{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T05:45:37Z","timestamp":1773121537919,"version":"3.50.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,11,25]],"date-time":"2019-11-25T00:00:00Z","timestamp":1574640000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"NHGRI","doi-asserted-by":"publisher","award":["R00HG008399"],"award-info":[{"award-number":["R00HG008399"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Genomic Innovator Award","award":["R35HG010717"],"award-info":[{"award-number":["R35HG010717"]}]},{"name":"Centers for Excellence in Genomic Science"},{"name":"CEGS","award":["RM1HG009490"],"award-info":[{"award-number":["RM1HG009490"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Clustered regularly interspaced short palindromic repeats (CRISPR) technologies allow for facile genomic modification in a site-specific manner. A key step in this process is the in silico design of single guide RNAs to efficiently and specifically target a site of interest. To this end, it is necessary to enumerate all potential off-target sites within a given genome that could be inadvertently altered by nuclease-mediated cleavage. Currently available software for this task is limited by computational efficiency, variant support or annotation, and assessment of the functional impact of potential off-target effects.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To overcome these limitations, we have developed CRISPRitz, a suite of software tools to support the design and analysis of CRISPR\/CRISPR-associated (Cas) experiments. Using efficient data structures combined with parallel computation, we offer a rapid, reliable, and exhaustive search mechanism to enumerate a comprehensive list of putative off-target sites. As proof-of-principle, we performed a head-to-head comparison with other available tools on several datasets. This analysis highlighted the unique features and superior computational performance of CRISPRitz including support for genomic searching with DNA\/RNA bulges and mismatches of arbitrary size as specified by the user as well as consideration of genetic variants (variant-aware). In addition, graphical reports are offered for coding and non-coding regions that annotate the potential impact of putative off-target sites that lie within regions of functional genomic annotation (e.g. insulator and chromatin accessible sites from the ENCyclopedia Of DNA Elements [ENCODE] project).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software is freely available at: https:\/\/github.com\/pinellolab\/CRISPRitzhttps:\/\/github.com\/InfOmics\/CRISPRitz.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz867","type":"journal-article","created":{"date-parts":[[2019,11,22]],"date-time":"2019-11-22T04:23:55Z","timestamp":1574396635000},"page":"2001-2008","source":"Crossref","is-referenced-by-count":66,"title":["CRISPRitz: rapid, high-throughput and variant-aware <i>in silico<\/i> off-target site identification for CRISPR genome editing"],"prefix":"10.1093","volume":"36","author":[{"given":"Samuele","family":"Cancellieri","sequence":"first","affiliation":[{"name":"Computer Science Department, University of Verona , Verona 37134, Italy"}]},{"given":"Matthew C","family":"Canver","sequence":"additional","affiliation":[{"name":"Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital , Charlestown, MA 02129, USA"},{"name":"Department of Pathology, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}]},{"given":"Nicola","family":"Bombieri","sequence":"additional","affiliation":[{"name":"Computer Science Department, University of Verona , Verona 37134, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9843-7638","authenticated-orcid":false,"given":"Rosalba","family":"Giugno","sequence":"additional","affiliation":[{"name":"Computer Science Department, University of Verona , Verona 37134, Italy"}]},{"given":"Luca","family":"Pinello","sequence":"additional","affiliation":[{"name":"Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital , Charlestown, MA 02129, USA"},{"name":"Department of Pathology, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,11,25]]},"reference":[{"key":"2023062312014731100_btz867-B1","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1145\/360825.360855","article-title":"Efficient string matching: an aid to bibliographic search","volume":"18","author":"Aho","year":"1975","journal-title":"Commun. 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