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 · 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 · 70
Zebrafish functional xenograft vasculature platform identifies PF-502 as a durable vasculature normalization drug.
PMID 37680473 · PMC10480778 · iScience · 2023 · 8 claims · 8 setups
The zebrafish functional xenograft vasculature platform (zFXVP) enables visualization and quantification of structurally and functionally realistic tumor vasculature formation.
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Has reproduction · 78
Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.
PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups
KCTD16, CD3D and GSDMB are succinylation-related prognostic genes in BLCA
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Has reproduction · 59
Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach.
PMID 38253993 · PMC10810249 · BMC bioinformatics · 2024 · 8 claims · 8 setups
The BGWO_SA_Ens algorithm (hybrid BGWO + simulated annealing with an ensemble classifier objective function) selects predictive breast cancer biomarker genes with high classification performance
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Stability analysis of mixtures of mutagenetic trees.
PMID 18366778 · PMC2335279 · BMC bioinformatics · 2008 · 7 claims · 5 setups
Mutagenetic trees mixture models capture multiple alternative pathways of ordered accumulation of genetic events (e.g., HIV resistance mutations, cancer chromosomal aberrations).
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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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Expression profiling of drug response--from genes to pathways.
PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups
Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.
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Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa.
PMID 19890396 · PMC2767505 · PloS one · 2009 · 8 claims · 4 setups
Rifampicin resistance (rpoB) and pyrazinamide resistance (pncA) mutations occur at different nucleotide positions in the MDR and XDR strains, showing they were acquired independently and that the XDR strain did not evolve directly from this MDR strain.
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Has reproduction · 58
Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.
PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups
PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA
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targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.
PMID 19099550 · PMC2651862 · BMC systems biology · 2008 · 8 claims · 8 setups
A comprehensive in silico target identification pipeline (targetTB) integrating interactome, reactome, essentiality, sequence and structural analyses can identify high-confidence drug targets for Mtb
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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 · 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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Structure of protein interaction networks and their implications on drug design.
PMID 19876376 · PMC2760708 · PLoS computational biology · 2009 · 8 claims · 6 setups
Budding yeast and human PINs are scale-rich and configured as highly optimized tolerance (HOT) networks similar to Internet router-level topology, rather than scale-free networks formed by preferential attachment.
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Has reproduction · 61
Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data.
PMID 33575569 · PMC7671354 · NAR genomics and bioinformatics · 2020 · 8 claims · 5 setups
Omics Playground is a user-friendly, interactive self-service bioinformatics platform for in-depth analysis, visualization and interpretation of transcriptomics and proteomics data without coding
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Has reproduction · 80
Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.
PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups
The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences
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Public health genomics: translating obesity genomics research into population health benefits.
PMID 19037221 · PMC2736102 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 6 setups
Obesity genomics research is mostly in the discovery phase (T1); a four-phase translational framework (T1-T4) is needed to move discoveries to population health impact
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Toxicogenomics: an emerging discipline.
PMID 12460812 · PMC1241126 · Environmental health perspectives · 2002 · 8 claims · 6 setups
Toxicogenomics applies genomic tools (microarrays, proteomics, metabolomics) to characterize how cells and organisms respond to chemical/drug exposures.
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The use of neuroproteomics in drug abuse research.
PMID 19926406 · PMC3947580 · Drug and alcohol dependence · 2010 · 8 claims · 8 setups
Neuroproteomic technologies (2D-DIGE, iTRAQ, ICAT, etc.) enable identification of protein-level changes underlying effects of drugs of abuse such as amphetamine, morphine, cocaine, and alcohol.
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Has reproduction · 68
Molecular subtype of recurrent implantation failure reveals distinct endometrial etiology of female infertility.
PMID 40660214 · PMC12257665 · Journal of translational medicine · 2025 · 8 claims · 8 setups
RIF endometrial samples segregate into two reproducible molecular subtypes: an immune-driven subtype (RIF-I) and a metabolic-driven subtype (RIF-M)
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Has reproduction · 75
Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.
PMID 38163105 · PMC10757018 · Heliyon · 2024 · 7 claims · 8 setups
Chemokines CCL2 and CXCL5 mediate a shear stress-induced 'Endothelial-Monocyte-Neutrophil' axis that contributes to aortic dissection development.