{"id":"https://openalex.org/W2587588342","doi":"https://doi.org/10.1186/s12859-017-1512-4","title":"Not all predicted CRISPR\u2013Cas systems are equal: isolated cas genes and classes of CRISPR like elements","display_name":"Not all predicted CRISPR\u2013Cas systems are equal: isolated cas genes and classes of CRISPR like elements","publication_year":2017,"publication_date":"2017-02-06","ids":{"openalex":"https://openalex.org/W2587588342","doi":"https://doi.org/10.1186/s12859-017-1512-4","mag":"2587588342","pmid":"https://pubmed.ncbi.nlm.nih.gov/28166719"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1512-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1512-4","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-017-1512-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100406698","display_name":"Quan Zhang","orcid":"https://orcid.org/0000-0003-1127-5969"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Quan Zhang","raw_affiliation_strings":["School of Informatics and Computing, Indiana University, 150 S. Woodlawn Ave, Bloomington, IN, 47405, USA"],"affiliations":[{"raw_affiliation_string":"School of Informatics and Computing, Indiana University, 150 S. Woodlawn Ave, Bloomington, IN, 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082620694","display_name":"Yuzhen Ye","orcid":"https://orcid.org/0000-0003-3707-3185"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuzhen Ye","raw_affiliation_strings":["School of Informatics and Computing, Indiana University, 150 S. Woodlawn Ave, Bloomington, IN, 47405, USA. yye@indiana.edu","School of Informatics and Computing, Indiana University, 150 S. Woodlawn Ave, Bloomington, IN, 47405, USA"],"affiliations":[{"raw_affiliation_string":"School of Informatics and Computing, Indiana University, 150 S. Woodlawn Ave, Bloomington, IN, 47405, USA. yye@indiana.edu","institution_ids":[]},{"raw_affiliation_string":"School of Informatics and Computing, Indiana University, 150 S. Woodlawn Ave, Bloomington, IN, 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100406698"],"corresponding_institution_ids":["https://openalex.org/I4210119109"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":10.1839,"has_fulltext":false,"cited_by_count":199,"citation_normalized_percentile":{"value":0.98824048,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"18","issue":"1","first_page":"92","last_page":"92"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":1.0,"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":1.0,"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":0.9506999850273132,"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/T12134","display_name":"Insect symbiosis and bacterial influences","score":0.9422000050544739,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/crispr","display_name":"CRISPR","score":0.9633785486221313},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6617380380630493},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.647997260093689},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6153637170791626},{"id":"https://openalex.org/keywords/locus","display_name":"Locus (genetics)","score":0.5547981262207031},{"id":"https://openalex.org/keywords/trans-activating-crrna","display_name":"Trans-activating crRNA","score":0.5399970412254333},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5337100625038147},{"id":"https://openalex.org/keywords/crispr-interference","display_name":"CRISPR interference","score":0.5088882446289062},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4940967857837677},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.43424713611602783},{"id":"https://openalex.org/keywords/cas9","display_name":"Cas9","score":0.32160770893096924}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.9633785486221313},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6617380380630493},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.647997260093689},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6153637170791626},{"id":"https://openalex.org/C84597430","wikidata":"https://www.wikidata.org/wiki/Q106227","display_name":"Locus (genetics)","level":3,"score":0.5547981262207031},{"id":"https://openalex.org/C84356384","wikidata":"https://www.wikidata.org/wiki/Q7833575","display_name":"Trans-activating crRNA","level":5,"score":0.5399970412254333},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5337100625038147},{"id":"https://openalex.org/C154055011","wikidata":"https://www.wikidata.org/wiki/Q28208918","display_name":"CRISPR interference","level":5,"score":0.5088882446289062},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4940967857837677},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.43424713611602783},{"id":"https://openalex.org/C132455925","wikidata":"https://www.wikidata.org/wiki/Q16965677","display_name":"Cas9","level":4,"score":0.32160770893096924}],"mesh":[{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013297","descriptor_name":"Streptococcus pyogenes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013297","descriptor_name":"Streptococcus pyogenes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013297","descriptor_name":"Streptococcus pyogenes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048249","descriptor_name":"Streptococcus thermophilus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048249","descriptor_name":"Streptococcus thermophilus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048249","descriptor_name":"Streptococcus thermophilus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":"Q000235","qualifier_name":"genetics","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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-017-1512-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1512-4","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28166719","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28166719","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:iu.tind.io:359","is_oa":false,"landing_page_url":"http://iu.tind.io/record/359","pdf_url":null,"source":{"id":"https://openalex.org/S4306402656","display_name":"IUScholarWorks Open (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://iu.tind.io/record/359","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5294841","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5294841","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1512-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1512-4","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5791983296","display_name":null,"funder_award_id":"1262588","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G616933693","display_name":null,"funder_award_id":"1R01AI108888","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W201727952","https://openalex.org/W1519266993","https://openalex.org/W1969324119","https://openalex.org/W1978094899","https://openalex.org/W2004432131","https://openalex.org/W2006877162","https://openalex.org/W2007153971","https://openalex.org/W2010986636","https://openalex.org/W2013018092","https://openalex.org/W2013950535","https://openalex.org/W2015607962","https://openalex.org/W2019197162","https://openalex.org/W2019670881","https://openalex.org/W2041113404","https://openalex.org/W2048883964","https://openalex.org/W2057092463","https://openalex.org/W2060573994","https://openalex.org/W2062521268","https://openalex.org/W2069689025","https://openalex.org/W2077190448","https://openalex.org/W2087089981","https://openalex.org/W2087942159","https://openalex.org/W2097065948","https://openalex.org/W2098023550","https://openalex.org/W2101983500","https://openalex.org/W2105187403","https://openalex.org/W2105329815","https://openalex.org/W2112606126","https://openalex.org/W2112814753","https://openalex.org/W2113211604","https://openalex.org/W2114499303","https://openalex.org/W2120546567","https://openalex.org/W2126511681","https://openalex.org/W2127391962","https://openalex.org/W2131527797","https://openalex.org/W2134023754","https://openalex.org/W2135598273","https://openalex.org/W2135621733","https://openalex.org/W2137675802","https://openalex.org/W2137721714","https://openalex.org/W2138116029","https://openalex.org/W2142813640","https://openalex.org/W2149635735","https://openalex.org/W2153355254","https://openalex.org/W2156125289","https://openalex.org/W2160786977","https://openalex.org/W2163241233","https://openalex.org/W2165869860","https://openalex.org/W2168933209","https://openalex.org/W2169244146","https://openalex.org/W2180561742","https://openalex.org/W2194181707","https://openalex.org/W2199695484","https://openalex.org/W2277208675","https://openalex.org/W2399809721","https://openalex.org/W2470052926","https://openalex.org/W4235939910"],"related_works":["https://openalex.org/W3146454725","https://openalex.org/W2140658947","https://openalex.org/W1531424361","https://openalex.org/W4379600106","https://openalex.org/W3195673132","https://openalex.org/W4323308326","https://openalex.org/W3209892036","https://openalex.org/W4220960485","https://openalex.org/W2317788533","https://openalex.org/W2564226239"],"abstract_inverted_index":{"This":[0],"is":[1],"the":[2,21,34],"first":[3],"systematic":[4],"study":[5],"to":[6,19,29],"collect":[7],"and":[8],"characterize":[9],"false-CRISPR":[10],"elements.":[11],"We":[12],"demonstrated":[13],"that":[14],"false-CRISPRs":[15],"could":[16],"be":[17,30],"used":[18],"reduce":[20],"false":[22],"annotation":[23,35],"of":[24,36],"CRISPRs,":[25],"therefore":[26],"showing":[27],"them":[28],"useful":[31],"for":[32],"improving":[33],"CRISPR-Cas":[37],"systems.":[38]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":25},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":22},{"year":2019,"cited_by_count":34},{"year":2018,"cited_by_count":26},{"year":2017,"cited_by_count":8}],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2025-10-10T00:00:00"}
