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 · 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 · 83
Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress.
PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 7 claims · 4 setups
A metabolite-centric reporter pathway analysis (RPAm) can infer cold-stress-associated metabolites and pathways in Arabidopsis directly from transcriptome data without metabolome data
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Has reproduction · 59
Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.
PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 7 claims · 8 setups
Eight gene modules linked to metastasis were identified via scored network analysis and validated through pathway databases.
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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 · 79
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.
PMID 33705981 · PMC9403021 · Genomics, proteomics & bioinformatics · 2021 · 8 claims · 6 setups
TSUNAMI is a freely accessible web-based tool suite that mines gene co-expression network (GCN) modules from public (GEO, TCGA) or user-uploaded numerical omics data and performs downstream gene set enrichment analysis.
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Has reproduction · 89
Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features.
PMID 37509188 · PMC10377046 · Biomolecules · 2023 · 8 claims · 3 setups
Graph Random Forest (GRF) embeds graph/network information directly into the decision-tree building process by splitting on features in the k-hop neighborhood of a data-driven head-splitting node.
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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 · 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 · 86
Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.
PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups
RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.
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Has reproduction · 71
Artificial intelligence-guided discovery of gastric cancer continuum.
PMID 36692601 · PMC9871434 · Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2023 · 8 claims · 8 setups
A Boolean implication network built from GSE66229 yields a GC-BoNE gene signature (Boolean paths C#11-2-4-14 and C#7-13-14) that classifies tumor vs normal/adjacent-normal gastric samples
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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 · 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 · 51
SGCP: a spectral self-learning method for clustering genes in co-expression networks.
PMID 38956463 · PMC11221046 · BMC bioinformatics · 2024 · 7 claims · 4 setups
SGCP, a spectral self-learning method, yields gene co-expression modules with higher GO enrichment than WGCNA, CoExpNets, and CEMiTool across 12 real gene expression datasets.
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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 · 85
A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.
PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups
EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)
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Has reproduction · 75
Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.
PMID 34143800 · PMC8213194 · PloS one · 2021 · 7 claims · 6 setups
306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified across three independent GEO datasets in EOC vs normal ovarian tissue.
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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 · 75
ResnetAge: A Resnet-Based DNA Methylation Age Prediction Method.
PMID 38247911 · PMC10813502 · Bioengineering (Basel, Switzerland) · 2023 · 8 claims · 4 setups
ResnetAge, a ResNet-based neural network using 22,278 shared Illumina 27K/450K CpG sites, predicts DNA methylation age from beta values.
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Has reproduction · 80
Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.
PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups
Combining WGCNA-derived hub genes with a VAE-derived 10-dimensional representation as features for an SVM classifier achieves high accuracy (0.9692) and AUC (0.9981) for colorectal cancer prediction.
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Has reproduction · 78
T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.
PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups
Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification