ArticleBMC bioinformatics2011
ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
22 citing papers in PubMed, 50 citations in OpenAlex.
- Unlocking the potential of CRISPR tools and databases for precision genome editing.Frontiers in plant science · 2025Review
- Advancements in genome editing tools for genetic studies and crop improvement.Frontiers in plant science · 2024Review
- Compact zinc finger base editors that edit mitochondrial or nuclear DNA in vitro and in vivo.Nature communications · 2022Article
- Tools for experimental and computational analyses of off-target editing by programmable nucleases.Nature protocols · 2021Review
- Generation of cryopreserved macrophages from normal and genetically engineered human pluripotent stem cells for disease modelling.PloS one · 2021Article
- Functional analysis of the ABCs of eye color in Helicoverpa armigera with CRISPR/Cas9-induced mutations.Scientific reports · 2017Article
- Long-Term Assessment of AAV-Mediated Zinc Finger Nuclease Expression in the Mouse Brain.Frontiers in molecular neuroscience · 2017Article
- Multidimensional Genome-wide Analyses Show Accurate FVIII Integration by ZFN in Primary Human Cells.Molecular therapy : the journal of the American Society of Gene Therapy · 2016Article
- Lentivector Knockdown of CCR5 in Hematopoietic Stem and Progenitor Cells Confers Functional and Persistent HIV-1 Resistance in Humanized Mice.Journal of virology · 2015Article
- Dual-reporter surrogate systems for efficient enrichment of genetically modified cells.Cellular and molecular life sciences : CMLS · 2015Article
- Excision of Expanded GAA Repeats Alleviates the Molecular Phenotype of Friedreich's Ataxia.Molecular therapy : the journal of the American Society of Gene Therapy · 2015Article
- COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites.Molecular therapy. Nucleic acids · 2014Article
- Development of synthetic selfish elements based on modular nucleases in Drosophila melanogaster.Nucleic acids research · 2014Article
- Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases.Bioinformatics (Oxford, England) · 2014Article
- Mouse genome engineering using designer nucleases.Journal of visualized experiments : JoVE · 2014Article
- An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage.Nucleic acids research · 2014Article
- Bacterial cellular engineering by genome editing and gene silencing.International journal of molecular sciences · 2014Review
- Nanomedicine: tiny particles and machines give huge gains.Annals of biomedical engineering · 2014Review
- Zinc-finger-nucleases mediate specific and efficient excision of HIV-1 proviral DNA from infected and latently infected human T cells.Nucleic acids research · 2013Article
- Repeatable construction method for engineered zinc finger nuclease based on overlap extension PCR and TA-cloning.PloS one · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundZinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model organisms. ZFN specificity is not absolute; therefore, it is essential to select ZFN target sites without similar genomic off-target sites. It is important to assay for off-target cleavage events at sites similar to the target sequence.
resultsZFN-Site is a web interface that searches multiple genomes for ZFN off-target sites. Queries can be based on the target sequence or can be expanded using degenerate specificity to account for known ZFN binding preferences. ZFN off-target sites are outputted with links to genome browsers, facilitating off-target cleavage site screening. We verified ZFN-Site using previously published ZFN half-sites and located their target sites and their previously described off-target sites. While we have tailored this tool to ZFNs, ZFN-Site can also be used to find potential off-target sites for other nucleases, such as TALE nucleases.
conclusionsZFN-Site facilitates genome searches for possible ZFN cleavage sites based on user-defined stringency limits. ZFN-Site is an improvement over other methods because the FetchGWI search engine uses an indexed search of genome sequences for all ZFN target sites and possible off-target sites matching the half-sites and stringency limits. Therefore, ZFN-Site does not miss potential off-target sites.
Indexed as
Identifiers
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.