{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T17:35:43Z","timestamp":1780680943843,"version":"3.54.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2018,6,1]],"date-time":"2018-06-01T00:00:00Z","timestamp":1527811200000},"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\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 HG008728"],"award-info":[{"award-number":["R01 HG008728"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 HG008927"],"award-info":[{"award-number":["R01 HG008927"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001006","name":"Breast Cancer Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001006","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001006","name":"BCRF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001006","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Center for Genetic Medicine Research"},{"name":"Gilbert Family Neurofibromatosis Institute at Children\u2019s National Health System"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genome-wide clustered, regularly interspaced, short palindromic repeat (CRISPR)-Cas9 screen has been widely used to interrogate gene functions. However, the rules to design better libraries beg further refinement.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We found single guide RNA (sgRNA) outliers are characterized by higher G-nucleotide counts, especially in regions distal from the PAM motif and are associated with stronger off-target activities. Furthermore, using non-targeting sgRNAs as negative controls lead to strong bias, which can be mitigated by using sgRNAs targeting multiple \u2018safe harbor\u2019 regions. Custom-designed screens confirmed our findings and further revealed that 19\u2009nt sgRNAs consistently gave the best signal-to-noise ratio. Collectively, our analysis motivated the design of a new genome-wide CRISPR\/Cas9 screen library and uncovered some intriguing properties of the CRISPR-Cas9 system.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The MAGeCK workflow is available open source at https:\/\/bitbucket.org\/liulab\/mageck_nest under the MIT license.<\/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\/bty450","type":"journal-article","created":{"date-parts":[[2018,5,31]],"date-time":"2018-05-31T03:42:39Z","timestamp":1527738159000},"page":"4095-4101","source":"Crossref","is-referenced-by-count":60,"title":["Improved design and analysis of CRISPR knockout screens"],"prefix":"10.1093","volume":"34","author":[{"given":"Chen-Hao","family":"Chen","sequence":"first","affiliation":[{"name":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA"},{"name":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA"},{"name":"Biological and Biomedical Science Program, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tengfei","family":"Xiao","sequence":"additional","affiliation":[{"name":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA"},{"name":"Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Xu","sequence":"additional","affiliation":[{"name":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA"},{"name":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA"},{"name":"Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Jiang","sequence":"additional","affiliation":[{"name":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA"},{"name":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clifford A","family":"Meyer","sequence":"additional","affiliation":[{"name":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA"},{"name":"Department of Biostatistics and Computational Biology, Dana-Farber 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