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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Adipose proteome analysis: focus on mediators of insulin resistance.
PMID 19086862 · PMC2651673 · Expert review of proteomics · 2008 · 8 claims · 5 setups
Ectopic lipid accumulation in liver and muscle, resulting from impaired adipose tissue lipid-storage capacity, is more directly associated with insulin resistance than adipose tissue mass itself.
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The use of proteomics in biomarker discovery in neurodegenerative diseases.
PMID 15920295 · PMC3850612 · Disease markers · 2005 · 8 claims · 8 setups
A combination of low CSF-β-amyloid(1-42) with high CSF-tau and high CSF-phospho-tau is associated with an AD diagnosis
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Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.
PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups
A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers
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Has reproduction · 78
Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.
PMID 41953002 · PMC13053772 · iScience · 2026 · 7 claims · 8 setups
An integrated framework of bioinformatics, machine learning, and ΔG clustering can prioritize PAHs for AD-associated neurotoxicity.
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Has reproduction · 83
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.
PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups
Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs
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Cohesin regulates alternative splicing.
PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups
Cohesin regulates alternative splicing independently of its effects on transcription.
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A global proteomics approach identifies novel phosphorylated signaling proteins in GPVI-activated platelets: involvement of G6f, a novel platelet Grb2-binding membrane adapter.
PMID 16941570 · PMC1869047 · Proteomics · 2006 · 8 claims · 7 setups
96 proteins undergo post-translational modification (phosphorylation) in response to CRP stimulation of human platelets, including 11 proteins not previously identified in platelets
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Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.
PMID 18973825 · PMC7185545 · Drug discovery today · 2008 · 8 claims · 8 setups
Abundant plasma proteins (albumin, IgG, transferrin) act as 'molecular sponges' that bind and transport low molecular weight proteins/peptides and drugs, extending their half-life by preventing rapid renal clearance.
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Has reproduction · 50
Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.
PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups
829 genes are overexpressed in the oscular region of increased calcite spicule formation in S. ciliatum
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Has reproduction · 81
Identification of Proteins Deregulated by Platinum-Based Chemotherapy as Novel Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer.
PMID 33777753 · PMC7991912 · Frontiers in oncology · 2021 · 7 claims · 8 setups
Cisplatin exposure induces significant deregulation of protein expression networks in NSCLC cells
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The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.
PMID 17932789 · PMC2140095 · Journal of structural and functional genomics · 2007 · 8 claims · 6 setups
A family-based target selection approach (rather than genome-wide or fold-novelty based selection) maximizes cross-member methodological transfer and biological insight
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Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.
PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups
Current syndromic disease classification lacks specificity despite historically serving clinicians well
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HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.
PMID 18714345 · PMC2500163 · PloS one · 2008 · 7 claims · 4 setups
HIV infection of a human T-cell line differentially regulates 18 proteins involved in lipid metabolism.
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Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.
PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups
Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation
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Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.
PMID 19693676 · PMC2824116 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 7 setups
Proteomic screening of human synaptosomes identifies a set of proteins differentially expressed in HIV/AIDS brain
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Has reproduction · 69
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.
PMID 34601390 · PMC8483812 · Computers in biology and medicine · 2021 · 8 claims · 8 setups
COVID-19 and neurological diseases (NDs) share pathophysiological connections that influence disease progression and severity
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Has reproduction · 100
Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.
PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups
KYNU expression is decreased in melanoma despite a high KYNU mutation rate in the TCGA database
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Has reproduction · 84
Network Controllability Reveals Key Mitigation Points for Tumor-Promoting Signaling in Tumor-Educated Platelets.
PMID 41226816 · PMC12609506 · International journal of molecular sciences · 2025 · 8 claims · 6 setups
TEPs in NSCLC show 111 upregulated and 108 downregulated genes versus non-cancer control platelets, enriched in ECM interaction, cytoskeleton, immune signaling, and platelet activation pathways.
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Aberrations of the p14(ARF) and p16(INK4a) genes in renal cell carcinomas.
PMID 11749694 · PMC5926680 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 6 setups
Homozygous co-deletion of p14ARF and p16INK4a is frequent in RCC cell lines (5 of 6 lines)
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KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.
PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups
KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.