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 47

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

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

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

Full-text index only

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
Human metapneumovirus, Australia, 2001-2004.

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

Full-text index only

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

nasopharyngeal npa hmpv-positive reverse direct multiplex
Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.

PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups

Has reproduction · 64

A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs

peripheral genome blood bulk illumina ion
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

Full-text index only

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
Emergence of recombinant forms of HIV: dynamics and scaling.

PMID 17967052 · PMC2041978 · PLoS computational biology · 2007 · 7 claims · 5 setups

Full-text index only

A detailed mathematical model incorporating multiple cell infections and recombination quantitatively captures experimental observations of recombinant HIV emergence dynamics in vitro

cd4+ scid-hu splenocytes computational single-round replication-competent proviral
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

Has reproduction · 71

TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

blood cynomolgus external gene differential principal
Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups

Has reproduction · 75

RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.

pbmcs pbmc aligned bulk read transcript
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

Full-text index only

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
Early days: genomics and human responses to infection.

PMID 16679048 · PMC7108404 · Current opinion in microbiology · 2006 · 8 claims · 8 setups

Full-text index only

DNA microarray-based transcript profiling of primate/human responses to infection has begun to yield new insights into host-pathogen interactions but is limited by unresolved methodological challenges.

peripheral liver gastric brain microarray
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.

PMID 34601390 · PMC8483812 · Computers in biology and medicine · 2021 · 8 claims · 8 setups

Has reproduction · 69

COVID-19 and neurological diseases (NDs) share pathophysiological connections that influence disease progression and severity

peripheral hippocampal spinal peritumoral microarray protein-protein
Lack of Toll-like receptor 4 and 2 polymorphisms in Korean patients with bacteremia.

PMID 17179672 · PMC2721950 · Journal of Korean medical science · 2006 · 7 claims · 4 setups

Full-text index only

No TLR4 Asp299Gly or Thr399Ile polymorphisms were detected in either bacteremia patients or healthy volunteers

peripheral pcr bacteremia pcr-rflp sequencing blood
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

Full-text index only

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

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

Full-text index only

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
Tipping the balance in autoimmune disease.

PMID 18001485 · PMC2246277 · Genome biology · 2007 · 8 claims · 8 setups

Full-text index only

Human autoimmune diseases are fundamentally diseases of immune dysfunction, evidenced by predisposing genes being immune-function genes, some shared and some unique across MS, T1D, SLE, CD and RA

patients congenic nzm2410 mrl-lpr snp induced genetic
Mitochondrial D-loop mutations and deletion profiles of cancerous and noncancerous liver tissue in hepatitis B virus-infected liver.

PMID 15785740 · PMC2361973 · British journal of cancer · 2005 · 8 claims · 2 setups

Full-text index only

D-loop mutation frequency is significantly higher in both noncancerous and tumour liver tissue of HCC/HBV patients than in normal control liver

liver pcr
Application of ProteinChip array profiling in serum biomarker discovery for patients suffering from severe acute respiratory syndrome.

PMID 18220240 · PMC7120874 · Methods in molecular biology (Clifton, N.J.) · 2007 · 8 claims · 5 setups

Full-text index only

SELDI-TOF-MS ProteinChip array profiling of serum can identify differentially expressed protein biomarkers in SARS-CoV infected patients versus controls.

serum sars seldi-tof-ms ion serial
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

Full-text index only

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
Comparative analysis of the tear protein profile in mycotic keratitis patients.

PMID 18385783 · PMC2268856 · Molecular vision · 2008 · 8 claims · 5 setups

Full-text index only

A glutaredoxin-related protein is expressed only in the tears of fungal keratitis patients and is absent in control tears.

pooled in-gel peptide 2de two-dimensional maldi-tof post
Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

PMID 19903332 · PMC3091321 · Genome biology · 2009 · 6 claims · 5 setups

Full-text index only

A candidate 37-transcript diagnostic signature distinguishes septicemic melioidosis from sepsis caused by other organisms with 100% accuracy in the training set and 78%/80% accuracy in two independent validation sets

blood whole-genome unsupervised class
Gene expression profiles of HIV-1-infected glia and brain: toward better understanding of the role of astrocytes in HIV-1-associated neurocognitive disorders.

PMID 19697136 · PMC3107560 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 6 setups

Full-text index only

Astrocyte gene expression dysregulation resulting from HIV-1 exposure may contribute to HIV-1 neuropathogenesis

fetal astrocytes brain macaque rapid microarray correlational

Experiments

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

Human metapneumovirus, Australia, 2001-2004.

Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.

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

Emergence of recombinant forms of HIV: dynamics and scaling.

Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

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.

Early days: genomics and human responses to infection.

Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.

Lack of Toll-like receptor 4 and 2 polymorphisms in Korean patients with bacteremia.

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

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

Tipping the balance in autoimmune disease.

Mitochondrial D-loop mutations and deletion profiles of cancerous and noncancerous liver tissue in hepatitis B virus-infected liver.

Application of ProteinChip array profiling in serum biomarker discovery for patients suffering from severe acute respiratory syndrome.

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.

Comparative analysis of the tear protein profile in mycotic keratitis patients.

Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

Gene expression profiles of HIV-1-infected glia and brain: toward better understanding of the role of astrocytes in HIV-1-associated neurocognitive disorders.