{"id":"https://openalex.org/W2805951293","doi":"https://doi.org/10.1093/bioinformatics/bty450","title":"Improved design and analysis of CRISPR knockout screens","display_name":"Improved design and analysis of CRISPR knockout screens","publication_year":2018,"publication_date":"2018-05-31","ids":{"openalex":"https://openalex.org/W2805951293","doi":"https://doi.org/10.1093/bioinformatics/bty450","mag":"2805951293","pmid":"https://pubmed.ncbi.nlm.nih.gov/29868757"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty450","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty450","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/4095/26676675/bty450.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/4095/26676675/bty450.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032575688","display_name":"Chen-Hao Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chen-Hao Chen","raw_affiliation_strings":["Biological and Biomedical Science Program, Harvard Medical School, Boston, MA, USA","Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological and Biomedical Science Program, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032987260","display_name":"Tengfei Xiao","orcid":"https://orcid.org/0000-0001-5704-9882"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tengfei Xiao","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101969428","display_name":"Han Xu","orcid":"https://orcid.org/0000-0002-8654-461X"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Han Xu","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA","Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025010135","display_name":"Peng Jiang","orcid":"https://orcid.org/0000-0002-7828-5486"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peng Jiang","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021521447","display_name":"Clifford A. Meyer","orcid":"https://orcid.org/0000-0002-8321-2839"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Clifford A Meyer","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100318133","display_name":"Wei Li","orcid":"https://orcid.org/0000-0002-2163-7903"},"institutions":[{"id":"https://openalex.org/I1336742384","display_name":"Children's National","ror":"https://ror.org/03wa2q724","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1336742384"]},{"id":"https://openalex.org/I193531525","display_name":"George Washington University","ror":"https://ror.org/00y4zzh67","country_code":"US","type":"education","lineage":["https://openalex.org/I193531525"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei Li","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","Center for Genetic Medicine Research, Children\u2019s National Health System, Washington, DC, USA","Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA","Department of Genomics and Precision Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, USA","Center for Genetic Medicine Research, Children's National Health System, Washington, DC, USA"],"raw_orcid":"https://orcid.org/0000-0002-2163-7903","affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Center for Genetic Medicine Research, Children\u2019s National Health System, Washington, DC, USA","institution_ids":["https://openalex.org/I1336742384"]},{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Genomics and Precision Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, USA","institution_ids":["https://openalex.org/I193531525"]},{"raw_affiliation_string":"Center for Genetic Medicine Research, Children's National Health System, Washington, DC, USA","institution_ids":["https://openalex.org/I1336742384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033532061","display_name":"Myles Brown","orcid":"https://orcid.org/0000-0002-8213-1658"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Myles Brown","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045575546","display_name":"X. Shirley Liu","orcid":"https://orcid.org/0000-0003-4736-7339"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"X Shirley Liu","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5033532061","https://openalex.org/A5045575546","https://openalex.org/A5100318133"],"corresponding_institution_ids":["https://openalex.org/I1336742384","https://openalex.org/I136199984","https://openalex.org/I193531525","https://openalex.org/I4210117453"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.5259,"has_fulltext":true,"cited_by_count":72,"citation_normalized_percentile":{"value":0.93818605,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"34","issue":"23","first_page":"4095","last_page":"4101"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9923999905586243,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9923999905586243,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.000699999975040555,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/crispr","display_name":"CRISPR","score":0.9696095585823059},{"id":"https://openalex.org/keywords/cas9","display_name":"Cas9","score":0.7077782154083252},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5814239978790283},{"id":"https://openalex.org/keywords/genome-editing","display_name":"Genome editing","score":0.5755802989006042},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5395449995994568},{"id":"https://openalex.org/keywords/guide-rna","display_name":"Guide RNA","score":0.5333122611045837},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5043362379074097},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4905545115470886},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4814440608024597},{"id":"https://openalex.org/keywords/subgenomic-mrna","display_name":"Subgenomic mRNA","score":0.46274808049201965},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4493728280067444},{"id":"https://openalex.org/keywords/palindrome","display_name":"Palindrome","score":0.4444003999233246},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3864307999610901},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3670170307159424},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.23322200775146484},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.19816792011260986},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12357023358345032}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.9696095585823059},{"id":"https://openalex.org/C132455925","wikidata":"https://www.wikidata.org/wiki/Q16965677","display_name":"Cas9","level":4,"score":0.7077782154083252},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5814239978790283},{"id":"https://openalex.org/C144501496","wikidata":"https://www.wikidata.org/wiki/Q5533489","display_name":"Genome editing","level":4,"score":0.5755802989006042},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5395449995994568},{"id":"https://openalex.org/C97702854","wikidata":"https://www.wikidata.org/wiki/Q4039747","display_name":"Guide RNA","level":5,"score":0.5333122611045837},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5043362379074097},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4905545115470886},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4814440608024597},{"id":"https://openalex.org/C189819185","wikidata":"https://www.wikidata.org/wiki/Q384283","display_name":"Subgenomic mRNA","level":4,"score":0.46274808049201965},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4493728280067444},{"id":"https://openalex.org/C44667518","wikidata":"https://www.wikidata.org/wiki/Q12321","display_name":"Palindrome","level":4,"score":0.4444003999233246},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3864307999610901},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3670170307159424},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.23322200775146484},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.19816792011260986},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12357023358345032}],"mesh":[{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017394","descriptor_name":"RNA, Guide, Kinetoplastida","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty450","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty450","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/4095/26676675/bty450.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29868757","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29868757","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:5839772","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6247926","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty450","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty450","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/4095/26676675/bty450.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.4399999976158142,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G373423763","display_name":null,"funder_award_id":"R01 HG008927","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4834479356","display_name":null,"funder_award_id":"R01 HG008927","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5749038469","display_name":null,"funder_award_id":"R01 HG008728","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G6182328826","display_name":null,"funder_award_id":"R01 HG008728","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8288036582","display_name":null,"funder_award_id":"NIH R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8416827599","display_name":null,"funder_award_id":"HG008728","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306260","display_name":"Breast Cancer Research Foundation","ror":"https://ror.org/0348ff195"},{"id":"https://openalex.org/F4320317457","display_name":"Children's National Hospital","ror":"https://ror.org/03wa2q724"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2805951293.pdf","grobid_xml":"https://content.openalex.org/works/W2805951293.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1635615463","https://openalex.org/W1855348513","https://openalex.org/W1879165674","https://openalex.org/W1934704664","https://openalex.org/W1944525636","https://openalex.org/W1968342623","https://openalex.org/W1973260880","https://openalex.org/W1977955083","https://openalex.org/W1982846895","https://openalex.org/W1982873976","https://openalex.org/W2003797386","https://openalex.org/W2026520402","https://openalex.org/W2036176224","https://openalex.org/W2045435533","https://openalex.org/W2064815984","https://openalex.org/W2097360283","https://openalex.org/W2100122648","https://openalex.org/W2106296224","https://openalex.org/W2108038398","https://openalex.org/W2131395804","https://openalex.org/W2132212985","https://openalex.org/W2136544377","https://openalex.org/W2138164217","https://openalex.org/W2146511318","https://openalex.org/W2177540144","https://openalex.org/W2179438025","https://openalex.org/W2180291937","https://openalex.org/W2201689894","https://openalex.org/W2252568502","https://openalex.org/W2270544154","https://openalex.org/W2272131637","https://openalex.org/W2338215681","https://openalex.org/W2411238967","https://openalex.org/W2414684615","https://openalex.org/W2461013690","https://openalex.org/W2523099503","https://openalex.org/W2544093984","https://openalex.org/W2584033231","https://openalex.org/W2611446801","https://openalex.org/W2735132087","https://openalex.org/W2740403143","https://openalex.org/W4294541781"],"related_works":["https://openalex.org/W1751510803","https://openalex.org/W3015098563","https://openalex.org/W4311050706","https://openalex.org/W4324031050","https://openalex.org/W2128758977","https://openalex.org/W3110102429","https://openalex.org/W3006121361","https://openalex.org/W1978917197","https://openalex.org/W2939056872","https://openalex.org/W4232405569"],"abstract_inverted_index":{"Motivation:":[0],"Genome-wide":[1],"clustered,":[2],"regularly":[3],"interspaced,":[4],"short":[5],"palindromic":[6],"repeat":[7],"(CRISPR)-Cas9":[8],"screen":[9,109],"has":[10],"been":[11],"widely":[12],"used":[13],"to":[14,21,65],"interrogate":[15],"gene":[16],"functions.":[17],"However,":[18],"the":[19,47,94,102,117,133],"rules":[20],"design":[22,103],"better":[23],"libraries":[24],"beg":[25],"further":[26,86],"refinement.":[27],"Results:":[28],"We":[29],"found":[30],"single":[31],"guide":[32],"RNA":[33],"(sgRNA)":[34],"outliers":[35],"are":[36,51,140],"characterized":[37],"by":[38,72],"higher":[39],"G-nucleotide":[40],"counts,":[41],"especially":[42],"in":[43],"regions":[44],"distal":[45],"from":[46],"PAM":[48],"motif":[49],"and":[50,85,111,121],"associated":[52],"with":[53],"stronger":[54],"off-target":[55],"activities.":[56],"Furthermore,":[57],"using":[58,73],"non-targeting":[59],"sgRNAs":[60,74,91],"as":[61],"negative":[62],"controls":[63],"lead":[64],"strong":[66],"bias,":[67],"which":[68],"can":[69],"be":[70],"mitigated":[71],"targeting":[75],"multiple":[76],"'safe":[77],"harbor'":[78],"regions.":[79],"Custom-designed":[80],"screens":[81],"confirmed":[82],"our":[83,99],"findings":[84],"revealed":[87],"that":[88],"19":[89],"nt":[90],"consistently":[92],"gave":[93],"best":[95],"signal-to-noise":[96],"ratio.":[97],"Collectively,":[98],"analysis":[100],"motivated":[101],"of":[104,116],"a":[105],"new":[106],"genome-wide":[107],"CRISPR/Cas9":[108],"library":[110],"uncovered":[112],"some":[113],"intriguing":[114],"properties":[115],"CRISPR-Cas9":[118],"system.":[119],"Availability":[120],"implementation:":[122],"The":[123],"MAGeCK":[124],"workflow":[125],"is":[126],"available":[127,141],"open":[128],"source":[129],"at":[130,142],"https://bitbucket.org/liulab/mageck_nest":[131],"under":[132],"MIT":[134],"license.":[135],"Supplementary":[136,138],"information:":[137],"data":[139],"Bioinformatics":[143],"online.":[144]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":24},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}