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 · 49
LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.
PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 7 claims · 8 setups
LRP1 is the top hub gene with the highest diagnostic performance for distinguishing ectopic from eutopic endometrium in EMS
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Has reproduction
Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.
PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups
The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells
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Has reproduction · 50
Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma.
PMID 33420019 · PMC7794422 · Nature communications · 2021 · 8 claims · 8 setups
SNAI2 is highly expressed in FN-RMS tumors and cell lines compared to normal tissue
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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 · 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
TFEB deficiency attenuates mitochondrial degradation upon brown adipose tissue whitening at thermoneutrality.
PMID 33516944 · PMC7903014 · Molecular metabolism · 2021 · 7 claims · 8 setups
BAT whitening at thermoneutrality is associated with TFEB-dependent mitochondrial degradation.
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Has reproduction · 45
Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.
PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 7 setups
Eight distinct T cell populations are identifiable in CRC tumor tissue and seven in peripheral blood by unsupervised clustering of scRNA-seq data.
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Has reproduction · 100
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.
PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups
WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.
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Has reproduction · 75
geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.
PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 4 setups
geneshot is a gene-level metagenomic bioinformatics tool that clusters de novo assembled protein-coding genes into co-abundant gene groups (CAGs) to reduce dimensionality and generate testable hypotheses from WGS microbiome data
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Has reproduction · 53
Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.
PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 7 claims · 5 setups
A computational framework integrating independently measured CNV (DNA sequencing) and single-cell RNA-seq from the same patients identifies recurrent concordant copy number gain and gene upregulation (CNG-UP) events and functional modules at the single-cell level.
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Has reproduction · 84
Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.
PMID 34599324 · PMC8557840 · Genome biology and evolution · 2021 · 8 claims · 6 setups
The divergence of the MT+ and MT- alleles predates speciation events within the Ostreococcus genus
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Has reproduction · 95
Pathway-targeting gene matrix for Drosophila gene set enrichment analysis.
PMID 34710184 · PMC8553153 · PloS one · 2021 · 8 claims · 4 setups
Gene matrix files for GSEA are largely unavailable for Drosophila, limiting pathway-level enrichment analysis in this model organism
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Has reproduction · 59
Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.
PMID 36093058 · PMC9459695 · iScience · 2022 · 8 claims · 8 setups
PFA-perfusion-based isolation preserves the true in vivo chromatin accessibility state, avoiding artifacts caused by tissue dissociation-induced activation
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Has reproduction · 50
auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication.
PMID 36078102 · PMC9454499 · Cells · 2022 · 8 claims · 7 setups
auts2a and auts2b originate from the teleost-specific whole genome duplication (TGD)
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Has reproduction · 43
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.
PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups
TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.
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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 · 54
Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.
PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups
Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes
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Has reproduction · 89
Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.
PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups
Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM
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Has reproduction · 87
NK2R control of energy expenditure and feeding to treat metabolic diseases.
PMID 39537932 · PMC11602716 · Nature · 2024 · 8 claims · 8 setups
NK2R activation is sufficient to suppress appetite centrally and increase energy expenditure peripherally
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Has reproduction · 71
Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.
PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups
Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.