citHeader("Please cite the paper below for the CRISPRseek package.")

citEntry(entry="Article",
	title="CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems",
	author="Lihua Julie Zhu, Benjamin R. Holmes, Neil Aronin, Michael H. Brodsky",
	journal="PLoS one",
	volume=9,
	year=2014,
	number=9,
	url="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172692/",
	PubMedID="PMC4172692",
	abstract="CRISPR-Cas systems are a diverse family of RNA-protein complexes in bacteria that target foreign DNA sequences for cleavage. Derivatives of these complexes have been engineered to cleave specific target sequences depending on the sequence of a CRISPR-derived guide RNA (gRNA) and the source of the Cas9 protein. Important considerations for the design of gRNAs are to maximize aimed activity at the desired target site while minimizing off-target cleavage. Because of the rapid advances in the understanding of existing CRISPR-Cas9-derived RNA-guided nucleases and the development of novel RNA-guided nuclease systems, it is critical to have computational tools that can accommodate a wide range of different parameters for the design of target-specific RNA-guided nuclease systems. We have developed CRISPRseek, a highly flexible, open source software package to identify gRNAs that target a given input sequence while minimizing off-target cleavage at other sites within any selected genome. CRISPRseek will identify potential gRNAs that target a sequence of interest for CRISPR-Cas9 systems from different bacterial species and generate a cleavage score for potential off-target sequences utilizing published or user-supplied weight matrices with position-specific mismatch penalty scores. Identified gRNAs may be further filtered to only include those that occur in paired orientations for increased specificity and/or those that overlap restriction enzyme sites. For applications where gRNAs are desired to discriminate between two related sequences, CRISPRseek can rank gRNAs based on the difference between predicted cleavage scores in each input sequence. CRISPRseek is implemented as a Bioconductor package within the R statistical programming environment, allowing it to be incorporated into computational pipelines to automate the design of gRNAs for target sequences identified in a wide variety of genome-wide analyses. CRISPRseek is available under the GNU General Public Licence v3.0 at http://www.bioconductor.org.",
	textVersion="Zhu LJ, Holmes BR, Aronin N, Brodsky MH (2014) CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems. PLoS ONE 9(9): e108424. doi:10.1371/journal.pone.0108424"
)
citEntry(entry="Article",
        title="Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology",
        author="Lihua Julie Zhu",
        journal="Front. Biol.",
        volume=10,
        year=2015,
        number=4,
        abstract="CRISPR-Cas (Clustered, Regularly Interspaced, Short Palindromic Repeats CRISPR-associated (Cas)) RNA guided endonuclease has emerged as the most effective and widely used genome editing technology, which has become the most exciting and rapidly advancing research field. Efficient genome editing by the CRISPR-Cas9 system has been demonstrated in many species, and several labs have established CRISPR-Cas9 as a screening tool for systematic genetic analysis, similar to shRNA screening.  At least three companies have been founded to leverage this technology for therapeutic uses. To facilitate the implementation of this technology, many software tools have been developed to identify guide RNAs that effectively target a desired genomic region. Here, I provide an overview of the technology, focusing on guide RNA design principles, available software tools and their strengths and weaknesses.",
        textVersion="Lihua Julie Zhu (2015). Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology. Front. Biol.,  10(4): 289-296"
)
