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).

Publications 1.3k Datasets 392.5k Experiments 21

System / cell line: analysis ✕ Assay: extracellular ✕ Clear

A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.

PMID 37852185 · PMC10591064 · Cell reports. Medicine · 2023 · 8 claims · 8 setups

Has reproduction · 65

A 3-lncRNA urine extracellular vesicle classifier (Clnc: AC015987.1, CTD-2589M5.4, RP11-363E6.3) detects high-grade PCa with higher accuracy than PCA3, mpMRI, PCPT-RC 2.0, and ERSPC-RC

urinary tcga paired urine sequencing lncrna qrt-pcr
Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.

PMID 36015199 · PMC9413912 · Pharmaceutics · 2022 · 8 claims · 8 setups

Has reproduction · 19

Shared differentially expressed genes link glioblastoma with ischemic stroke and with moyamoya disease, revealing molecular associations among the diseases.

glioblastoma ischemic moyamoya shared bulk microarray gene
Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

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The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

tlr4 mus chimpanzee baboon genomic coding sequence
Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

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Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

gingivalis whole-cell comparative gene
Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.

PMID 35320603 · PMC9323552 · Global change biology · 2022 · 8 claims · 7 setups

Has reproduction · 39

Glacier shrinkage (decreasing glacier influence) accelerates downstream organic matter decomposition rates in glacier-fed streams

benthic sediment subset stream extracellular chlorophyll-a 16s
Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

PMID 15361934 · PMC515368 · PLoS biology · 2004 · 7 claims · 8 setups

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The HIF-1/VHL-1/EGL-9 hydroxylase pathway is tightly conserved in C. elegans

elegans whole-genome rnase pharmacological
Liver-specific paraoxonase-1 alleviates regulatory T cell-driven immunosuppression via metabolic reprogramming in hepatocellular carcinoma.

PMID 41387425 · PMC12701056 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 66

PON1 expression is downregulated in HCC tumor tissue and low PON1 is associated with worse prognosis

hcc paired hepa1-6 pon1-nc bioinformatic immunohistochemistry orthotopic
Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

PMID 18312646 · PMC2270869 · Retrovirology · 2008 · 8 claims · 7 setups

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Infectivity of recombinant viruses carrying different Env proteins from the same patient varies over an approximately 10-fold range, even among viruses with similar tropism.

env u373 mt4-r5 u373-r5 phylogenetic infectivity flow
Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism.

PMID 31825657 · PMC7099524 · American journal of physiology. Cell physiology · 2020 · 8 claims · 8 setups

Has reproduction · 64

L6, C2C12, and primary human myotubes show substantial heterogeneity in transcriptomic and metabolic profiles

c2c12 transcriptomic proliferation brdu
A mouse plasma peptide atlas as a resource for disease proteomics.

PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

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A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

plasma peptides fully tissues lc-ms anion database
Aggregation propensity of the human proteome.

PMID 18927604 · PMC2557143 · PLoS computational biology · 2008 · 8 claims · 7 setups

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Long proteins have, on average, less intense/pronounced aggregation peaks than short proteins

proteome non-membrane proteins membrane sequence-based correlation statistical
Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints.

PMID 35624178 · PMC9142503 · Nature communications · 2022 · 7 claims · 5 setups

Has reproduction · 84

pcSecYeast, a proteome-constrained genome-scale model integrating metabolism, translation, and detailed secretory pathway processing (translocation, PTMs, folding, misfolding, degradation), was constructed for S. cerevisiae

cerevisiae genome-scale unit expression
From linear genome sequence to three-dimensional organization of the cell nucleus.

PMID 12620101 · PMC153456 · Genome biology · 2003 · 8 claims · 8 setups

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Chromosome conformation capture (3C) can quantify in vivo physical interaction frequencies between genomic loci by crosslinking, digestion, and intramolecular ligation followed by PCR

saccharomyces mitotic nucleoplasm hela chromosome translocation stretched
A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

PMID 19997597 · PMC2781549 · PloS one · 2009 · 8 claims · 7 setups

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The majority of proteins expressed in growing and non-growing S. aureus cells can be identified and quantified by a metabolic labeling proteomic approach

aureus 2-d 1-d gelc-ms
Proteomic characterization of HIV-modulated membrane receptors, kinases and signaling proteins involved in novel angiogenic pathways.

PMID 19712456 · PMC2754444 · Journal of translational medicine · 2009 · 7 claims · 5 setups

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31 HIV-modulated cellular proteins were identified as functionally associated with signaling events involved in angiogenesis

rh9 hiv-infected identified subtractive mass enzyme-linked
Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.

PMID 12697062 · PMC156599 · BMC genetics · 2003 · 8 claims · 6 setups

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Rabbit MYOC encodes a 490 amino acid, 54,882-Da protein that is 84% identical overall to human myocilin

rabbit gtm66 myoc myocilin cdna sds-page transfection
Purinergic adipocyte-macrophage crosstalk promotes degeneration of thermogenic brown adipose tissue.

PMID 41261284 · PMC12715258 · EMBO reports · 2025 · 8 claims · 8 setups

Has reproduction · 78

Imbalanced sympathetic/thermogenic activation (via UCP1 deficiency or pharmacological futile thermogenesis) causes BAT inflammation, fibrosis and degeneration

bat wild-type brown histology qrt-pcr norepinephrine
A chromosomally integrated bacteriophage in invasive meningococci.

PMID 15967821 · PMC2212043 · The Journal of experimental medicine · 2005 · 8 claims · 7 setups

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An 8-kb genetic island (NMA1792-NMA1799) is specifically associated with hyperinvasive meningococcal clonal complexes

meningitidis culture czech patients comparative pcr nuclease
Comparative genomics search for losses of long-established genes on the human lineage.

PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

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A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

dog genome chimp gorilla comparative overlap visual
Activation instead of blocking mesolimbic dopaminergic reward circuitry is a preferred modality in the long term treatment of reward deficiency syndrome (RDS): a commentary.

PMID 19014506 · PMC2615745 · Theoretical biology & medical modelling · 2008 · 8 claims · 6 setups

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A biphasic treatment approach—acute DA receptor blocking followed by long-term DA release/activation at the NAc—is needed to treat RDS without inducing abnormal mood or craving.

kidney alcohol-preferring obese rodents receptor dna-directed meta-analysis

Experiments

A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.

Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.

Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.

Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

Liver-specific paraoxonase-1 alleviates regulatory T cell-driven immunosuppression via metabolic reprogramming in hepatocellular carcinoma.

Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism.

A mouse plasma peptide atlas as a resource for disease proteomics.

Aggregation propensity of the human proteome.

Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints.

From linear genome sequence to three-dimensional organization of the cell nucleus.

A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

Proteomic characterization of HIV-modulated membrane receptors, kinases and signaling proteins involved in novel angiogenic pathways.

Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.

Purinergic adipocyte-macrophage crosstalk promotes degeneration of thermogenic brown adipose tissue.

A chromosomally integrated bacteriophage in invasive meningococci.

Comparative genomics search for losses of long-established genes on the human lineage.

Activation instead of blocking mesolimbic dopaminergic reward circuitry is a preferred modality in the long term treatment of reward deficiency syndrome (RDS): a commentary.