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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Asthma investigators begin to reap the fruits of genomics.
PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups
Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.
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Proteomic analysis of serum in lung cancer induced by 3-methylcholanthrene.
PMID 19794824 · PMC2753780 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 4 setups
141 protein spots are differentially expressed between normal rat sera and MCA-induced lung cancer rat sera (82 overexpressed, 59 underexpressed)
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Has reproduction · 83
Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.
PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups
188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways
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Has reproduction · 77
Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.
PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups
457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis
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Has reproduction · 93
Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.
PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups
5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)
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Has reproduction · 71
Transcriptomic Study on the Lungs of Broilers with Ascites Syndrome.
PMID 36611783 · PMC9817706 · Animals : an open access journal from MDPI · 2023 · 8 claims · 6 setups
1442 genes were differentially expressed in AS broiler lung vs normal lung (614 up-regulated, 828 down-regulated)
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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 · 100
miR-4478 Accelerates Nucleus Pulposus Cells Apoptosis Induced by Oxidative Stress by Targeting MTH1.
PMID 36130054 · PMC9897280 · Spine · 2023 · 7 claims · 8 setups
miR-4478 is upregulated in nucleus pulposus tissues from IVDD patients and is degeneration-degree-associated
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Has reproduction · 71
Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.
PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 7 claims · 6 setups
An 18-gene mitophagy-related prognostic signature was identified by machine learning and used to build a prognostic risk score model for ALS.
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Has reproduction · 68
Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.
PMID 35819852 · PMC9433101 · The Journal of clinical investigation · 2022 · 8 claims · 8 setups
Chronic wound-edge tissue exhibits genome-wide DNA hypermethylation, with hypermethylation more prominent than hypomethylation across differentially methylated regions.
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Has reproduction · 53
Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.
PMID 35425715 · PMC9004628 · Frontiers in oncology · 2022 · 8 claims · 7 setups
Patient-derived colorectal cancer organoids (CRCOs) can be established from surgical CRC tissue with an 82% success rate (41/50)
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Has reproduction · 64
Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.
PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups
Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI
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Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.
PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups
Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.
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Has reproduction · 50
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.
PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups
Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.
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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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Interpretation of genomic data: questions and answers.
PMID 18582627 · PMC2528831 · Seminars in hematology · 2008 · 8 claims · 6 setups
The main challenge in using genomic technology in cancer research is not managing the volume of data but the proper design, analysis, and reporting of studies.
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Senescence marker protein 30 in acute liver failure: validation of a mass spectrometry proteomics assay.
PMID 18507831 · PMC2435529 · BMC gastroenterology · 2008 · 8 claims · 6 setups
Plasma SMP30 protein levels are selectively elevated in GalN/LPS-induced ALF mice
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Has reproduction · 78
Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.
PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups
In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.
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Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.
PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups
Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.
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Has reproduction · 62
Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments.
PMID 32093613 · PMC7041296 · BMC genomics · 2020 · 7 claims · 3 setups
The Equivalent Change Index (ECI), a gene-level statistic ranging from -1 to 1, quantifies whether a gene was changed to the same (1) or completely opposite (-1) degree across two experiments relative to their controls.