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 · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
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Has reproduction · 68
Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.
PMID 35819852 · PMC9433101 · The Journal of clinical investigation · 2022 · 8 claims · 8 setups
Chronic wound-edge tissue shows genome-wide DNA hypermethylation compared with unwounded skin
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Has reproduction · 74
Microglia-containing cerebral organoids derived from induced pluripotent stem cells for the study of neurological diseases.
PMID 36936782 · PMC10014280 · iScience · 2023 · 8 claims · 8 setups
A novel protocol using FGF/EGF/heparin growth factor supplementation and 10% CO2 culture generates cerebral organoids containing neurons, astrocytes, and microglia from iPSCs/hESCs
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Has reproduction · 69
Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma.
PMID 39355255 · PMC11442245 · Frontiers in immunology · 2024 · 8 claims · 8 setups
66 consensus immunotherapy prognostic genes (CITPGs) were identified from the intersection of WGCNA modules, immunotherapy responder-vs-non-responder DEGs, and tumor-vs-normal DEGs
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Has reproduction · 93
Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.
PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups
24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).
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Full-text index only
Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.
PMID 35949126 · PMC9682560 · Anatolian journal of cardiology · 2022 · 7 claims · 7 setups
10 key genes (TCF7L2, CACNA1C, NRP1, GABBR2, FANCC, DCK, CCDC88C, TCF12, ABLIM1, PBX1) are regulated by both aberrant DNA methylation and miRNA activity in atherosclerosis
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Has reproduction · 92
Benefit of using interaction effects for the analysis of high-dimensional time-response or dose-response data for two-group comparisons.
PMID 38012163 · PMC10682470 · Scientific reports · 2023 · 5 claims · 1 setups
Interaction effects are often the mathematical equivalent of the biological research question in gene expression studies but are frequently not considered in practice.
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Has reproduction · 86
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.
PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 7 claims · 4 setups
TNBC can be divided into four gene-expression-defined subtypes: BLIA, BLIS, MES, and LAR
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Has reproduction · 70
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).
PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups
AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella
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Has reproduction · 69
Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.
PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups
Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis
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Has reproduction · 62
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.
PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 8 claims · 5 setups
A DNN model built on 34 top-ranked hub genes achieves the highest prediction accuracy (AUC 92.11%) for distinguishing primary from bone-metastasized tumors
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Has reproduction · 73
Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.
PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups
Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.
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Has reproduction · 67
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.
PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups
PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons
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Has reproduction · 53
Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.
PMID 35425715 · PMC9004628 · Frontiers in oncology · 2022 · 8 claims · 7 setups
Patient-derived colorectal cancer organoids (CRCOs) can be established from surgical CRC tissue with an 82% success rate (41/50)
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Has reproduction · 73
Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.
PMID 37161060 · PMC10170109 · Scientific reports · 2023 · 8 claims · 8 setups
Mitophagy affects tumour development, immune cell infiltration, and prognosis in HPV-associated HNSCC
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Has reproduction · 73
A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.
PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups
COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity
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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 · 61
Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.
PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups
Twelve HIA-related genes were identified that are transcriptionally activated by HIF1A/HIF2A and functionally implicated in angiogenesis in CRC
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Has reproduction · 93
Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.
PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups
5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)
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Has reproduction · 84
Network Controllability Reveals Key Mitigation Points for Tumor-Promoting Signaling in Tumor-Educated Platelets.
PMID 41226816 · PMC12609506 · International journal of molecular sciences · 2025 · 8 claims · 6 setups
TEPs from NSCLC patients show 111 upregulated and 108 downregulated genes compared to platelets from non-cancer donors