ArticleGenome research2011
Biome representational in silico karyotyping.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed, 20 citations in OpenAlex.
- Paucibacterial Microbiome and Resident DNA Virome of the Healthy Conjunctiva.Investigative ophthalmology & visual science · 2016Trial
- Association of Seasonal Hyperacute Panuveitis Syndrome withOphthalmology science · 2026Article
- Findings and methodologies in oral phageome research: a systematic review.Journal of oral microbiology · 2024Review
- Methodologic Considerations for Studying the Ocular Surface Microbiome.Ophthalmology science · 2023Review
- Molecular Diagnostics for Ocular Infectious Diseases: LXXVIII Edward Jackson Memorial Lecture.American journal of ophthalmology · 2022Review
- Elevated levels of Merkel cell polyoma virus in the anophthalmic conjunctiva.Scientific reports · 2021Article
- Comprehensive pathogen detection for ocular infections.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2021Article
- Prognostic Utility of Whole-Genome Sequencing and Polymerase Chain Reaction Tests of Ocular Fluids in Postprocedural Endophthalmitis.American journal of ophthalmology · 2020Article
- Potential Role of Ocular Microbiome, Host Genotype, Tear Cytokines, and Environmental Factors in Corneal Infiltrative Events in Contact Lens Wearers.Investigative ophthalmology & visual science · 2018Article
- Emerging techniques for pathogen discovery in endophthalmitis.Current opinion in ophthalmology · 2015Review
- Identification of torque teno virus in culture-negative endophthalmitis by representational deep DNA sequencing.Ophthalmology · 2015Observational
- Does the microbiome play a causal role in spondyloarthritis?Clinical rheumatology · 2014Review
- Article
- Role of molecular diagnostics in ocular microbiology.Current ophthalmology reports · 2013Article
- Microsporidia and Acanthamoeba: the role of emerging corneal pathogens.Eye (London, England) · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
Metagenomic characterization of complex biomes remains challenging. Here we describe a modification of digital karyotyping-biome representational in silico karyotyping (BRISK)-as a general technique for analyzing a defined representation of all DNA present in a sample. BRISK utilizes a Type IIB DNA restriction enzyme to create a defined representation of 27-mer DNAs in a sample. Massively parallel sequencing of this representation allows for construction of high-resolution karyotypes and identification of multiple species within a biome. Application to normal human tissue demonstrated linear recovery of tags by chromosome. We apply this technique to the biome of the oral mucosa and find that greater than 25% of recovered DNA is nonhuman. DNA from 41 microbial species could be identified from oral mucosa of two subjects. Of recovered nonhuman sequences, fewer than 30% are currently annotated. We characterized seven prevalent unknown sequences by chromosome walking and find these represent novel microbial sequences including two likely derived from novel phage genomes. Application of BRISK to archival tissue from a nasopharyngeal carcinoma resulted in identification of Epstein-Barr virus infection. These results suggest that BRISK is a powerful technique for the analysis of complex microbiomes and potentially for pathogen discovery.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.