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 17

System / cell line: genomic ✕ Assay: polymerase ✕ Clear

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
Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.

PMID 34551434 · PMC8501979 · Nucleic acids research · 2021 · 6 claims · 4 setups

Has reproduction · 75

rNTP incorporation is preferentially found on the leading strand in yeast cells expressing wild-type replicative DNA polymerases

saccharomyces model ribose-seq emriboseq rhii-hyden-seq
High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

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WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

genomic whole-genome same call snp technical genotype
Filtering high-throughput protein-protein interaction data using a combination of genomic features.

PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

saccharomyces bank caenorhabditis homo yeast mass naive
Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector.

PMID 17317684 · PMC1874629 · Nucleic acids research · 2007 · 7 claims · 7 setups

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Gene-Collector is a method for multiplex nucleic acid amplification that specifically circularizes only correctly paired (cognate) PCR primer products on a Collector probe, degrading non-cognate artifacts by exonuclease treatment.

genomic multiplex circularized circular multiplex probe-guided exonuclease
Systems biology of gene regulation fulfills its promise.

PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups

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Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.

unspecified embryonic five yeast chip-chip chip-pet computational
From linear genome sequence to three-dimensional organization of the cell nucleus.

PMID 12620101 · PMC153456 · Genome biology · 2003 · 8 claims · 8 setups

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Chromosome conformation capture (3C) can quantify in vivo physical interaction frequencies between genomic loci by crosslinking, digestion, and intramolecular ligation followed by PCR

saccharomyces mitotic nucleoplasm hela chromosome translocation stretched
Human PMS2 deficiency is associated with impaired immunoglobulin class switch recombination.

PMID 18824584 · PMC2571921 · The Journal of experimental medicine · 2008 · 8 claims · 8 setups

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Homozygous deleterious PMS2 mutations are associated with a B cell-intrinsic CSR deficiency in three patients

pbls fibroblasts cd19+ rt-pcr genomic western
Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

mcf7 arabidopsis specified different chip-seq microarray array-based
p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

PMID 11875738 · PMC2375302 · British journal of cancer · 2002 · 8 claims · 6 setups

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p53 status can be reliably determined by yeast functional assay from single frozen sections of trucut biopsies

frozen plasmids single extracted p53 sanger laser
Differential analysis for high density tiling microarray data.

PMID 17892592 · PMC2231405 · BMC bioinformatics · 2007 · 8 claims · 6 setups

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gSAM, a generalized extension of Significance Analysis of Microarrays (SAM), uses a piece-wise function to segment genome-wide differential response by protein-coding vs non-coding regions and by 5' vs 3' vs intra-genic bias within genes, rather than treating a gene as an atomic unit.

hl60 profiling chip-on-chip
Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

PMID 20021669 · PMC2803178 · BMC genetics · 2009 · 8 claims · 8 setups

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WGA DNA from archived serum samples produced low genotyping call rates and is unsuitable for high-resolution genotyping on SNP 6.0 arrays

wga non-amplified archived serum-derived snp purification whole-genome
Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

PMID 19133980 · PMC4303606 · British journal of haematology · 2009 · 7 claims · 6 setups

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Downregulation of GR mRNA in the resistant myeloma cell line is caused by a block to transcriptional elongation within intron B of the GR gene

mm.1s pcr demethylating quantitative
Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.

PMID 22119442 · PMC3250924 · Cell · 2011 · 8 claims · 8 setups

Has reproduction · 68

viRNA-mediated silencing of the FR1gfp Flock House virus is transmitted to RNAi-deficient (rde-1 or rde-4 homozygous) progeny and persists for many ensuing generations, i.e. an acquired antiviral trait is inherited.

transgenic elegans four gfp genetic template-independence
Systems biology and the host response to viral infection.

PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

lung cd4 rhesus kshv microarray quantitative genomic
CoMoDis: composite motif discovery in mammalian genomes.

PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups

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CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif

ncbi35 gata-1 gene imr90 computational microarray seed-motif-anchored
Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

PMID 19811662 · PMC2766370 · Molecular cancer · 2009 · 7 claims · 6 setups

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LCN-HRM enables detection and sequencing-based characterisation of low-level mutations that are undetectable by direct sequencing alone

hct116 ffpe genomic tx84 dideoxynucleotide high lcn-hrm

Experiments

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

Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.

High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector.

Systems biology of gene regulation fulfills its promise.

From linear genome sequence to three-dimensional organization of the cell nucleus.

Human PMS2 deficiency is associated with impaired immunoglobulin class switch recombination.

Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

Differential analysis for high density tiling microarray data.

Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.

Systems biology and the host response to viral infection.

CoMoDis: composite motif discovery in mammalian genomes.

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.