ArticlePLoS computational biology2007
Comprehensive DNA signature discovery and validation.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed, 78 citations in OpenAlex.
- Seqwin: ultrafast identification of signature sequences in microbial genomes.Bioinformatics (Oxford, England) · 2026Article
- Seqwin: Ultrafast identification of signature sequences in microbial genomes.bioRxiv : the preprint server for biology · 2025Article
- Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity.PloS one · 2024Article
- Multicenter Preparedness Exercise Enables Rapid Development of Cluster-Specific PCR-Based Screening Assays from Bacterial Genomic Data.Journal of clinical microbiology · 2023Article
- Single Nucleotide Polymorphism-Based Real-Time PCR Screening Assay for Rapid Tracking of Bacterial Infection Clusters To Complement Whole-Genome Sequencing Efforts during Outbreak Investigations.Microbiology spectrum · 2022Article
- Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.Nature biotechnology · 2022Article
- End-point RT-PCR based on a conservation landscape for SARS-COV-2 detection.Scientific reports · 2022Article
- Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary RegulatedMicroorganisms · 2021Review
- Development of qPCR Detection Assay for Potato PathogenPlants (Basel, Switzerland) · 2021Article
- Comparative genome analysis using sample-specific string detection in accurate long reads.Bioinformatics advances · 2021Article
- On DNA Signatures, Their Dual-Use Potential for GMO Counterfeiting, and a Cyber-Based Security Solution.Frontiers in bioengineering and biotechnology · 2019Article
- Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases.BMC veterinary research · 2017Article
- Validation and Application of a Real-time PCR Protocol for the Specific Detection and Quantification of Clavibacter michiganensis subsp. sepedonicus in Potato.The plant pathology journal · 2015Article
- DNA Sequence Signatures for Rapid Detection of Six Target Bacterial Pathogens Using PCR Assays.Microbiology insights · 2015Article
- An algorithm of discovering signatures from DNA databases on a computer cluster.BMC bioinformatics · 2014Article
- Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR.BMC microbiology · 2014Article
- Microbial genomic taxonomy.BMC genomics · 2013Article
- Identification of DNA signatures suitable for use in development of real-time PCR assays by whole-genome sequence approaches: use of Streptococcus pyogenes in a pilot study.Journal of clinical microbiology · 2012Article
- Identification of a pheA gene associated with Streptococcus mitis by using suppression subtractive hybridization.Applied and environmental microbiology · 2012Article
- Biodefense Oriented Genomic-Based Pathogen Classification Systems: Challenges and Opportunities.Journal of bioterrorism & biodefense · 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
9 authors at 3 institutions in 1 country.
Funding
Abstract
DNA signatures are nucleotide sequences that can be used to detect the presence of an organism and to distinguish that organism from all other species. Here we describe Insignia, a new, comprehensive system for the rapid identification of signatures in the genomes of bacteria and viruses. With the availability of hundreds of complete bacterial and viral genome sequences, it is now possible to use computational methods to identify signature sequences in all of these species, and to use these signatures as the basis for diagnostic assays to detect and genotype microbes in both environmental and clinical samples. The success of such assays critically depends on the methods used to identify signatures that properly differentiate between the target genomes and the sample background. We have used Insignia to compute accurate signatures for most bacterial genomes and made them available through our Web site. A sample of these signatures has been successfully tested on a set of 46 Vibrio cholerae strains, and the results indicate that the signatures are highly sensitive for detection as well as specific for discrimination between these strains and their near relatives. Our approach, whereby the entire genomic complement of organisms are compared to identify probe targets, is a promising method for diagnostic assay development, and it provides assay designers with the flexibility to choose probes from the most relevant genes or genomic regions. The Insignia system is freely accessible via a Web interface and has been released as open source software at: http://insignia.cbcb.umd.edu.
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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.