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).

• Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

  PMID 20018283 · PMC2845297 · Atherosclerosis · 2010 · 8 claims · 7 setups

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  The ADIPOQ locus is the only major gene locus for plasma adiponectin, reaching genome-wide significance in combined and sex-stratified analyses

  population-based cohorts gwa plasma genome-wide replication candidate

• Multilocus analysis of SNP and metabolic data within a given pathway.

  PMID 16412218 · PMC1382210 · BMC genomics · 2006 · 8 claims · 7 setups

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  The combinatorial partitioning method (CPM) with optimal thresholds can identify SNPs associated with quantitative metabolite levels rather than only categorical traits.

  healthy plasma genomic chi-square combinatorial leave-one-out

• Metabolic profiling during malaria reveals the role of the aryl hydrocarbon receptor in regulating kidney injury.

  PMID 33021470 · PMC7538157 · eLife · 2020 · 8 claims · 8 setups

  Has reproduction · 62

  Plasma AHR ligands derived from heme metabolism (biliverdin, bilirubin) and tryptophan/kynurenine pathway metabolites increase during acute Pc malaria in mice and acute cerebral malaria in humans

  c57bl pediatric littermate untargeted targeted bilirubin

• A biomarker panel for peripheral arterial disease.

  PMID 18687758 · PMC3133945 · Vascular medicine (London, England) · 2008 · 7 claims · 6 setups

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  β2-microglobulin (β2M) and cystatin C had the highest correlation with ABI among all plasma markers tested, higher than age, smoking, or diabetes status

  plasma fasting subjects biomarker nephelometric clinical ankle-brachial

• The cold-induced lipokine 12,13-diHOME promotes fatty acid transport into brown adipose tissue.

  PMID 28346411 · PMC5699924 · Nature medicine · 2017 · 8 claims · 8 setups

  Has reproduction · 78

  12,13-diHOME is a cold-induced lipokine that stimulates BAT activity

  plasma bat serum mice lc-ms correlation 18f-fdg

• Reduced 5-FU clearance in a patient with low DPD activity due to heterozygosity for a mutant allele of the DPYD gene.

  PMID 11953843 · PMC2364178 · British journal of cancer · 2002 · 7 claims · 5 setups

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  Heterozygosity for the IVS14+1G>A DPYD splice-site mutation is associated with markedly reduced 5-FU clearance and severe 5-FU toxicity in the index patient.

  plasma peripheral pbm genomic reversed-phase pharmacokinetic dpd

• HIV-1 evolution following transmission to an HLA-B*5801-positive patient.

  PMID 19909081 · PMC2779566 · The Journal of infectious diseases · 2009 · 8 claims · 8 setups

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  Multiple escape mutations developed rapidly in HLA-B*5801-restricted epitopes in Gag, Nef, and Pol following transmission

  plasma transmitter subject genomic full-length population ifn-γ

• Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome.

  PMID 19722698 · PMC2783519 · Journal of proteome research · 2009 · 7 claims · 6 setups

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  Tandem IgY7-SuperMix separation nearly doubles overall proteome coverage compared to IgY7 flow-through alone (523 vs 263 confidently identified proteins)

  plasma identified lc-ms sds-page spike-in

• HIV-1 sequence evolution in vivo after superinfection with three viral strains.

  PMID 17716368 · PMC2020475 · Retrovirology · 2007 · 8 claims · 8 setups

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  gag and env-V3 nucleotide evolution follows a similar pattern in all three strains: low substitution rate in the first 2-3 years of infection, then an increase driven mainly by synonymous substitutions

  blood seminal pbmcs biological strain-specific bulk in-house

• New perspectives on an old disease: proteomics in cancer research.

  PMID 17472735 · PMC1895992 · Genome biology · 2007 · 8 claims · 8 setups

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  The HUPO Plasma Proteome Project has catalogued over 3,020 non-redundant gene products (>7,000 proteins/isoforms) in human plasma, many originating from tissues/organs rather than being plasma-intrinsic.

  plasma breast tumor genetically shotgun proteomics glycopeptide

• LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise.

  PMID 17386085 · PMC1847688 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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  LIMPIC is a computational method for detecting protein peaks from linear-mode MALDI-TOF-MS data using background noise reduction and baseline removal followed by non-uniform threshold peak detection and multi-spectra detection-rate classification.

  in-vitro plasma maldi-tof signal baseline

• A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

  PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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  GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

  plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion

• Fibrinogen Yecheon: congenital dysfibrinogenemia with gamma methionine-310 to threonine substitution.

  PMID 19949684 · PMC2775876 · Journal of Korean medical science · 2009 · 7 claims · 6 setups

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  A novel de novo heterozygous FGG mutation (c.1007T>C) causing γ Met310Thr substitution was identified in a Korean patient, named 'fibrinogen Yecheon'

  plasma coagulation fibrinogen pcr

• A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation.

  PMID 19888438 · PMC2771280 · Journal of biomedicine & biotechnology · 2010 · 6 claims · 6 setups

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  iTRAQ labelling combined with OFFGEL fractionation improves proteome coverage of human plasma compared to iTRAQ alone or no iTRAQ

  pooled plasma prefractionated immunodepleted itraq 1-dimensional fluorescence-based

• Cold-Induced Lipoprotein Clearance in Cyp7b1-Deficient Mice.

  PMID 35478959 · PMC9038073 · Frontiers in cell and developmental biology · 2022 · 7 claims · 8 setups

  Has reproduction · 83

  Cyp7b1 deficiency blunts cold-induced hepatic Cyp7b1 upregulation and plasma bile acid synthesis

  liver plasma interscapular bat qrt-pcr western bile

• Brown fat activation reduces hypercholesterolaemia and protects from atherosclerosis development.

  PMID 25754609 · PMC4366535 · Nature communications · 2015 · 7 claims · 8 setups

  Has reproduction

  β3-AR agonist-mediated BAT activation reduces plasma triglycerides and cholesterol and protects against atherosclerosis development in APOE*3-Leiden.CETP mice.

  e3l.cetp interscapular liver aortic indirect histology plasma

• Perspectives of targeted mass spectrometry for protein biomarker verification.

  PMID 19818677 · PMC2795387 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  SRM/MRM mass spectrometry can quantify targeted proteotypic peptides as surrogates for candidate biomarker proteins in complex plasma samples

  proteins standard plasma sera srm multiplexed immunoaffinity-srm

• Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

  PMID 15502245 · PMC3839274 · Disease markers · 2004 · 7 claims · 3 setups

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  Standardization of specimen collection, handling, storage, and choice of serum vs. plasma/anticoagulant is essential for comparable proteomic biomarker discovery.

  plasma ppp reference identification quantitative specimen

• Contributions of proteomics to understanding phagosome maturation.

  PMID 18331591 · PMC2613258 · Cellular microbiology · 2008 · 8 claims · 8 setups

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  Proteomic studies across many species have identified hundreds of proteins associated with phagosomes, revealing conserved functional classes (vATPase subunits, GTPases, hydrolases, SNAREs, Rabs, cytoskeletal proteins).

  macrophage dictyostelium drosophila entamoeba quantitative 2dge prefractionation

• On the holobiont 'predictome' of immunocompetence in pigs.

  PMID 37127575 · PMC10150480 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 8 setups

  Has reproduction · 40

  Holobiont (combined genotype + microbiome) models performed better than partial models (genotype-only or microbiome-only) overall

  duroc fecal plasma serum snp 16s immunoglobulin