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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Full-text index only
FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data.
PMID 17204155 · PMC1774579 · BMC bioinformatics · 2007 · 6 claims · 5 setups
FLAME captures non-linear relationships and non-globular clusters by approximating fuzzy membership from each object's nearest neighbors rather than global centroids
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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 · 84
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.
PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 6 claims · 7 setups
DeepProg, an ensemble of deep-learning and machine-learning models, robustly predicts patient survival subtypes from multi-omics data and explicitly models survival as the objective while predicting new patient risks
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Gene expression and isoform variation analysis using Affymetrix Exon Arrays.
PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups
The Exon Array performs comparably to 3'-targeted platforms (Illumina, U133) at the gene expression level, though interplatform correlation is slightly lower than between the two 3' platforms.
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Comparison of prognostic gene expression signatures for breast cancer.
PMID 18717985 · PMC2533026 · BMC genomics · 2008 · 8 claims · 5 setups
The three prognostic signatures (70-gene, 76-gene, GGI) show similar prognostic performance for predicting DMFS despite differing gene identity and development approach
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Has reproduction
Endogenous Fatty Acid Synthesis Drives Brown Adipose Tissue Involution.
PMID 33440156 · PMC8240962 · Cell reports · 2021 · 8 claims · 8 setups
Endogenous fatty acid synthesis (DNL), regulated by ChREBP, is the central driver of BAT whitening/involution at thermoneutrality.
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Has reproduction · 78
Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynthesis.
PMID 38317086 · PMC10845750 · BMC plant biology · 2024 · 8 claims · 6 setups
Drought stress significantly increases MDA, proline, soluble sugar, and crude protein content and antioxidative enzyme (SOD, POD, CAT) activity in A. chinensis seedlings
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Has reproduction · 74
SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation.
PMID 42146899 · PMC13176606 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups
SpaGene improves average PCC and SSIM and reduces RMSE compared to 6 baseline methods (SpaGE, gimVI, Tangram, VISTA, spRefine, stDiff) across 8 diverse ST-SC dataset pairs under gene-holdout evaluation.
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Has reproduction · 66
Responses of peritubular macrophages and the testis transcriptome profiles of peripubertal and adult rodents exposed to an acute dose of MEHP.
PMID 38113427 · PMC10901151 · Toxicological sciences : an official journal of the Society of Toxicology · 2024 · 8 claims · 7 setups
MEHP exposure previously increased PTMφ numbers 6-fold in peripubertal Fischer rats
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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
Using random walks to identify cancer-associated modules in expression data.
PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups
Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.
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Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.
PMID 17038195 · PMC1618849 · BMC genomics · 2006 · 8 claims · 6 setups
EXPOLDB is a novel database integrating human gene expression variability data (including monozygotic twin comparisons) with (TG/CA)n repeat polymorphism information
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Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.
PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups
An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set
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Has reproduction · 62
Metatranscriptomics of the human oral microbiome during health and disease.
PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups
Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.
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Has reproduction · 59
Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.
PMID 33958982 · PMC8093778 · Frontiers in neuroscience · 2021 · 7 claims · 8 setups
Fourteen gene modules were consistently associated with ReHo across three independent fMRI datasets.
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Has reproduction · 71
Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.
PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 7 claims · 8 setups
CAI is positively correlated with translational efficiency, supporting its use as a proxy for viral mRNA translation in cell types.
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Has reproduction · 71
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.
PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 7 claims · 7 setups
AML patients can be categorized into two distinct PANRG-based clusters with differing prognosis and immune characteristics
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Has reproduction · 100
The mouse gastric surface epithelial cell and its response to early Helicobacter pylori infection.
PMID 41824631 · PMC13020875 · Virulence · 2026 · 8 claims · 5 setups
LCM followed by RNA-Seq is a feasible methodology for characterizing gastric SMCs and their host response to H. pylori infection in vivo
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Has reproduction · 53
Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.
PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 7 claims · 5 setups
A computational framework integrating independently measured CNV (DNA sequencing) and single-cell RNA-seq from the same patients identifies recurrent concordant copy number gain and gene upregulation (CNG-UP) events and functional modules at the single-cell level.