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 · 78
Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.
PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 5 claims · 6 setups
CIBERSORTx can combine scRNA-seq-derived signatures with bulk HCC transcriptomes to estimate proportions of 11 TIL subsets and infer cell-type-specific gene expression.
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Has reproduction · 35
Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.
PMID 32365491 · PMC7281456 · Cancers · 2020 · 8 claims · 8 setups
ZBTB38 mRNA expression is significantly lower in prostate cancer than in normal/benign prostate tissue, and further reduced in metastatic versus localised tumours
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Has reproduction · 95
MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.
PMID 29901703 · PMC6025204 · GigaScience · 2018 · 6 claims · 7 setups
A two-step 'omni' RNA-seq pipeline (MetaMap) combining STAR human alignment with CLARK-S metagenomic classification can quantify archaeal, bacterial, and viral reads from the non-human read fraction of human RNA-seq data
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Has reproduction · 53
PulmonDB: a curated lung disease gene expression database.
PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 7 claims · 6 setups
PulmonDB is a curated, web-based relational database (plus R package) integrating microarray and RNA-seq gene expression data with controlled-vocabulary annotation for COPD and IPF.
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Has reproduction · 62
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.
PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 7 claims · 5 setups
A DNN model using the top 34 betweenness-centrality-ranked hub genes predicts bone metastasis with AUC of 92.11% on the GEO validation data.
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Has reproduction · 57
Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.
PMID 32019831 · PMC7002113 · mSystems · 2020 · 8 claims · 7 setups
Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are diverse and abundant in the halite endolithic microbial community, with 1,538 total ncRNAs discovered across Archaea and Bacteria.
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Has reproduction · 45
De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.
PMID 29451882 · PMC5815590 · PloS one · 2018 · 7 claims · 7 setups
This is the first de novo transcriptomic analysis of Cornus officinalis, providing fundamental gene and biosynthetic pathway information.
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Has reproduction · 20
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.
PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups
AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats
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Has reproduction · 70
GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses.
PMID 33758032 · PMC8547006 · mSystems · 2021 · 7 claims · 6 setups
GAUGE automatically annotates GEO microbial microarray and RNA-seq data sets, increasing the percentage amenable to analysis from 4% to 33%.
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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 · 78
Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynthesis.
PMID 38317086 · PMC10845750 · BMC plant biology · 2024 · 8 claims · 6 setups
Drought stress significantly increases MDA, proline, soluble sugar, and crude protein content and antioxidative enzyme (SOD, POD, CAT) activity in A. chinensis seedlings
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Has reproduction · 63
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups
RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO
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Has reproduction
Identification of a novel 10 immune-related genes signature as a prognostic biomarker panel for gastric cancer.
PMID 34382341 · PMC8446556 · Cancer medicine · 2021 · 7 claims · 6 setups
A 10 immune-related gene signature (BMPR1B, GHR, IL11RA, INHBB, NPR3, OBP2A, PTN, R3HDML, TAC1, TPM2) was constructed via WGCNA combined with LASSO-Cox and predicts overall survival in gastric cancer
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Has reproduction · 83
Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.
PMID 40472802 · PMC12171563 · EBioMedicine · 2025 · 6 claims · 7 setups
AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy
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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 · 68
Molecular subtype of recurrent implantation failure reveals distinct endometrial etiology of female infertility.
PMID 40660214 · PMC12257665 · Journal of translational medicine · 2025 · 8 claims · 8 setups
RIF endometrial samples segregate into two reproducible molecular subtypes: an immune-driven subtype (RIF-I) and a metabolic-driven subtype (RIF-M)
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Has reproduction · 59
Application of Machine Learning in Predicting Hepatic Metastasis or Primary Site in Gastroenteropancreatic Neuroendocrine Tumors.
PMID 37887568 · PMC10605255 · Current oncology (Toronto, Ont.) · 2023 · 8 claims · 7 setups
Multi-gene random forest models classify primary tumor vs. liver metastasis samples with 100% accuracy in training/test cohorts and >90% accuracy in an independent validation cohort
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Has reproduction · 50
Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.
PMID 33746712 · PMC7966716 · Frontiers in molecular neuroscience · 2021 · 6 claims · 7 setups
A computational method using high-quality scRNA-seq reference data can estimate per-sample, per-cell-type off-target contamination coefficients in sctRNA-seq datasets.
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Has reproduction · 44
Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.
PMID 34532385 · PMC8421925 · Annals of translational medicine · 2021 · 8 claims · 7 setups
The brown co-expression module (775 genes) is the module most significantly associated with the chronic stage of SCI
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Has reproduction · 61
Differentiation status determines the effects of IFNγ on the expression of PD-L1 and immunomodulatory genes in melanoma.
PMID 39736644 · PMC11687009 · Cell communication and signaling : CCS · 2024 · 6 claims · 8 setups
Dedifferentiation via MITF knockdown renders 624Mel melanoma cells hypersensitive to IFNγ, causing non-additive (synergistic) upregulation of IFNγ-induced immunoregulatory genes.