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 · 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 · 100
Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.
PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups
A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity
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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
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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Wiggle-predicting functionally flexible regions from primary sequence.
PMID 16839194 · PMC1500818 · PLoS computational biology · 2006 · 7 claims · 6 setups
A GNM-derived, correlation-weighted 'FF score' can objectively define functionally flexible regions (FFRs) that match experimentally confirmed flexible/functional regions (hinges, recognition loops, catalytic loops).
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Detection of venous thromboembolism by proteomic serum biomarkers.
PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups
A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays
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Has reproduction · 69
Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma.
PMID 39355255 · PMC11442245 · Frontiers in immunology · 2024 · 8 claims · 8 setups
66 consensus immunotherapy prognostic genes (CITPGs) were identified from the intersection of WGCNA modules, immunotherapy responder-vs-non-responder DEGs, and tumor-vs-normal DEGs
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Protein ranking by semi-supervised network propagation.
PMID 16723003 · PMC1810311 · BMC bioinformatics · 2006 · 8 claims · 5 setups
RankProp, a diffusion-based network propagation algorithm on a PSI-BLAST-derived protein similarity network, significantly outperforms local search methods (BLAST/PSI-BLAST) at detecting remote homologs.
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Has reproduction · 50
Dissecting lncRNA-mRNA competitive regulatory network in human islet tissue exosomes of a type 1 diabetes model reveals exosome miRNA markers.
PMID 36440209 · PMC9682028 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups
lncRNA-mRNA ceRNA networks differ substantially between control and cytokine-treated islet exosomes, sharing lncRNAs more than mRNAs, implying state-dependent regulatory functions
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Has reproduction · 97
Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.
PMID 37883426 · PMC10602290 · PloS one · 2023 · 6 claims · 7 setups
TAA/TAV pathogenesis is more associated with immune-related gene expression than TAA/BAV, with two WGCNA gene modules (brown and blue) enriched for immune functions.
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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 · 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 · 50
STAT1 and IL-7 as potential diagnostic biomarkers for distinguishing high-grade from low-grade serous ovarian cancer: a multi-cohort analysis.
PMID 42058211 · PMC13120972 · Frontiers in immunology · 2026 · 7 claims · 6 setups
STAT1 and IL-7 are differentially expressed immune-related genes that can distinguish HGSOC from LGSOC and may serve as ancillary diagnostic biomarkers.
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Has reproduction · 98
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.
PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups
maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors
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Has reproduction · 78
Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.
PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups
A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response
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Has reproduction · 44
Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.
PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups
DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection
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Has reproduction · 49
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.
PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups
ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC
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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 · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.
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Has reproduction · 85
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.
PMID 38157249 · PMC10781479 · Aging · 2023 · 6 claims · 7 setups
A nine-gene oxidative stress-related scoring (OSRS) model (AREG, CES1, CSTA, FDCSP, JCHAIN, IFFO2, PGLYRP4, SPOCK2, SPINK6) predicts overall survival in HNSCC.