{"id":"https://openalex.org/W2902305894","doi":"https://doi.org/10.1021/acs.jcim.8b00368","title":"Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network","display_name":"Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network","publication_year":2018,"publication_date":"2018-11-28","ids":{"openalex":"https://openalex.org/W2902305894","doi":"https://doi.org/10.1021/acs.jcim.8b00368","mag":"2902305894","pmid":"https://pubmed.ncbi.nlm.nih.gov/30485088"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.8b00368","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00368","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5100372201","display_name":"Xue Li","orcid":"https://orcid.org/0000-0002-4515-6792"},"institutions":[{"id":"https://openalex.org/I3017480383","display_name":"Southwest Medical University","ror":"https://ror.org/00g2rqs52","country_code":"CN","type":"funder","lineage":["https://openalex.org/I3017480383"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Xue","raw_affiliation_strings":["School of Public Health, Southwest Medical University, Luzhou, Sichuan, China"],"affiliations":[{"raw_affiliation_string":"School of Public Health, Southwest Medical University, Luzhou, Sichuan, China","institution_ids":["https://openalex.org/I3017480383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101402777","display_name":"Bin Tang","orcid":"https://orcid.org/0000-0002-4251-1867"},"institutions":[{"id":"https://openalex.org/I3017480383","display_name":"Southwest Medical University","ror":"https://ror.org/00g2rqs52","country_code":"CN","type":"funder","lineage":["https://openalex.org/I3017480383"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Tang","raw_affiliation_strings":["Basic Medical College, Southwest Medical University, Luzhou, Sichuan, China"],"affiliations":[{"raw_affiliation_string":"Basic Medical College, Southwest Medical University, Luzhou, Sichuan, China","institution_ids":["https://openalex.org/I3017480383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100344298","display_name":"Wei Chen","orcid":"https://orcid.org/0000-0001-5451-6430"},"institutions":[{"id":"https://openalex.org/I1301076528","display_name":"City Of Hope National Medical Center","ror":"https://ror.org/00w6g5w60","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei Chen","raw_affiliation_strings":["Integrative Genomics Core, City of Hope National Medical Center, Duarte, California 91010, United States"],"affiliations":[{"raw_affiliation_string":"Integrative Genomics Core, City of Hope National Medical Center, Duarte, California 91010, United States","institution_ids":["https://openalex.org/I1301076528"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061944036","display_name":"Jiesi Luo","orcid":"https://orcid.org/0000-0002-1199-7024"},"institutions":[{"id":"https://openalex.org/I3017480383","display_name":"Southwest Medical University","ror":"https://ror.org/00g2rqs52","country_code":"CN","type":"funder","lineage":["https://openalex.org/I3017480383"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiesi Luo","raw_affiliation_strings":["Key Laboratory for Aging and Regenerative Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory for Aging and Regenerative Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China","institution_ids":["https://openalex.org/I3017480383"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5061944036","https://openalex.org/A5100344298"],"corresponding_institution_ids":["https://openalex.org/I1301076528","https://openalex.org/I3017480383"],"apc_list":null,"apc_paid":null,"fwci":2.9415,"has_fulltext":false,"cited_by_count":105,"citation_normalized_percentile":{"value":0.92265143,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"59","issue":"1","first_page":"615","last_page":"624"},"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":0.992900013923645,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9904999732971191,"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":0.8388575911521912},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7246195077896118},{"id":"https://openalex.org/keywords/cas9","display_name":"Cas9","score":0.6623772978782654},{"id":"https://openalex.org/keywords/guide-rna","display_name":"Guide RNA","score":0.6074323654174805},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5594592690467834},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5347954630851746},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.49342575669288635},{"id":"https://openalex.org/keywords/genome-editing","display_name":"Genome editing","score":0.45495572686195374},{"id":"https://openalex.org/keywords/genome-engineering","display_name":"Genome engineering","score":0.4494851529598236},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4467504620552063},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20114010572433472},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1715206503868103},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1360040307044983}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.8388575911521912},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7246195077896118},{"id":"https://openalex.org/C132455925","wikidata":"https://www.wikidata.org/wiki/Q16965677","display_name":"Cas9","level":4,"score":0.6623772978782654},{"id":"https://openalex.org/C97702854","wikidata":"https://www.wikidata.org/wiki/Q4039747","display_name":"Guide RNA","level":5,"score":0.6074323654174805},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5594592690467834},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5347954630851746},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.49342575669288635},{"id":"https://openalex.org/C144501496","wikidata":"https://www.wikidata.org/wiki/Q5533489","display_name":"Genome editing","level":4,"score":0.45495572686195374},{"id":"https://openalex.org/C145290725","wikidata":"https://www.wikidata.org/wiki/Q5533489","display_name":"Genome engineering","level":5,"score":0.4494851529598236},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4467504620552063},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20114010572433472},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1715206503868103},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1360040307044983}],"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":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"D017394","descriptor_name":"RNA, Guide, Kinetoplastida","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.8b00368","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00368","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:30485088","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30485088","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G920474130","display_name":null,"funder_award_id":"21803045","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1869792624","https://openalex.org/W1879165674","https://openalex.org/W1912701812","https://openalex.org/W1915704240","https://openalex.org/W1968342623","https://openalex.org/W1982846895","https://openalex.org/W1984578972","https://openalex.org/W1988101725","https://openalex.org/W2026592619","https://openalex.org/W2036176224","https://openalex.org/W2045435533","https://openalex.org/W2050480410","https://openalex.org/W2064815984","https://openalex.org/W2067036696","https://openalex.org/W2074798818","https://openalex.org/W2088338354","https://openalex.org/W2096261947","https://openalex.org/W2101234009","https://openalex.org/W2101749257","https://openalex.org/W2102636708","https://openalex.org/W2107959600","https://openalex.org/W2120503144","https://openalex.org/W2127862779","https://openalex.org/W2134100064","https://openalex.org/W2134298288","https://openalex.org/W2152505144","https://openalex.org/W2164695230","https://openalex.org/W2180291937","https://openalex.org/W2198606573","https://openalex.org/W2199695484","https://openalex.org/W2221022144","https://openalex.org/W2252568502","https://openalex.org/W2345512687","https://openalex.org/W2461013690","https://openalex.org/W2502949459","https://openalex.org/W2523099503","https://openalex.org/W2594532403","https://openalex.org/W2786426577","https://openalex.org/W2786494334","https://openalex.org/W2790102940","https://openalex.org/W2919115771","https://openalex.org/W2962949934"],"related_works":["https://openalex.org/W2603161682","https://openalex.org/W2960163646","https://openalex.org/W2807464733","https://openalex.org/W2516842346","https://openalex.org/W2134268326","https://openalex.org/W2903635918","https://openalex.org/W2437118042","https://openalex.org/W2337751047","https://openalex.org/W4320033130","https://openalex.org/W2667943050"],"abstract_inverted_index":{"The":[0],"CRISPR-Cas9":[1,45,128],"system":[2],"derived":[3],"from":[4,95],"adaptive":[5],"immunity":[6],"in":[7,139,150,154,169,220],"bacteria":[8],"and":[9,118,157,179,187,206,211,235,239],"archaea":[10],"has":[11],"been":[12,64],"developed":[13,65],"into":[14],"a":[15,36,54,86,102],"powerful":[16],"tool":[17],"for":[18,39,126],"genome":[19,240],"engineering":[20],"with":[21],"wide-ranging":[22],"applications.":[23],"Optimizing":[24],"single-guide":[25],"RNA":[26],"(sgRNA)":[27],"design":[28,201],"to":[29,53,70,81,89,112,144,161,199,231],"improve":[30],"efficiency":[31],"of":[32,74,123,167,183,196,202,224],"target":[33,56,165],"cleavage":[34],"is":[35],"key":[37],"step":[38],"successful":[40],"gene":[41,57],"editing":[42],"using":[43],"the":[44,72,107,115,121,127,133,142,155,159,164,176,181,194,200,222,248],"system.":[46,129],"Because":[47],"not":[48,152],"all":[49],"sgRNAs":[50,93,125,149,168,225],"that":[51,132,216,226],"cognate":[52],"given":[55],"are":[58],"equally":[59],"effective,":[60],"computational":[61],"tools":[62],"have":[63],"based":[66,105],"on":[67,106],"experimental":[68],"data":[69],"increase":[71],"likelihood":[73],"selecting":[75],"effective":[76,234],"sgRNAs.":[77],"Despite":[78],"considerable":[79],"efforts":[80],"date,":[82],"it":[83],"still":[84],"remains":[85],"big":[87],"challenge":[88],"accurately":[90,162],"predict":[91,163],"functional":[92,124],"directly":[94],"large-scale":[96],"sequence":[97,116,185],"data.":[98],"We":[99,130,191,214],"propose":[100],"DeepCas9,":[101],"deep-learning":[103],"framework":[104],"convolutional":[108,177],"neural":[109],"network":[110],"(CNN),":[111],"automatically":[113],"learn":[114],"determinants":[117],"further":[119,174],"enable":[120,232],"identification":[122],"show":[131,180],"CNN":[134],"method":[135,198],"outperforms":[136],"previous":[137],"methods":[138],"both":[140],"(i)":[141],"ability":[143,160],"correctly":[145],"identify":[146],"highly":[147],"active":[148],"experiments":[151],"used":[153],"training":[156],"(ii)":[158],"efficacies":[166],"different":[170],"organisms.":[171],"Besides,":[172],"we":[173],"visualize":[175],"kernels":[178],"match":[182],"identified":[184],"signatures":[186],"known":[188],"nucleotide":[189],"preferences.":[190],"finally":[192],"demonstrate":[193],"application":[195],"our":[197],"next-generation":[203],"genome-scale":[204],"CRISPRi":[205],"CRISPRa":[207],"libraries":[208],"targeting":[209],"human":[210],"mouse":[212],"genomes.":[213],"expect":[215],"DeepCas9":[217,242],"will":[218],"assist":[219],"reducing":[221],"numbers":[223],"must":[227],"be":[228,244],"experimentally":[229],"validated":[230],"more":[233],"efficient":[236],"genetic":[237],"screens":[238],"engineering.":[241],"can":[243],"freely":[245],"accessed":[246],"via":[247],"Internet":[249],"at":[250],"https://github.com/lje00006/DeepCas9":[251],".":[252]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":28},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":9}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
