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 71

Assay: antigen ✕ Clear

Autoantibody profiling for the study and treatment of autoimmune disease.

PMID 12223102 · PMC128938 · Arthritis research · 2002 · 8 claims · 8 setups

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Custom-fabricated antigen microarrays (spotted on poly-L-lysine-coated glass slides) enable multiplex profiling of autoantibody responses in autoimmune disease sera.

serum antigen-antibody antigens fetal spotted elisa microarray
SePaCS--a web-based application for classification of seroreactivity profiles.

PMID 17478503 · PMC1933220 · Nucleic acids research · 2007 · 8 claims · 4 setups

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SePaCS is a freely available web-based tool that trains and applies multiple classification methods (4 Naive Bayes variants, SVM with RBF kernel, LDA, DLDA) to seroreactivity profiles and outputs results as a summary table plus a detailed PDF report

blood computational seroreactivity supervised mutual
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
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
Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study.

PMID 18205922 · PMC2374452 · Arthritis research & therapy · 2008 · 7 claims · 4 setups

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A standardized 3D in vitro alginate bead model of chondrocytes stimulated with synovial fibroblast supernatants can be used to profile RA-related cartilage destruction genes

sv40 articular differentially antibody-based oligonucleotide real-time
Molecular cloning and characterisation of the RESA gene, a marker of genetic diversity of Plasmodium falciparum.

PMID 19816792 · PMC2900597 · Molecular biology reports · 2010 · 8 claims · 8 setups

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RESA was cloned from a P. falciparum Dd2 expression library screened with human immune sera, yielding a 1,336 bp insert with a 936 bp ORF encoding a 317-aa protein.

falciparum falciparum-infected coli sera cdna sequencing pcr
Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers.

PMID 15502247 · PMC3839398 · Disease markers · 2004 · 8 claims · 8 setups

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Proteomics approaches (2D Western blot, protein microarray, multiplex ELISA) can identify tumor antigen-directed autoantibodies as candidate cancer biomarkers

lung pancreatic hepatocellular renal gel microarray multiplex
Toward the use of genomics to study microevolutionary change in bacteria.

PMID 19855823 · PMC2756242 · PLoS genetics · 2009 · 7 claims · 5 setups

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The clonal population structure of bacteria, combined with occasional DNA import, provides a powerful context for identifying genetic bases of adaptive phenotypes via association studies.

neisseria campylobacter helicobacter sequence multilocus phylogeny-based
Multiple genetic alterations cause frequent and heterogeneous human histocompatibility leukocyte antigen class I loss in cervical cancer.

PMID 10727458 · PMC2193119 · The Journal of experimental medicine · 2000 · 8 claims · 8 setups

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Tumor-associated HLA class I alterations were present in 90% of cervical cancer lesions tested

cervical frozen genomic peripheral multiparameter flow immunohistochemistry
From Pasteur to genomics: progress and challenges in infectious diseases.

PMID 15516917 · PMC7096024 · Nature medicine · 2004 · 8 claims · 8 setups

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Genomic sequencing has revealed the blueprint of most pathogens, enabling new diagnostics, therapeutics and vaccines including for previously uncultivable agents.

bacterial neisseria sars hiv-infected whole-genome reverse nucleic
HIT: a versatile proteomics platform for multianalyte phenotyping of cytokines, intracellular proteins and surface molecules.

PMID 18849997 · PMC3334282 · Nature medicine · 2008 · 8 claims · 8 setups

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HIT uses oligonucleotide-tagged (Fab- or mSA-conjugated) antibodies, T7 polymerase amplification, and DNA microarray hybridization to indirectly measure multiple analytes in a fluid-phase multiplex format

hsp70-coated hsp70 secreted jurkat fluid-phase multiplex hit
Novel approaches for identifying target antigens of autoreactive human B and T cells.

PMID 19763575 · PMC2845891 · Seminars in immunopathology · 2009 · 8 claims · 8 setups

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CD8+ T cells infiltrating MS brain and IM muscle tissue show clonal expansions consistent with antigen-driven selection

muscle brain morphologically autopsy cdr3-spectratyping single-cell immunohistochemistry
Detection of an Ala601Thr mutation of plasminogen gene in 3 out of 36 Korean patients with deep vein thrombosis.

PMID 12692411 · PMC3055032 · Journal of Korean medical science · 2003 · 7 claims · 3 setups

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Dysplasminogenemia was identified in 3 of 36 (8.3%) unrelated Korean DVT patients.

plasma genomic amidolytic immunoturbidimetric pcr
Biocomputing enters its adolescence.

PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

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A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

bank antibody-antigen yeast genome protein-protein empirical integrative
Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PMID 16519801 · PMC1421398 · BMC biotechnology · 2006 · 8 claims · 8 setups

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The Creator Splice system (5' intron splicing) significantly increases protein expression levels compared to the standard Creator system

hek293t mammalian coli vector immunoblot fluorescence bacterial
Late onset thrombosis in a case of severe protein S deficiency due to compound heterozygosity for PROS1 mutations.

PMID 18433462 · PMC2632602 · Journal of thrombosis and haemostasis : JTH · 2008 · 6 claims · 6 setups

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A novel 14 bp deletion in intervening sequence L (putative branch point of intron L), which likely impairs PROS1 pre-mRNA splicing, was found in all family members with low free protein S.

plasma genomic apc free ps-direct
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
Serum S100A6 concentration predicts peritoneal tumor burden in mice with epithelial ovarian cancer and is associated with advanced stage in patients.

PMID 19888321 · PMC2765613 · PloS one · 2009 · 8 claims · 8 setups

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Serum S100A6 concentration correlates with peritoneal tumor burden in a mouse OVCA xenograft model, based on inverse regression calibration against bioluminescent imaging data.

serum skov-3 pooled ovca lc-ms antigen whole-animal
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 41

Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative
De novo identification of CD4(+) T cell epitopes.

PMID 38658646 · PMC11093748 · Nature methods · 2024 · 7 claims · 8 setups

Has reproduction · 83

SABR-IIs (chimeric receptors linking a covalently attached peptide-MHC-II to CD28-CD3ζ signaling domains) present epitopes to CD4+ T cells and induce a readable NFAT-GFP/CD69 signal upon cognate TCR recognition

nfat-gfp hla-dq8 5kc daudi nfat-gfp co-incubation species

Experiments

Autoantibody profiling for the study and treatment of autoimmune disease.

SePaCS--a web-based application for classification of seroreactivity profiles.

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

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

Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study.

Molecular cloning and characterisation of the RESA gene, a marker of genetic diversity of Plasmodium falciparum.

Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers.

Toward the use of genomics to study microevolutionary change in bacteria.

Multiple genetic alterations cause frequent and heterogeneous human histocompatibility leukocyte antigen class I loss in cervical cancer.

From Pasteur to genomics: progress and challenges in infectious diseases.

HIT: a versatile proteomics platform for multianalyte phenotyping of cytokines, intracellular proteins and surface molecules.

Novel approaches for identifying target antigens of autoreactive human B and T cells.

Detection of an Ala601Thr mutation of plasminogen gene in 3 out of 36 Korean patients with deep vein thrombosis.

Biocomputing enters its adolescence.

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

Late onset thrombosis in a case of severe protein S deficiency due to compound heterozygosity for PROS1 mutations.

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

Serum S100A6 concentration predicts peritoneal tumor burden in mice with epithelial ovarian cancer and is associated with advanced stage in patients.

RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

De novo identification of CD4(+) T cell epitopes.