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 28

System / cell line: infection ✕ Assay: positive ✕ Clear

Tissue plasminogen activator and plasminogen activator inhibitor type 1 gene polymorphism in patients with gastric ulcer complicated with bleeding.

PMID 12589088 · PMC3054991 · Journal of Korean medical science · 2003 · 6 claims · 5 setups

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The t-PA I/D or D/D genotype is significantly associated with duodenal (vs gastric) ulcer location

genomic randomly patients endoscopic allele-specific pcr logistic
Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis.

PMID 18635889 · PMC2556453 · American journal of respiratory and critical care medicine · 2008 · 7 claims · 5 setups

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The TLR1 −7202A/G (rs5743551) G allele is associated with elevated TLR1-mediated cytokine production ex vivo

blood expressing intensive patients tlr-agonist nf-κb surface
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 8 setups

Has reproduction · 89

SARS-CoV-2 infection induces a strong interferon-driven antiviral response in the nasopharynx, with up-regulation of viral sensors, T cell/NK chemokines, and antiviral effectors

nasopharyngeal airway patient-matched swab shotgun gsea biological
Human metapneumovirus, Australia, 2001-2004.

PMID 16965711 · PMC3291208 · Emerging infectious diseases · 2006 · 8 claims · 5 setups

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HMPV had a 7.1% average annual incidence among 10,025 respiratory samples tested over 4 years

nasopharyngeal npa hmpv-positive reverse direct multiplex
Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

PMID 19025632 · PMC2630941 · Virology journal · 2008 · 8 claims · 4 setups

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Twelve gp41 sites (outside the overlapping rev exon2 reading frame) show positive selection conserved across multiple HIV-1 M subtypes/CRFs, making them candidate targets for broadly protective vaccines.

gp41 hiv-1 recombination site-specific comparative
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
A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

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Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

serum plasmids coli pcr oligonucleotide chip
Spotted-fever group Rickettsia in Dermacentor variabilis, Maryland.

PMID 15496254 · PMC3320417 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

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SFG Rickettsia infection prevalence in Maryland D. variabilis was 3.8% (15/392)

dermacentor tick-derived glta field pcr single sequencing
Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

PMID 19889143 · PMC3032083 · Journal of viral hepatitis · 2010 · 7 claims · 8 setups

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O-HBV-associated mutations in PreS/S/polymerase regions likely contribute to undetectable HBsAg by interfering with serologic detection, altering antigen secretion, and/or decreasing replicative fitness

serum hbv full-length o-hbv nested phylogenetic quasispecies
Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.

PMID 17052347 · PMC1622754 · BMC infectious diseases · 2006 · 8 claims · 4 setups

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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

hep-2 archival pneumoniae immunohistochemistry western gel
Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

hiv-1 four simulated population-based maximum bayesian
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 7 claims · 7 setups

Has reproduction

Differential DNA methylation occurs predominantly in intergenic regions and low methylated regions (LMRs), highlighting the role of distal regulatory elements in COVID-19 severity.

nasal aggregated genes differentially whole-genome methylation tiling
Genetic variants of Ehrlichia phagocytophila, Rhode Island and Connecticut.

PMID 11996680 · PMC3369764 · Emerging infectious diseases · 2002 · 7 claims · 6 setups

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All 50 E. phagocytophila-positive samples from Bridgeport, CT (1996-1998) had 16S rRNA sequences identical to the human agent (EP-ha).

ixodes white-footed eastern pcr-positive nested sequencing cloning
The regulation of endocytosis by kinases: cell biology meets genomics.

PMID 16420682 · PMC1414100 · Genome biology · 2005 · 8 claims · 4 setups

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A genome-wide kinase RNAi screen reveals extensive and complex regulation of endocytosis by the human kinome.

hela rnai fluorescent fluorescence
Using DNA microarrays to study host-microbe interactions.

PMID 10998383 · PMC2627958 · Emerging infectious diseases · 2000 · 8 claims · 8 setups

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DNA microarrays can measure transcript levels and detect sequence polymorphisms for every gene simultaneously in microbial genomes

streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene
Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

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PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag
The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

PMID 18778482 · PMC2563025 · Retrovirology · 2008 · 8 claims · 7 setups

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Intra-host nucleotide diversity of the HIV-2 C2V3C3 region increases over the course of chronic infection in most patients

pbmcs clonal env deduced nested maximum-likelihood positive
Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil.

PMID 10081673 · PMC2627691 · Emerging infectious diseases · 1999 · 8 claims · 8 setups

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Among 79 HIV-1 infected patients, 3 (3.8%) had dual infections, 6 (7.6%) had recombinant infections, and 70 (88.6%) had single-subtype infections

pbmc uncultured pcr-amplified aligned rflp heteroduplex nested
Detection of p53 mutations in precancerous gastric tissue.

PMID 14520466 · PMC2394306 · British journal of cancer · 2003 · 8 claims · 6 setups

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p53 mutations can be detected in precancerous gastritis and intestinal metaplasia tissue using the restriction site mutation (RSM) assay

gastric enzyme-resistant gastritis pylori-positive restriction sequencing electron
Concurrent genotyping of Helicobacter pylori virulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA.

PMID 18842150 · PMC2577186 · BMC microbiology · 2008 · 7 claims · 8 setups

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MDA-amplified DNA from minute gastric biopsy specimens enables concurrent PCR-based genotyping of bacterial (H. pylori) and human host genes from a single DNA source

mda-amplified pylori-positive multiplex pyrosequencing pcr

Experiments

Tissue plasminogen activator and plasminogen activator inhibitor type 1 gene polymorphism in patients with gastric ulcer complicated with bleeding.

Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis.

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

Human metapneumovirus, Australia, 2001-2004.

Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

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

A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

Spotted-fever group Rickettsia in Dermacentor variabilis, Maryland.

Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.

Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

Genetic variants of Ehrlichia phagocytophila, Rhode Island and Connecticut.

The regulation of endocytosis by kinases: cell biology meets genomics.

Using DNA microarrays to study host-microbe interactions.

Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil.

Detection of p53 mutations in precancerous gastric tissue.

Concurrent genotyping of Helicobacter pylori virulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA.