{"id":"https://openalex.org/W2953155660","doi":"https://doi.org/10.1093/bioinformatics/bty1061","title":"CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity","display_name":"CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity","publication_year":2019,"publication_date":"2019-01-02","ids":{"openalex":"https://openalex.org/W2953155660","doi":"https://doi.org/10.1093/bioinformatics/bty1061","mag":"2953155660","pmid":"https://pubmed.ncbi.nlm.nih.gov/30615056"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty1061","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1061","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068452155","display_name":"Houxiang Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I83328450","display_name":"Miami University","ror":"https://ror.org/05nbqxr67","country_code":"US","type":"education","lineage":["https://openalex.org/I83328450"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Houxiang Zhu","raw_affiliation_strings":["Department of Biology, Miami University, Oxford, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Miami University, Oxford, OH, USA","institution_ids":["https://openalex.org/I83328450"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101531536","display_name":"Chun Liang","orcid":"https://orcid.org/0000-0003-1996-6027"},"institutions":[{"id":"https://openalex.org/I83328450","display_name":"Miami University","ror":"https://ror.org/05nbqxr67","country_code":"US","type":"education","lineage":["https://openalex.org/I83328450"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chun Liang","raw_affiliation_strings":["Department of Biology, Miami University, Oxford, OH, USA","Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Miami University, Oxford, OH, USA","institution_ids":["https://openalex.org/I83328450"]},{"raw_affiliation_string":"Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA","institution_ids":["https://openalex.org/I83328450"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101531536"],"corresponding_institution_ids":["https://openalex.org/I83328450"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.103,"has_fulltext":false,"cited_by_count":86,"citation_normalized_percentile":{"value":0.95006452,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"35","issue":"16","first_page":"2783","last_page":"2789"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9961000084877014,"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":0.9961000084877014,"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/T12610","display_name":"RNA regulation and disease","score":0.0006000000284984708,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00019999999494757503,"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":0.9713066816329956},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.577752947807312},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5341016054153442},{"id":"https://openalex.org/keywords/guide-rna","display_name":"Guide RNA","score":0.5189868807792664},{"id":"https://openalex.org/keywords/trans-activating-crrna","display_name":"Trans-activating crRNA","score":0.4601294696331024},{"id":"https://openalex.org/keywords/genome-editing","display_name":"Genome editing","score":0.4498252272605896},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3538825213909149},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23814281821250916},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10043847560882568}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.9713066816329956},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.577752947807312},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5341016054153442},{"id":"https://openalex.org/C97702854","wikidata":"https://www.wikidata.org/wiki/Q4039747","display_name":"Guide RNA","level":5,"score":0.5189868807792664},{"id":"https://openalex.org/C84356384","wikidata":"https://www.wikidata.org/wiki/Q7833575","display_name":"Trans-activating crRNA","level":5,"score":0.4601294696331024},{"id":"https://openalex.org/C144501496","wikidata":"https://www.wikidata.org/wiki/Q5533489","display_name":"Genome editing","level":4,"score":0.4498252272605896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3538825213909149},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23814281821250916},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10043847560882568}],"mesh":[{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004720","descriptor_name":"Endonucleases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004720","descriptor_name":"Endonucleases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004720","descriptor_name":"Endonucleases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004720","descriptor_name":"Endonucleases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017394","descriptor_name":"RNA, Guide, Kinetoplastida","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","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":false},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","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":false},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty1061","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1061","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30615056","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30615056","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W1968342623","https://openalex.org/W1972476556","https://openalex.org/W1973260880","https://openalex.org/W1977709885","https://openalex.org/W1982846895","https://openalex.org/W1982873976","https://openalex.org/W1988075836","https://openalex.org/W1992116297","https://openalex.org/W1992783297","https://openalex.org/W1995497292","https://openalex.org/W2001845502","https://openalex.org/W2003171404","https://openalex.org/W2014639769","https://openalex.org/W2021767455","https://openalex.org/W2028543816","https://openalex.org/W2058792860","https://openalex.org/W2064815984","https://openalex.org/W2066099080","https://openalex.org/W2070172761","https://openalex.org/W2072309186","https://openalex.org/W2073412341","https://openalex.org/W2077659966","https://openalex.org/W2086561953","https://openalex.org/W2103123883","https://openalex.org/W2104654654","https://openalex.org/W2104703176","https://openalex.org/W2108234281","https://openalex.org/W2110260408","https://openalex.org/W2114850508","https://openalex.org/W2115188287","https://openalex.org/W2119387367","https://openalex.org/W2119771879","https://openalex.org/W2121633690","https://openalex.org/W2122941722","https://openalex.org/W2126259097","https://openalex.org/W2127862779","https://openalex.org/W2131395804","https://openalex.org/W2132401721","https://openalex.org/W2133702185","https://openalex.org/W2134298288","https://openalex.org/W2152505144","https://openalex.org/W2153635508","https://openalex.org/W2163090183","https://openalex.org/W2164604555","https://openalex.org/W2164695230","https://openalex.org/W2165869860","https://openalex.org/W2166802172","https://openalex.org/W2167155938","https://openalex.org/W2170551349","https://openalex.org/W2252568502","https://openalex.org/W2338878549","https://openalex.org/W2341405505","https://openalex.org/W2408159711","https://openalex.org/W2409121249","https://openalex.org/W2410526873","https://openalex.org/W2412316478","https://openalex.org/W2465120080","https://openalex.org/W2470889463","https://openalex.org/W2550079706","https://openalex.org/W2553118607","https://openalex.org/W2559979550","https://openalex.org/W2560230043","https://openalex.org/W2563521043","https://openalex.org/W2563593003","https://openalex.org/W2588570791","https://openalex.org/W2588577496","https://openalex.org/W2597038011","https://openalex.org/W2607120679","https://openalex.org/W2610391087","https://openalex.org/W2614935095","https://openalex.org/W2623910725","https://openalex.org/W2786426577","https://openalex.org/W2953385017","https://openalex.org/W2989794628"],"related_works":["https://openalex.org/W2022419379","https://openalex.org/W1690029344","https://openalex.org/W4378347774","https://openalex.org/W4220960485","https://openalex.org/W1966021055","https://openalex.org/W2152806488","https://openalex.org/W4200553529","https://openalex.org/W4375955993","https://openalex.org/W2667943050","https://openalex.org/W2117924928"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"Clustered":[2],"Regularly":[3],"Interspaced":[4],"Short":[5],"Palindromic":[6],"Repeats":[7],"(CRISPR)-Cpf1":[8],"system":[9,23,100],"has":[10],"been":[11],"successfully":[12],"applied":[13],"in":[14,60,112,121],"genome":[15,113],"editing.":[16,114],"However,":[17],"target":[18,52,72,104],"efficiency":[19,73,105],"of":[20,57],"the":[21,37,55,81,98],"CRISPR-Cpf1":[22,39,83,99],"varies":[24],"among":[25],"different":[26],"guide":[27],"RNA":[28],"(gRNA)":[29],"sequences.":[30],"RESULTS:":[31],"In":[32],"this":[33],"study,":[34],"we":[35],"reanalyzed":[36],"published":[38],"gRNAs":[40,96],"data":[41,134],"and":[42,46,106,124],"found":[43],"many":[44],"sequence":[45],"structural":[47],"features":[48],"related":[49],"to":[50,70,91],"their":[51],"efficiency.":[53],"With":[54],"aid":[56],"Random":[58],"Forest":[59],"feature":[61],"selection,":[62],"a":[63],"support":[64],"vector":[65],"machine":[66],"model":[67],"was":[68],"created":[69],"predict":[71],"for":[74,97],"any":[75],"given":[76],"gRNAs.":[77],"We":[78],"have":[79],"developed":[80],"first":[82],"web":[84],"service":[85],"application,":[86],"CRISPR-DT":[87,108],"(CRISPR":[88],"DNA":[89],"Targeting),":[90],"help":[92],"users":[93],"design":[94],"optimal":[95],"by":[101],"considering":[102],"both":[103],"specificity.":[107],"will":[109],"empower":[110],"researchers":[111],"AVAILABILITY":[115],"AND":[116],"IMPLEMENTATION:":[117],"CRISPR-DT,":[118],"mainly":[119],"implemented":[120],"Perl,":[122],"PHP":[123],"JavaScript,":[125],"is":[126],"freely":[127],"available":[128,136],"at":[129,137],"http://bioinfolab.miamioh.edu/CRISPR-DT.":[130],"SUPPLEMENTARY":[131],"INFORMATION:":[132],"Supplementary":[133],"are":[135],"Bioinformatics":[138],"online.":[139]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":17},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":2}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}