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 · 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 · 75
An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.
PMID 33247935 · PMC7698665 · Database : the journal of biological databases and curation · 2020 · 8 claims · 6 setups
GETc enables discovery and visualization of time-course gene expression data and analytical results from GEO
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Has reproduction · 82
SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis.
PMID 30698691 · PMC6354025 · GigaScience · 2019 · 8 claims · 5 setups
SMAGEXP integrates the metaMA and metaRNASeq R packages into Galaxy to provide a unified tool suite for transcriptomics meta-analysis.
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Has reproduction · 73
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.
PMID 31110304 · PMC6527554 · Scientific reports · 2019 · 8 claims · 7 setups
GREIN is a web application providing user-friendly interfaces to manipulate, visualize, and analyze GEO RNA-seq data.
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Has reproduction
All of gene expression (AOE): An integrated index for public gene expression databases.
PMID 31978081 · PMC6980531 · PloS one · 2020 · 8 claims · 5 setups
AOE integrates publicly available gene expression data from GEO, ArrayExpress, and GEA into a single searchable index.
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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 · 74
Wide-Open: Accelerating public data release by automating detection of overdue datasets.
PMID 28594819 · PMC5464523 · PLoS biology · 2017 · 7 claims · 5 setups
Wide-Open is a general text-mining approach that automatically detects overdue datasets by scanning PubMed articles for dataset accession identifiers and querying repositories to determine if the datasets remain private.
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Has reproduction · 10
Effect of PAIP1 on the metastatic potential and prognostic significance in oral squamous cell carcinoma.
PMID 35153296 · PMC8841500 · International journal of oral science · 2022 · 8 claims · 8 setups
PAIP1 mRNA and protein levels are upregulated in OSCC/HNSCC compared to normal tissue.
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Has reproduction · 62
A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.
PMID 31290545 · PMC6616200 · Database : the journal of biological databases and curation · 2019 · 5 claims · 8 setups
A curated collection of 33 GEO transcriptome datasets relevant to IgE-mediated atopic diseases (allergies to primary immunodeficiencies) was assembled, encompassing 1860 transcriptome profiles.
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Has reproduction
D2H2: diabetes data and hypothesis hub.
PMID 38107655 · PMC10723036 · Bioinformatics advances · 2023 · 6 claims · 5 setups
D2H2 is a web portal hosting hundreds of curated, uniformly reprocessed diabetes-relevant transcriptomics datasets from GEO with per-study visualization, differential expression, and single-gene queries.
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Has reproduction · 80
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.
PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups
WGCNA identified 214 key genes in the blue module most correlated with LUAD
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Has reproduction · 80
MCPmed: a call for Model Context Protocol-enabled bioinformatics web services for LLM-driven discovery.
PMID 41729821 · PMC12927880 · Briefings in bioinformatics · 2026 · 6 claims · 3 setups
Adapting MCP to bioinformatics web server backends provides a standardized, machine-actionable semantic layer linking API endpoints to scientific concepts and metadata.
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Has reproduction · 88
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.
PMID 33937763 · PMC8061458 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups
Approximately two-thirds of compiled HM450K samples are from blood, one-quarter from brain, and roughly one-third from cancer patients.
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Has reproduction · 80
Curation of over 10 000 transcriptomic studies to enable data reuse.
PMID 33599246 · PMC7904053 · Database : the journal of biological databases and curation · 2021 · 8 claims · 6 setups
Gemma is a curated database and bioinformatics system that addresses metadata, probe annotation, and expression data inconsistencies in GEO to enable transcriptomic data reuse
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Has reproduction · 85
Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure.
PMID 35197930 · PMC8859149 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups
Robust Rank Aggregation (RRA) can integrate DEG lists from multiple independent RIF microarray datasets to identify robust DEGs.
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Has reproduction · 87
Identification of a novel lncRNA prognostic signature and analysis of functional lncRNA AC115619.1 in hepatocellular carcinoma.
PMID 37614318 · PMC10442647 · Frontiers in pharmacology · 2023 · 8 claims · 8 setups
A six-lncRNA prognostic signature (LINC02428, LINC02163, AC008549.1, AC115619.1, CASC9, LINC02362) predicts overall survival in HCC patients
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Has reproduction · 71
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.
PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 7 claims · 8 setups
Two distinct RNA modification patterns exist among BCa samples with radically different clinical outcomes and biological characteristics.
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Has reproduction · 66
Liver-specific paraoxonase-1 alleviates regulatory T cell-driven immunosuppression via metabolic reprogramming in hepatocellular carcinoma.
PMID 41387425 · PMC12701056 · Nature communications · 2025 · 8 claims · 8 setups
PON1 expression is downregulated in HCC tumor tissue and low PON1 is associated with worse prognosis
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Has reproduction · 71
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.
PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups
LUAD samples cluster into IRG-high and IRG-low groups, with the IRG-high group showing significantly better survival and greater immune cell infiltration.
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Has reproduction · 50
Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.
PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups
A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation