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 · 69
Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.
PMID 31533612 · PMC6751684 · BMC bioinformatics · 2019 · 7 claims · 8 setups
An ensemble feature selection method based on classifier consensus identifies a robust 100-miRNA signature from TCGA data.
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Has reproduction · 59
Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.
PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups
NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering
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Has reproduction · 77
Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.
PMID 24888378 · PMC4070569 · BMC genomics · 2014 · 8 claims · 8 setups
Ribo-Zero-Seq removes rRNA with efficiency comparable to poly(A)-based mRNA-Seq in both FF and FFPE RNA, whereas DSN-Seq leaves significantly more rRNA and shows greater variation.
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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 by a discriminative index (DI) score representing classification power for distinguishing given groups, enabling intuitive selection of optimal biomarker genes.
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Has reproduction · 77
Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.
PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups
457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis
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Has reproduction
Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.
PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 7 claims · 8 setups
Tabular ML classifiers (TabNet, XGBoost, LightGBM) trained on tumor-only-derived features achieve state-of-the-art somatic vs germline classification, with AUC>94% on TCGA holdout and AUC>85% on metastatic melanoma.
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Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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Has reproduction · 76
High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.
PMID 37388735 · PMC10303802 · Frontiers in immunology · 2023 · 8 claims · 8 setups
Almost 90% of TCGA EC tumors exhibit DNA methylation age deceleration (DNAmad) relative to patient chronological age as assessed by the Horvath clock
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Has reproduction · 73
Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.
PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups
N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort
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Has reproduction · 63
Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.
PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups
Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes
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Has reproduction · 32
Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.
PMID 41407883 · PMC12712020 · Communications biology · 2025 · 8 claims · 8 setups
PTRs are highly conserved across 44 AML samples and 30 different human tissues, indicating broadly conserved post-transcriptional mechanisms
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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 · 61
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems.
PMID 32374865 · PMC7319446 · Nucleic acids research · 2020 · 8 claims · 3 setups
miEAA 2.0 supports miRNA/precursor enrichment input from ten frequently investigated organisms, expanding beyond the human-only first release.
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Has reproduction · 79
Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.
PMID 34911933 · PMC8674326 · Nature communications · 2021 · 7 claims · 4 setups
Shared chromatin accessibility features among low-grade (Gleason pattern 3) prostate cancer cells are lost in high-grade (Gleason pattern 4) tumours.
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Has reproduction · 50
Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.
PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups
A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database
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Has reproduction · 79
The relationship between PLOD1 expression level and glioma prognosis investigated using public databases.
PMID 34040895 · PMC8127981 · PeerJ · 2021 · 8 claims · 8 setups
PLOD1 mRNA expression is significantly higher in glioma tissue than in normal brain tissue
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Has reproduction · 79
TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis.
PMID 40124621 · PMC11929507 · PeerJ · 2025 · 8 claims · 8 setups
TGF-β signaling pathway activity is significantly increased in fibroblasts from cervical cancer samples compared to normal samples and correlates with tumor proliferation and differentiation.
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Has reproduction · 67
An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.
PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 7 setups
An individualized causal analysis framework can discover tumor-specific intercellular communication networks (ICNs) from transcriptomic data
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Has reproduction · 66
A global database for modeling tumor-immune cell communication.
PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups
TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures
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Has reproduction
Unlocking the microbial studies through computational approaches: how far have we reached?
PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups
Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.