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 · 50
In vivo microscopy reveals macrophage polarization locally promotes coherent microtubule dynamics in migrating cancer cells.
PMID 32665556 · PMC7360550 · Nature communications · 2020 · 8 claims · 8 setups
Cancer cells in vivo display higher coherent orientation of MT dynamics along their major axis compared to 2D in vitro cultures
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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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Full-text index only
Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.
PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups
A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.
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Has reproduction · 87
Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.
PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups
TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.
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Has reproduction · 23
Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.
PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups
The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies
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Has reproduction · 74
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups
An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead
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Has reproduction · 60
A comparative analysis of blastoid models through single-cell transcriptomics.
PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups
EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.
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Has reproduction · 65
A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.
PMID 37852185 · PMC10591064 · Cell reports. Medicine · 2023 · 8 claims · 8 setups
A 3-lncRNA urine extracellular vesicle classifier (Clnc: AC015987.1, CTD-2589M5.4, RP11-363E6.3) detects high-grade PCa with higher accuracy than PCA3, mpMRI, PCPT-RC 2.0, and ERSPC-RC
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Has reproduction · 79
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.
PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups
196 R. leguminosarum sv. trifolii strains form a five-species complex (gsA-gsE) with generally little recent between-species gene transfer, aside from a few highly mobile genetic regions
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Has reproduction · 64
Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes.
PMID 38566006 · PMC10985947 · Genetics, selection, evolution : GSE · 2024 · 7 claims · 7 setups
Significant genetic introgression from commercial European pigs (EP) into the Lijiang pig (LJP) and other domestic Chinese pig breeds was detected.
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Has reproduction · 95
A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.
PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups
RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA
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Has reproduction · 71
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.
PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups
TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.
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Has reproduction
Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.
PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 8 claims · 8 setups
A three-class WSI cluster (C0/C1/C2) derived via mini batch K-means clustering on Inception V3-extracted image features is significantly associated with overall survival and is an independent prognostic predictor in BLCA.
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Has reproduction · 67
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.
PMID 37994351 · PMC10663991 · F1000Research · 2023 · 8 claims · 6 setups
A comprehensive open-source R workflow combining trajectory inference (monocle3) and pseudo-bulk time course analysis (edgeR) can be applied to multi-sample scRNA-seq data of the mouse mammary gland.
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Has reproduction · 78
Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.
PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups
Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely
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Has reproduction · 65
Interpretable and integrative analysis of single-cell multiomics with scMKL.
PMID 40770488 · PMC12328712 · Communications biology · 2025 · 7 claims · 7 setups
scMKL outperforms SVM, EasyMKL, MLP, and XGBoost in classification accuracy (AUROC) across multiple single-cell cancer datasets
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Has reproduction · 84
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.
PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 8 claims · 7 setups
DeepProg is a novel ensemble framework of deep-learning and machine-learning approaches that robustly predicts patient survival subtypes using multi-omics data
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Has reproduction · 87
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.
PMID 34072576 · PMC8227486 · Genes · 2021 · 7 claims · 8 setups
A new consensus transcriptome of E. gracilis was assembled by combining reads from five independent RNA-seq studies (23 samples)
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Has reproduction · 64
Candidates for Balancing Selection in Leishmania donovani Complex Parasites.
PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups
Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)
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Has reproduction · 30
Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.
PMID 30503143 · PMC6327112 · Cell stem cell · 2019 · 8 claims · 8 setups
Single-cell transcriptomic analysis of GBA-N370S iPSC-derived dopamine neurons identifies a progressive axis of gene expression variation leading to endoplasmic reticulum stress.