 8 claims · 6 setups
BRCA1 and BRCA2 pathogenic mutation carriers have similar post-irradiation LCL gene expression profiles to each other, more so than to BRCAX samples without an LCS variant
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Has reproduction · 60
Core transcriptional signatures of phase change in the migratory locust.
PMID 31292921 · PMC6881432 · Protein & cell · 2019 · 8 claims · 7 setups
PhaseCore genes defined by AC-PCA contribution to phase differentiation predict phase status with >87.5% accuracy
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Has reproduction · 78
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).
PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups
METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.