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 · 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 · 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 · 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 · 41
Unveiling the immunometabolic landscape of colorectal cancer through PANoptosis-related gene expression.
PMID 41601652 · PMC12832467 · Frontiers in immunology · 2025 · 8 claims · 8 setups
A CPAN-index prognostic model built from 11 PANoptosis-related differentially expressed genes (CPAN_DEGs) stratifies CRC patients into high-risk and low-risk groups with distinct survival and immunophenotypes.
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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 · 7 setups
ZBTB38 expression is decreased in localised prostate cancer and further decreased in metastatic prostate cancer compared to non-cancerous prostate tissue
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Has reproduction · 59
Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.
PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups
NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering
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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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Has reproduction · 50
Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.
PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups
A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database
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Has reproduction · 51
A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.
PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups
An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73
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Has reproduction · 89
Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.
PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups
Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM
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Has reproduction · 73
Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.
PMID 32629858 · PMC7408437 · Cancers · 2020 · 8 claims · 8 setups
Unsupervised biclustering of 283 NB-specific immune genes stratifies HR-NB into two reproducible subtypes: ultra-high-risk (UHR-NB) and (revised) HR-NB.
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Has reproduction · 76
Exploration of the shared diagnostic genes and molecular mechanism between obesity and atherosclerosis via bioinformatic analysis.
PMID 39825072 · PMC11742665 · Scientific reports · 2025 · 8 claims · 8 setups
56 shared genes with consistent expression trend were identified between OB and AS by intersecting WGCNA key module genes with DEGs
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Has reproduction
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.
PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 8 claims · 5 setups
The nasal methylome shows differential DNA methylation in intergenic regions and low methylated regions (LMRs), highlighting distal regulatory/enhancer-like elements in COVID-19 gene regulation
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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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Full-text index only
Mining expressed sequence tags identifies cancer markers of clinical interest.
PMID 17078886 · PMC1635568 · BMC bioinformatics · 2006 · 8 claims · 6 setups
An EST-mining approach (Fisher Exact Test on tumor vs. non-tumor library hit counts) identifies differentially expressed transcripts with an estimated false discovery rate below 22% when human and mouse screens are combined.
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Has reproduction · 66
STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.
PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 6 claims · 4 setups
Low STAT3 expression in primary prostate cancer is associated with up-regulated OXPHOS and ribosomal biosynthesis at the transcriptomic level.
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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 · 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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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 · 84
A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex.
PMID 34253796 · PMC8275748 · Scientific reports · 2021 · 8 claims · 8 setups
The ERV locus HML6_3p21.31c is significantly upregulated in ALS post-mortem motor cortex after multiple-testing correction