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 · 75
Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.
PMID 38163105 · PMC10757018 · Heliyon · 2024 · 8 claims · 8 setups
Integration of three AD RNA-seq datasets identifies 150 common DEGs (100 down-regulated, 50 up-regulated) enriched for blood vessel morphogenesis, muscle structure/tissue development, and chemotaxis.
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Has reproduction · 78
SPRR1B+ keratinocytes prime oral mucosa for rapid wound healing via STAT3 activation.
PMID 39300285 · PMC11413210 · Communications biology · 2024 · 8 claims · 8 setups
A shared wound healing gene set (P2-WHGs, 146 genes) is constitutively expressed in uninjured oral mucosa but not in uninjured skin
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Full-text index only
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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Has reproduction · 59
Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.
PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups
Short-term stress and long-term adaptations share common metabolic pathways
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Has reproduction · 45
NUSAP1 Could be a Potential Target for Preventing NAFLD Progression to Liver Cancer.
PMID 35431924 · PMC9010788 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
NUSAP1 is a hub gene linking NAFLD fibrosis progression and NAFLD-associated HCC
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Has reproduction · 75
Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress.
PMID 40869111 · PMC12386182 · International journal of molecular sciences · 2025 · 8 claims · 6 setups
Meta-analysis of 21 experiments covering 58 HL conditions yielded ~218,000 DEG instances corresponding to ~19,000 unique A. thaliana genes
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Has reproduction · 69
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.
PMID 34601390 · PMC8483812 · Computers in biology and medicine · 2021 · 8 claims · 8 setups
COVID-19 and neurological diseases (NDs) share pathophysiological connections that influence disease progression and severity
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Has reproduction · 85
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.
PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups
Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) are associated with HCM by intersecting DEGs with MR-identified eQTLs
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Has reproduction · 50
Wx: a neural network-based feature selection algorithm for transcriptomic data.
PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups
The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.
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Has reproduction · 27
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups
A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.
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Has reproduction · 62
Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.).
PMID 36430273 · PMC9696714 · International journal of molecular sciences · 2022 · 8 claims · 3 setups
TM treatment of potato leaves produces widespread, time-dependent differential gene expression associated with ER stress and the UPR
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Has reproduction · 62
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.
PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups
Immature (day 7) CASK KO induced neurons show increased dendritic complexity/neurite overgrowth and upregulated gene networks for cell adhesion, neurite outgrowth, and cytoskeletal organization.
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Has reproduction · 19
Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.
PMID 36015199 · PMC9413912 · Pharmaceutics · 2022 · 8 claims · 7 setups
Glioblastoma, ischemic stroke, and moyamoya disease share molecular biomarkers and pathways indicating a pathological interconnection
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Has reproduction · 84
Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum.
PMID 41470732 · PMC12736803 · Plants (Basel, Switzerland) · 2025 · 7 claims · 8 setups
Drought and heat stress induce coordinated transcriptional reprogramming in potato and tomato: induction of molecular chaperone activity, oxidative stress responses, and immune signaling, with repression of photosynthetic and primary metabolic pathways reflecting energy reallocation.
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Has reproduction · 88
From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.
PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 8 claims · 7 setups
Flower buds in organogenesis, paradormancy, endodormancy and ecodormancy stages are each defined by expression of genes in specific pathways, and the transcriptional state accurately captures the dormancy state.
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Has reproduction · 75
FEM: mining biological meaning from cell level in single-cell RNA sequencing data.
PMID 34909283 · PMC8641482 · PeerJ · 2021 · 8 claims · 5 setups
The FEM algorithm converts a single-cell gene expression matrix into a functional expression matrix using multi-module gene set enrichment analysis, utilizing information from all expressed genes rather than discarding filtered genes.
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Has reproduction · 93
A comparison of the large-scale gene expression patterns in summer and fall migratory Pantala flavescens (Fabricius) in northern China.
PMID 39108562 · PMC11301579 · Ecology and evolution · 2024 · 8 claims · 4 setups
624 differentially expressed genes (DEGs) were identified between summer (M7) and fall (M10) migratory P. flavescens
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Has reproduction · 64
Integrated multi-omics analysis combined with clinical validation reveals that HLA-DRB5 and ODAPH are causal risk genes for keratoconus.
PMID 41803193 · PMC13179358 · Scientific reports · 2026 · 8 claims · 8 setups
2,884 differentially expressed genes (DEGs) were identified as the union of upregulated genes from two independent KC transcriptome datasets (GSE151631, GSE77938), enriched in cell adhesion, immune response, and TNF/IL-17 signaling pathways.
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Has reproduction · 100
Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.
PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups
iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action
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Has reproduction · 71
Transcriptome and machine learning analysis of the impact of COVID-19 on mitochondria and multiorgan damage.
PMID 38295140 · PMC10830027 · PloS one · 2024 · 6 claims · 7 setups
Potential cardiac, hepatic, and renal impairments in COVID-19 are associated with ACE2, inflammatory cytokine storms, and mitochondrial pathways.