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 27

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

Helicobacter pylori: after the genomes, back to biology.

PMID 12668641 · PMC2193897 · The Journal of experimental medicine · 2003 · 8 claims · 5 setups

Full-text index only

STM screening of 960 H. pylori mutants in gerbils identifies genes required for in vivo colonization

helicobacter diffuse signature-tagged genome yeast
Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

PMID 18485879 · PMC2405818 · Cell · 2008 · 8 claims · 8 setups

Full-text index only

A large-scale retroviral insertional mutagenesis screen identified 10,806 insertion sites implicating over 300 loci in tumorigenesis

p53 tumor tumors computational retroviral linker-mediated flow
Genetic requirement for pneumococcal ear infection.

PMID 18670623 · PMC2593789 · PloS one · 2007 · 7 claims · 8 setups

Full-text index only

STM screening of 5,280 S. pneumoniae ST556 mutants in a chinchilla middle ear infection model identified 169 genes required for ear infection

pneumoniae bioluminescent balb signature-tagged bioluminescent transmission
Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection.

PMID 35072628 · PMC8887901 · eLife · 2022 · 8 claims · 3 setups

Has reproduction · 57

mRNA vaccination induces antibody binding to additional Spike epitopes (NTD and CTD in S1) beyond those seen after mild infection (FP and SH-H in S2)

serum combined phage-dms principal
A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.

PMID 37936069 · PMC10629022 · BMC genomics · 2023 · 6 claims · 5 setups

Has reproduction

The glycosyltransferase gene AsRCOM is the most critical disease-resistance gene against agave purple curl leaf disease, and its overexpression significantly enhances resistance.

agave a.h11648 bulk wgcna qpcr
Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups

Has reproduction · 78

In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.

aeruginosa differentially paired rna-seq tn-seq computational
Use of functional genomics to understand influenza-host interactions.

PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups

Full-text index only

Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques

hela a549 lung texas cdna microarray infection
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
4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.

PMID 33301041 · PMC7708080 · Nucleic acids research · 2020 · 7 claims · 8 setups

Has reproduction · 78

A 4mC orphan MTase (lomA) is present only in the pathogenic (P) clade of Leptospira and methylates CTAG motifs.

interrogans canine syrian smrt bulk rt-qpcr
In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

Has reproduction · 95

icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning
CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

PMID 11556834 · PMC2375081 · British journal of cancer · 2001 · 7 claims · 6 setups

Full-text index only

Germ line CDKN2A mutations were found in 5 of 15 (33.3%) Italian melanoma-prone families, including one novel mutation (P48T) and three known pathogenic mutations (R24P, G101W, N71S)

genomic radiolabelled tig-er u2os sscp protein-protein retroviral
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
The application of genomics to emerging zoonotic viral diseases.

PMID 19855817 · PMC2734983 · PLoS pathogens · 2009 · 8 claims · 8 setups

Full-text index only

High-throughput sequencing, mRNA expression profiling, and SNP microarray analysis enable rapid identification and genomic characterization of emerging zoonotic pathogens and host responses to them.

siv-infected plasmacytoid migratory influenza transcriptional tlr fecal
Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

PMID 19706363 · PMC3525194 · Human genomics · 2009 · 8 claims · 6 setups

Full-text index only

A novel HPV type (HPV-85) was identified and phylogenetically characterized, showing closest relatedness to HPV-70/39/18/45/59 within the A7 genital HPV group

novel hpv gene h5n1 whole-genome intrinsic statistical
HIV-1 Nef binds the DOCK2-ELMO1 complex to activate rac and inhibit lymphocyte chemotaxis.

PMID 14737186 · PMC314466 · PLoS biology · 2004 · 8 claims · 8 setups

Full-text index only

HIV-1 Nef binds the DOCK2-ELMO1 complex (which also contains Rac) in T cells

jurkat hek resting ns1 two-step ni-nta anti-flag
Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

Full-text index only

PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

porcine paec umbilical huvec methyltransferase sds-page fragmentation
Quantitative membrane proteomics reveals new cellular targets of viral immune modulators.

PMID 17238276 · PMC1626102 · PLoS pathogens · 2006 · 8 claims · 8 setups

Full-text index only

SILAC-based quantitative membrane proteomics can identify novel targets of viral immunomodulators in an unbiased manner

hela silac immunoblot flow
Use of modified U1 snRNAs to inhibit HIV-1 replication.

PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups

Full-text index only

U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA

hiv-1 293t hela bioinformatic western reporter
TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

PMID 17526832 · PMC2884950 · Microbiology (Reading, England) · 2007 · 7 claims · 8 setups

Full-text index only

tccP2 is present in 26 of 27 (96.2%) EPEC 2 lineage strains and absent from all 34 EPEC 1 strains tested

clinical pcr-negative representative whole-cell conventional colony locus-specific
Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.

PMID 19014595 · PMC2615443 · Retrovirology · 2008 · 7 claims · 8 setups

Full-text index only

IN mutants V165A, A179P and KR186,7AA in the C-terminal region of the catalytic core domain fail to induce the lethal phenotype in HP16 yeast

saccharomyces hp16 293t cos-7 yeast immunoprecipitation chromatin

Experiments

Helicobacter pylori: after the genomes, back to biology.

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

Genetic requirement for pneumococcal ear infection.

Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection.

A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.

Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

Use of functional genomics to understand influenza-host interactions.

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.

4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.

In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

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

The application of genomics to emerging zoonotic viral diseases.

Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

HIV-1 Nef binds the DOCK2-ELMO1 complex to activate rac and inhibit lymphocyte chemotaxis.

Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

Quantitative membrane proteomics reveals new cellular targets of viral immune modulators.

Use of modified U1 snRNAs to inhibit HIV-1 replication.

TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.