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 22

System / cell line: e.g ✕ Assay: viral ✕ Clear

The application of genomics to emerging zoonotic viral diseases.

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

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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
The VIZIER project: preparedness against pathogenic RNA viruses.

PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups

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Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.

viruses virus coli soluble large-scale bioinformatic recombinant
Genomic sequencing of the severe acute respiratory syndrome-coronavirus.

PMID 16916263 · PMC7121524 · Methods in molecular biology (Clifton, N.J.) · 2006 · 7 claims · 7 setups

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PCR-based amplification and direct sequencing of SARS-CoV genome fragments is feasible from uncultured clinical specimens (serum, nasopharyngeal aspirate, stool), avoiding culture-derived artifacts and biohazard risk.

sars-cov extracted cdna pcr viral reverse real-time
Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

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CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

sputum phage metagenomes inferred metagenomic functional diversity
Structural genomics and drug discovery.

PMID 17488474 · PMC3822824 · Journal of cellular and molecular medicine · 2007 · 8 claims · 8 setups

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Membrane proteins represent ~70% of current drug targets but only just over 100 high-resolution structures exist for them, versus >30,000 total structures in public databases dominated by soluble proteins.

coli emre pichia sf9 cell-free bacterial inclusion
International research networks in viral structural proteomics: again, lessons from SARS.

PMID 18054092 · PMC2793675 · Antiviral research · 2008 · 8 claims · 8 setups

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International research networks (SPINE, VIZIER, FSPS, SEPSDA, SARS-DTV) coordinated a global effort to structurally characterize the SARS-CoV proteome

sars-cov x-ray nmr genome
Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups

Has reproduction · 88

Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life

zymo bacterial reference shotgun comparative reference
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.

PMID 35804320 · PMC9264741 · BMC bioinformatics · 2022 · 8 claims · 8 setups

Has reproduction · 99

getSequenceInfo (gSeqI) allows programmatic (CLI) or GUI-based retrieval of sequence data and metadata from GenBank, RefSeq, and ENA across Linux, MacOS, and Windows.

genome complete same coronavirus nuclescore resistance mlst
RNA interference in functional genomics and medicine.

PMID 12808314 · PMC3055057 · Journal of Korean medical science · 2003 · 8 claims · 7 setups

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RNAi is sequence-specific gene silencing induced by double-stranded RNA and is mediated by ~22-nt siRNAs generated from long dsRNA by the RNase III enzyme Dicer.

caenorhabditis drosophila mammalian postnatal dsrna biochemical synthetic
Technical challenges in using human induced pluripotent stem cells to model disease.

PMID 19951687 · PMC2921621 · Cell stem cell · 2009 · 8 claims · 8 setups

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hiPSCs generated from patient somatic cells (skin, blood) can be differentiated into disease-relevant cell types to model disease pathogenesis in vitro

ipscs humanized hemophilia parkinsonian tetraploid transplantation neuronal
The role of genomics in tracking the evolution of influenza A virus.

PMID 19855818 · PMC2739293 · PLoS pathogens · 2009 · 8 claims · 5 setups

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Antigenic drift, driven by selection for amino acid changes in exposed hemagglutinin epitope sites, is the main mechanism by which influenza A evades pre-existing immunity between pandemics.

hemagglutinin influenza ferrets nonsynonymous antigenic whole-genome
Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups

Has reproduction · 100

A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity

n×m common independent viral blood gene random
The role of genomics in the identification, prediction, and prevention of biological threats.

PMID 19855827 · PMC2757898 · PLoS biology · 2009 · 8 claims · 5 setups

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Genomics should be used proactively, not just reactively, to build biopreparedness against biological threats

bacillus escherichia sars pandemic whole-genome pangenomic low-resolution
Discovering the phylodynamics of RNA viruses.

PMID 19855824 · PMC2756585 · PLoS computational biology · 2009 · 8 claims · 8 setups

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A comprehensive 'discovery phase' integrating ecological and evolutionary dynamics of RNA viruses across scales is needed to achieve a full phylodynamic understanding

h3n2 influenza avian foot-and-mouth bayesian phylogenetic whole-genome
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.

PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups

Has reproduction · 68

A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.

hek293 coli dual genome-wide western
The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.

PMID 35371105 · PMC8964954 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 50

HCV E1E2 glycoproteins, and more so E2, down-modulate HIV-1 LTR activation in 293T, TZM-bl and Huh7 cells

293t tzm-bl tzm-bl-e1e2 hiv-1 pseudo-typed transcriptomic
Use of functional genomics to understand influenza-host interactions.

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

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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
Systems biology approaches for the study of multiple sclerosis.

PMID 18505469 · PMC3865652 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

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The MHC locus on chromosome 6p21 is the strongest genetic region linked to MS susceptibility.

patients lesion osteopontin monocyte-depleted genetic large-scale gene
Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

PMID 18258114 · PMC2600181 · Emerging infectious diseases · 2008 · 8 claims · 7 setups

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The nonstructural genes, especially NS5, are the most variable regions between highly and less neuroinvasive lineage 2 WNV strains

lineage mice patients complete phylogenetic nucleotide
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

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

fetal astrocytes brain macaque rapid microarray correlational

Experiments

The application of genomics to emerging zoonotic viral diseases.

The VIZIER project: preparedness against pathogenic RNA viruses.

Genomic sequencing of the severe acute respiratory syndrome-coronavirus.

Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

Structural genomics and drug discovery.

International research networks in viral structural proteomics: again, lessons from SARS.

Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.

RNA interference in functional genomics and medicine.

Technical challenges in using human induced pluripotent stem cells to model disease.

The role of genomics in tracking the evolution of influenza A virus.

Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

The role of genomics in the identification, prediction, and prevention of biological threats.

Discovering the phylodynamics of RNA viruses.

Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.

The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.

Use of functional genomics to understand influenza-host interactions.

Systems biology approaches for the study of multiple sclerosis.

Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

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