{"id":"https://openalex.org/W7163876747","doi":"https://doi.org/10.1093/bib/bbag216","title":"CRISPR-MBTF: a multi-branch transformer fusion framework for CRISPR-Cas9 off-target prediction","display_name":"CRISPR-MBTF: a multi-branch transformer fusion framework for CRISPR-Cas9 off-target prediction","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7163876747","doi":"https://doi.org/10.1093/bib/bbag216","pmid":"https://pubmed.ncbi.nlm.nih.gov/42261185"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag216","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/10.1093/bib/bbag216","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5138150066","display_name":"Ali Jahangiri-Sisakht","orcid":"https://orcid.org/0009-0005-9892-0140"},"institutions":[{"id":"https://openalex.org/I99861883","display_name":"University of Zanjan","ror":"https://ror.org/05e34ej29","country_code":"IR","type":"education","lineage":["https://openalex.org/I99861883"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Ali Jahangiri-Sisakht","raw_affiliation_strings":["Department of Computer Engineering, University of Zanjan , Zanjan 45371-38791 ,"],"raw_orcid":"https://orcid.org/0009-0005-9892-0140","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, University of Zanjan , Zanjan 45371-38791 ,","institution_ids":["https://openalex.org/I99861883"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070985292","display_name":"Leila Safari","orcid":"https://orcid.org/0000-0002-2872-0937"},"institutions":[{"id":"https://openalex.org/I99861883","display_name":"University of Zanjan","ror":"https://ror.org/05e34ej29","country_code":"IR","type":"education","lineage":["https://openalex.org/I99861883"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Leila Safari","raw_affiliation_strings":["Department of Computer Engineering, University of Zanjan , Zanjan 45371-38791 ,"],"raw_orcid":"https://orcid.org/0000-0002-2872-0937","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, University of Zanjan , Zanjan 45371-38791 ,","institution_ids":["https://openalex.org/I99861883"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025514517","display_name":"Roghayyeh Alipanahi","orcid":"https://orcid.org/0009-0005-7818-6794"},"institutions":[{"id":"https://openalex.org/I163205636","display_name":"Tabriz University of Medical Sciences","ror":"https://ror.org/04krpx645","country_code":"IR","type":"education","lineage":["https://openalex.org/I163205636"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Roghayyeh Alipanahi","raw_affiliation_strings":["Faculty of Pharmacy, Tabriz University of Medical Sciences , Golgasht Street, Tabriz, 5166/15731,"],"raw_orcid":"https://orcid.org/0009-0005-7818-6794","affiliations":[{"raw_affiliation_string":"Faculty of Pharmacy, Tabriz University of Medical Sciences , Golgasht Street, Tabriz, 5166/15731,","institution_ids":["https://openalex.org/I163205636"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5138150066"],"corresponding_institution_ids":["https://openalex.org/I99861883"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.51557801,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.994700014591217,"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":0.994700014591217,"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":0.002300000051036477,"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":0.00039999998989515007,"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":0.8029999732971191},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.7020999789237976},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5534999966621399},{"id":"https://openalex.org/keywords/cas9","display_name":"Cas9","score":0.4869000017642975},{"id":"https://openalex.org/keywords/genome-editing","display_name":"Genome editing","score":0.39309999346733093},{"id":"https://openalex.org/keywords/safer","display_name":"SAFER","score":0.36410000920295715},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.3614000082015991},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.34850001335144043}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.8029999732971191},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7135999798774719},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.7020999789237976},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5534999966621399},{"id":"https://openalex.org/C132455925","wikidata":"https://www.wikidata.org/wiki/Q16965677","display_name":"Cas9","level":4,"score":0.4869000017642975},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44269999861717224},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4043000042438507},{"id":"https://openalex.org/C144501496","wikidata":"https://www.wikidata.org/wiki/Q5533489","display_name":"Genome editing","level":4,"score":0.39309999346733093},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38029998540878296},{"id":"https://openalex.org/C2776654903","wikidata":"https://www.wikidata.org/wiki/Q2601463","display_name":"SAFER","level":2,"score":0.36410000920295715},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.3614000082015991},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.34850001335144043},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.34549999237060547},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.3244999945163727},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.2800000011920929},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.27639999985694885},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2736000120639801},{"id":"https://openalex.org/C171018156","wikidata":"https://www.wikidata.org/wiki/Q7370306","display_name":"Rotation formalisms in three dimensions","level":2,"score":0.27070000767707825},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.26899999380111694},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.2660999894142151},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26409998536109924},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.2624000012874603},{"id":"https://openalex.org/C44667518","wikidata":"https://www.wikidata.org/wiki/Q12321","display_name":"Palindrome","level":4,"score":0.26109999418258667},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2500999867916107}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"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":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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/bib/bbag216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag216","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42261185","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42261185","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13245737","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13245737/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag216","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1966716734","https://openalex.org/W2036176224","https://openalex.org/W2045435533","https://openalex.org/W2252568502","https://openalex.org/W2304268185","https://openalex.org/W2461013690","https://openalex.org/W2611134270","https://openalex.org/W2611661371","https://openalex.org/W2782551527","https://openalex.org/W2810756255","https://openalex.org/W2891210592","https://openalex.org/W2902305894","https://openalex.org/W2963192057","https://openalex.org/W2982510384","https://openalex.org/W2984059576","https://openalex.org/W3007485829","https://openalex.org/W3026606344","https://openalex.org/W3111011311","https://openalex.org/W4205143015","https://openalex.org/W4315650359","https://openalex.org/W4316466738","https://openalex.org/W4323666400","https://openalex.org/W4366551165","https://openalex.org/W4386202976","https://openalex.org/W4388789415","https://openalex.org/W4391033788","https://openalex.org/W4392213218","https://openalex.org/W4403904366","https://openalex.org/W4405910570","https://openalex.org/W4408937787"],"related_works":[],"abstract_inverted_index":{"Clustered":[0],"regularly":[1],"interspaced":[2],"short":[3],"palindromic":[4],"repeats":[5],"and":[6,48,56,72,91,135,155,174,183],"CRISPR-associated":[7],"protein":[8],"9":[9],"(CRISPR-Cas9)":[10],"is":[11,84],"a":[12,19,26,66,105,111,172],"revolutionary":[13],"genome":[14,186],"editing":[15,187],"technology":[16],"derived":[17],"from":[18],"bacterial":[20],"adaptive":[21],"immune":[22],"system":[23],"that":[24],"uses":[25],"single":[27],"guide":[28],"RNA":[29],"(sgRNA)":[30],"to":[31,36,87,121,145,177],"direct":[32],"the":[33,70,123,164,179],"Cas9":[34],"enzyme":[35],"specific":[37],"DNA":[38],"sequences":[39],"for":[40],"precise":[41],"genetic":[42,54],"modifications.":[43],"Its":[44],"ease":[45],"of":[46,75,81,166,181],"use":[47],"efficiency":[49],"has":[50],"accelerated":[51],"advancements":[52],"in":[53],"research":[55],"therapeutic":[57],"development.":[58],"However,":[59],"unintended":[60],"cleavage":[61],"at":[62],"off-target":[63,82],"sites":[64],"remains":[65],"significant":[67],"concern,":[68],"limiting":[69],"safety":[71],"broader":[73],"applicability":[74],"CRISPR-based":[76],"editing.":[77],"Accurate":[78],"computational":[79],"prediction":[80],"locations":[83],"therefore":[85],"essential":[86],"mitigate":[88],"potential":[89],"risks":[90],"improve":[92],"experimental":[93],"design.":[94],"In":[95],"this":[96],"study,":[97],"we":[98],"introduce":[99],"CRISPR":[100,128,167],"multi-branch":[101,112],"transformer":[102],"fusion":[103,119],"(CRISPR-MBTF),":[104],"novel":[106],"deep":[107],"learning-based":[108],"framework":[109],"employing":[110],"Transformer":[113],"architecture":[114],"combined":[115],"with":[116],"an":[117],"attention-based":[118],"mechanism":[120],"model":[122,139],"intricate":[124],"biological":[125],"context":[126],"influencing":[127],"activity.":[129],"By":[130],"capturing":[131],"subtle":[132],"sequence":[133,158],"patterns":[134,154],"contextual":[136],"dependencies,":[137],"our":[138],"achieves":[140],"enhanced":[141],"predictive":[142],"performance":[143],"compared":[144],"existing":[146],"approaches.":[147],"Additionally,":[148],"interpretability":[149],"analyses":[150],"uncover":[151],"biologically":[152],"meaningful":[153],"highlight":[156],"influential":[157],"regions,":[159],"offering":[160],"valuable":[161],"insights":[162],"into":[163],"determinants":[165],"specificity.":[168],"This":[169],"work":[170],"presents":[171],"robust":[173],"interpretable":[175],"tool":[176],"support":[178],"design":[180],"safer":[182],"more":[184],"effective":[185],"strategies.":[188]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-06-09T00:00:00"}