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 369

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Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups

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HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162

monocyte-derived mdm mdms western p24 seldi-tof sds-page
Development of animal models to test the fundamental basis of gene-environment interactions.

PMID 19037209 · PMC2703424 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 8 setups

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Selective breeding for low and high intrinsic aerobic treadmill running capacity produced divergent rat lines (LCR and HCR) that contrast in propensity for complex disease

nih-derived lcr carotid treadmill body maximal
Proteomic profiling of urine identifies specific fragments of SERPINA1 and albumin as biomarkers of preeclampsia.

PMID 18984079 · PMC2679897 · American journal of obstetrics and gynecology · 2008 · 8 claims · 7 setups

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Women with severe preeclampsia present a unique urinary proteomic fingerprint distinguishable from controls.

urine placenta placental seldi-tof tandem spiking
Proteomic analyses associate cystatin B with restricted HIV-1 replication in placental macrophages.

PMID 18951626 · PMC3867668 · Placenta · 2008 · 6 claims · 6 setups

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Placental macrophages support significantly lower HIV-1 replication than monocyte-derived macrophages

placental mdm hiv-1 seldi-tof sds-page
CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

PMID 18950538 · PMC2605473 · BMC bioinformatics · 2008 · 7 claims · 4 setups

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CompMoby identifies cis-regulatory binding sites at both transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factor

embryonic hela novo genome-wide
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

PMID 18940863 · PMC2602776 · Nucleic acids research · 2008 · 7 claims · 4 setups

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A novel Invader assay-based procedure can accurately determine SNP genotypes in trisomic genomic DNA samples in a simple, cost-effective manner

genomic same synthetic invader pyrosequencing hplc
The role of positive selection in determining the molecular cause of species differences in disease.

PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

orthologous omim meta-database panther comparative disease protein-protein
Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

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Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

pooled computational identified additional label-free lspad pathway-associated
The proteogenomic path towards biomarker discovery.

PMID 18764911 · PMC2574627 · Pediatric transplantation · 2008 · 8 claims · 8 setups

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Serum creatinine is a widely used but non-ideal biomarker for renal transplant monitoring because it lacks specificity and sensitivity for graft injury

renal urine breast chronic microarray immunoassay gel
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

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HIV infection of a human T-cell line differentially regulates 18 proteins involved in lipid metabolism.

t-cell identified gel maldi-tof bioinformatics
Human microglial cells synthesize albumin in brain.

PMID 18665237 · PMC2483733 · PloS one · 2008 · 8 claims · 8 setups

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Human microglial cells synthesize albumin de novo in the brain.

hmo6 microglial fetal alzheimer's immunocytochemistry immunohistochemistry tandem
Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

PMID 18588693 · PMC2446391 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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A decision tree built on 10 selected sequence-derived features classifies SAPs as Disease or Polymorphism with 82.6% accuracy and 0.607 MCC in cross-validation.

sap sequence-derived humvar same decision independent greedy
Primase-based whole genome amplification.

PMID 18559358 · PMC2490742 · Nucleic acids research · 2008 · 8 claims · 6 setups

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A primase-based Whole Genome Amplification (pWGA) method was developed using T7 gp4 primase to synthesize primers on-template, removing the requirement for synthetic primers

genomic plasmids circular agarose picogreen dye-terminator
Characterization of genome-wide p53-binding sites upon stress response.

PMID 18474530 · PMC2441782 · Nucleic acids research · 2008 · 7 claims · 7 setups

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Genome-wide ChIP-on-chip identified 1546 high-confidence p53-binding sites upon Actinomycin D treatment in U2OS cells

u2os saos-2 chip-on-chip chip-qpcr western
Spatial separation and bidirectional trafficking of proteins using a multi-functional reporter.

PMID 18384686 · PMC2359743 · BMC cell biology · 2008 · 8 claims · 8 setups

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β1Int-HaloTag fusion protein localizes to the cell membrane in a pattern similar to endogenous β1 integrin, indicating the fusion does not disrupt normal integrin surface expression

hela hek293 live immunocytochemistry live fluorescence
Anesthetics impact the resolution of inflammation.

PMID 18382663 · PMC2268966 · PloS one · 2008 · 8 claims · 8 setups

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Lidocaine delays and blocks key events in the resolution of acute inflammation

peritoneal cell-free zymosan-induced lipid apoptosis
Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

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Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

peripheral blood pooled trio gene quantitative promoter
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
A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

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A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

kidney same identified additional microarray significance fisher's

Experiments

Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

Development of animal models to test the fundamental basis of gene-environment interactions.

Proteomic profiling of urine identifies specific fragments of SERPINA1 and albumin as biomarkers of preeclampsia.

Proteomic analyses associate cystatin B with restricted HIV-1 replication in placental macrophages.

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

The role of positive selection in determining the molecular cause of species differences in disease.

Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

The proteogenomic path towards biomarker discovery.

HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.

Human microglial cells synthesize albumin in brain.

Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

Primase-based whole genome amplification.

Characterization of genome-wide p53-binding sites upon stress response.

Spatial separation and bidirectional trafficking of proteins using a multi-functional reporter.

Anesthetics impact the resolution of inflammation.

Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

Contributions of proteomics to understanding phagosome maturation.

A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.