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 · 64
VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data.
PMID 37180100 · PMC10172660 · Frontiers in immunology · 2023 · 7 claims · 7 setups
VIGET is a web portal that lets users select vaccines/ImmPort studies, run differential gene expression analysis, and perform Reactome-based pathway enrichment and functional interaction network construction
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Has reproduction · 75
Revealing the critical state and identifying individualized dynamic network biomarker for type 2 diabetes through advanced analysis methods on individual basis.
PMID 39890881 · PMC11785715 · Scientific reports · 2025 · 8 claims · 5 setups
sJSD, NIG, and TNFE methods can detect critical states/tipping points before disease deterioration using only a single sample
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Has reproduction · 100
Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.
PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups
Hsp90-dependent gene expression varies among different yeast strains
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Has reproduction · 90
A2TEA: Identifying trait-specific evolutionary adaptations.
PMID 37224329 · PMC10186066 · F1000Research · 2022 · 8 claims · 7 setups
A2TEA integrates gene family expansion analysis with differential expression data across species to identify genes that were targets of evolutionary adaptation to a given stress/treatment
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Has reproduction · 84
Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.
PMID 34643182 · PMC8555986 · eLife · 2021 · 8 claims · 8 setups
Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm/pSHF via an evolutionarily conserved intronic enhancer.
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Has reproduction · 71
Transcriptome and machine learning analysis of the impact of COVID-19 on mitochondria and multiorgan damage.
PMID 38295140 · PMC10830027 · PloS one · 2024 · 6 claims · 7 setups
Potential cardiac, hepatic, and renal impairments in COVID-19 are associated with ACE2, inflammatory cytokine storms, and mitochondrial pathways.
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Has reproduction · 69
COVID-19 vaccination atlas using an integrative systems vaccinology approach.
PMID 40456760 · PMC12130191 · NPJ vaccines · 2025 · 8 claims · 6 setups
mRNA vaccines induce transient but strong immune responses after booster doses
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Functional analysis of human hematopoietic stem cell gene expression using zebrafish.
PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups
277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow
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A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.
PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups
A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.
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Ontological Discovery Environment: a system for integrating gene-phenotype associations.
PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups
ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems
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Has reproduction · 84
Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.
PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups
A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts
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Has reproduction · 81
Transcriptome analysis reveals differential splicing events in IPF lung tissue.
PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups
873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.
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Has reproduction · 75
Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.
PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 7 setups
All three mouse models (hAβ-KI, 5xFAD, APP/PS1) share more differentially expressed genes, GO biological processes, and KEGG pathways with LOAD than with EOAD patients.
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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 · 83
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.
PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups
Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.
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Has reproduction · 58
Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.
PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups
EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD
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Increased DNA microarray hybridization specificity using sscDNA targets.
PMID 15847692 · PMC1090574 · BMC genomics · 2005 · 7 claims · 5 setups
A single round of ribo-SPIA amplification produces sufficient sscDNA for microarray hybridization from as little as 5 ng of starting total RNA
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Has reproduction · 100
Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.
PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups
Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.
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Has reproduction · 82
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis.
PMID 34019643 · PMC8218201 · Nucleic acids research · 2021 · 8 claims · 5 setups
eVITTA is a web-based toolbox with three modules (easyGEO, easyGSEA, easyVizR) that analyze, interpret, and compare transcriptome data from published NCBI GEO studies or new experiments