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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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 · 96
GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.
PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups
gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory
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Longitudinal analysis of early stage sarcopenia in aging rhesus monkeys.
PMID 18983905 · PMC2693938 · Experimental gerontology · 2009 · 8 claims · 6 setups
mtDNA deletion mutations induce ETS enzyme abnormalities (COXneg/SDHhyp phenotypes) linked to intra-fiber atrophy and fiber loss
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Has reproduction · 90
PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.
PMID 24747190 · PMC4411361 · Genomics, proteomics & bioinformatics · 2014 · 8 claims · 3 setups
PrimerSeq is a user-friendly stand-alone software with a GUI for systematic design and visualization of RT-PCR primers for alternative splicing analysis using user-provided RNA-seq data.
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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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In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach.
PMID 17559675 · PMC1913526 · BMC structural biology · 2007 · 8 claims · 4 setups
A rigid-body docking-based approach can predict mutational effects on binding energetics for three structurally distinct enzyme-proteic inhibitor systems (hRI-Ang, Bn-Bs, BPTI-β-Trypsin)
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Sys-BodyFluid: a systematical database for human body fluid proteome research.
PMID 18978022 · PMC2686600 · Nucleic acids research · 2009 · 6 claims · 4 setups
Sys-BodyFluid is a web-based database integrating proteomic data from 11 human body fluids (plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, milk, amniotic fluid), containing over 10,000 proteins
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Has reproduction · 91
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.
PMID 31217263 · PMC6686947 · G3 (Bethesda, Md.) · 2019 · 8 claims · 8 setups
De novo transcriptome assemblies were generated for larval P. cultripes and S. couchii, providing new genomic resources for spadefoot toads
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Has reproduction · 69
Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.
PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups
Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis
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Has reproduction
TFEB deficiency attenuates mitochondrial degradation upon brown adipose tissue whitening at thermoneutrality.
PMID 33516944 · PMC7903014 · Molecular metabolism · 2021 · 7 claims · 8 setups
BAT whitening at thermoneutrality is associated with TFEB-dependent mitochondrial degradation.
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Has reproduction
Effects of Pharmacological Thermogenic Adipocyte Activation on Metabolism and Atherosclerotic Plaque Regression.
PMID 30813320 · PMC6412269 · Nutrients · 2019 · 8 claims · 7 setups
Chronic dietary CL316,243 treatment reduces adiposity and enhances body weight loss independent of food intake in LDLR-deficient mice
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Genotypic analysis of two hypervariable human cytomegalovirus genes.
PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups
UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.
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Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
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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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Has reproduction · 78
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).
PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups
METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.
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Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.
PMID 17052347 · PMC1622754 · BMC infectious diseases · 2006 · 8 claims · 4 setups
TMA/IHC staining patterns of GroEL, GroES, GspD, Ndk and Pyk in cell pellets generally corresponded to differential regulation patterns previously found by 2D gel proteomic analysis of IFN-γ-induced persistence
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Has reproduction · 48
Irisin ameliorates obesity and insulin resistance via adipose tissue IL-33 and regulatory T cells.
PMID 41933175 · PMC13052164 · Nature metabolism · 2026 · 8 claims · 8 setups
Irisin modulates adipose tissue inflammation by increasing IL-33 production and preserving ST2+ regulatory T cells in white adipose tissues, thereby improving obesity and glucose intolerance.
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Systems analysis of bone.
PMID 20046860 · PMC2790199 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 7 setups
Fracture risk and skeletal traits are highly heritable, with over 350 QTLs mapped across the mouse genome and genes such as LRP5, Alox15, and Darc identified as regulators of bone mass.
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The role of proteomics in depression research.
PMID 19997739 · PMC2940035 · European archives of psychiatry and clinical neuroscience · 2010 · 8 claims · 8 setups
Proteomics offers a complementary, functional-endpoint approach that can elucidate MDD pathophysiological mechanisms and biomarkers beyond transcriptomic/targeted studies
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Has reproduction · 89
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.
PMID 32718933 · PMC7467002 · G3 (Bethesda, Md.) · 2020 · 7 claims · 8 setups
Across datasets re-analyzed with a unified workflow, there is a general lack of global Wolbachia gene regulation.