{"id":"https://openalex.org/W3162924147","doi":"https://doi.org/10.3390/e23050608","title":"Prediction of sgRNA Off-Target Activity in CRISPR/Cas9 Gene Editing Using Graph Convolution Network","display_name":"Prediction of sgRNA Off-Target Activity in CRISPR/Cas9 Gene Editing Using Graph Convolution Network","publication_year":2021,"publication_date":"2021-05-14","ids":{"openalex":"https://openalex.org/W3162924147","doi":"https://doi.org/10.3390/e23050608","mag":"3162924147","pmid":"https://pubmed.ncbi.nlm.nih.gov/34069050"},"language":"en","primary_location":{"id":"doi:10.3390/e23050608","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e23050608","pdf_url":"https://www.mdpi.com/1099-4300/23/5/608/pdf?version=1620992029","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1099-4300/23/5/608/pdf?version=1620992029","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076698009","display_name":"Prasoon Kumar Vinodkumar","orcid":null},"institutions":[{"id":"https://openalex.org/I56085075","display_name":"University of Tartu","ror":"https://ror.org/03z77qz90","country_code":"EE","type":"education","lineage":["https://openalex.org/I56085075"]}],"countries":["EE"],"is_corresponding":false,"raw_author_name":"Prasoon Kumar Vinodkumar","raw_affiliation_strings":["iCV Lab, Institute of Technology, University of Tartu, 51009 Tartu, Estonia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"iCV Lab, Institute of Technology, University of Tartu, 51009 Tartu, Estonia","institution_ids":["https://openalex.org/I56085075"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003249945","display_name":"Cagri Ozcinar","orcid":"https://orcid.org/0000-0003-4915-2251"},"institutions":[{"id":"https://openalex.org/I56085075","display_name":"University of Tartu","ror":"https://ror.org/03z77qz90","country_code":"EE","type":"education","lineage":["https://openalex.org/I56085075"]}],"countries":["EE"],"is_corresponding":false,"raw_author_name":"Cagri Ozcinar","raw_affiliation_strings":["iCV Lab, Institute of Technology, University of Tartu, 51009 Tartu, Estonia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"iCV Lab, Institute of Technology, University of Tartu, 51009 Tartu, Estonia","institution_ids":["https://openalex.org/I56085075"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005605270","display_name":"Gholamreza Anbarjafari","orcid":"https://orcid.org/0000-0001-8460-5717"},"institutions":[{"id":"https://openalex.org/I56085075","display_name":"University of Tartu","ror":"https://ror.org/03z77qz90","country_code":"EE","type":"education","lineage":["https://openalex.org/I56085075"]}],"countries":["EE"],"is_corresponding":true,"raw_author_name":"Gholamreza Anbarjafari","raw_affiliation_strings":["PwC Advisory Finland, 00180 Helsinki, Finland","iCV Lab, Institute of Technology, University of Tartu, 51009 Tartu, Estonia"],"raw_orcid":"https://orcid.org/0000-0001-8460-5717","affiliations":[{"raw_affiliation_string":"PwC Advisory Finland, 00180 Helsinki, Finland","institution_ids":[]},{"raw_affiliation_string":"iCV Lab, Institute of Technology, University of Tartu, 51009 Tartu, Estonia","institution_ids":["https://openalex.org/I56085075"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5005605270"],"corresponding_institution_ids":["https://openalex.org/I56085075"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2227},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2227},"fwci":0.8883,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.71649823,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"23","issue":"5","first_page":"608","last_page":"608"},"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":0.9968000054359436,"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":0.9876999855041504,"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":0.8379722237586975},{"id":"https://openalex.org/keywords/genome-editing","display_name":"Genome editing","score":0.7140089273452759},{"id":"https://openalex.org/keywords/cas9","display_name":"Cas9","score":0.703895628452301},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6800510287284851},{"id":"https://openalex.org/keywords/guide-rna","display_name":"Guide RNA","score":0.6423327922821045},{"id":"https://openalex.org/keywords/subgenomic-mrna","display_name":"Subgenomic mRNA","score":0.6190564036369324},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4772327244281769},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3750227093696594},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3178500235080719},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2596435546875}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.8379722237586975},{"id":"https://openalex.org/C144501496","wikidata":"https://www.wikidata.org/wiki/Q5533489","display_name":"Genome editing","level":4,"score":0.7140089273452759},{"id":"https://openalex.org/C132455925","wikidata":"https://www.wikidata.org/wiki/Q16965677","display_name":"Cas9","level":4,"score":0.703895628452301},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6800510287284851},{"id":"https://openalex.org/C97702854","wikidata":"https://www.wikidata.org/wiki/Q4039747","display_name":"Guide RNA","level":5,"score":0.6423327922821045},{"id":"https://openalex.org/C189819185","wikidata":"https://www.wikidata.org/wiki/Q384283","display_name":"Subgenomic mRNA","level":4,"score":0.6190564036369324},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4772327244281769},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3750227093696594},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3178500235080719},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2596435546875}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3390/e23050608","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e23050608","pdf_url":"https://www.mdpi.com/1099-4300/23/5/608/pdf?version=1620992029","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},{"id":"pmid:34069050","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34069050","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":"Entropy (Basel, Switzerland)","raw_type":null},{"id":"pmh:oai:doaj.org/article:24e1fe557416410ab1b476ecf0cbba88","is_oa":true,"landing_page_url":"https://doaj.org/article/24e1fe557416410ab1b476ecf0cbba88","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Entropy, Vol 23, Iss 5, p 608 (2021)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1099-4300/23/5/608/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/e23050608","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Entropy; Volume 23; Issue 5; Pages: 608","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8156774","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8156774","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":"Entropy (Basel)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/e23050608","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e23050608","pdf_url":"https://www.mdpi.com/1099-4300/23/5/608/pdf?version=1620992029","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W3162924147.pdf"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1608084731","https://openalex.org/W1922040927","https://openalex.org/W1973260880","https://openalex.org/W1982846895","https://openalex.org/W1984064827","https://openalex.org/W1990149668","https://openalex.org/W1990487336","https://openalex.org/W2003797386","https://openalex.org/W2011582941","https://openalex.org/W2030994161","https://openalex.org/W2036176224","https://openalex.org/W2045435533","https://openalex.org/W2051255304","https://openalex.org/W2063148079","https://openalex.org/W2064815984","https://openalex.org/W2077659966","https://openalex.org/W2085993152","https://openalex.org/W2095950258","https://openalex.org/W2097627856","https://openalex.org/W2118746294","https://openalex.org/W2131527797","https://openalex.org/W2133464522","https://openalex.org/W2139314409","https://openalex.org/W2140601463","https://openalex.org/W2149402050","https://openalex.org/W2163241233","https://openalex.org/W2247762492","https://openalex.org/W2252568502","https://openalex.org/W2273244674","https://openalex.org/W2461013690","https://openalex.org/W2726053863","https://openalex.org/W2727455004","https://openalex.org/W2778800886","https://openalex.org/W2782551527","https://openalex.org/W2810756255","https://openalex.org/W2889833989","https://openalex.org/W2891210592","https://openalex.org/W2902305894","https://openalex.org/W2905224888","https://openalex.org/W2973300930","https://openalex.org/W2977272800","https://openalex.org/W2981368271","https://openalex.org/W2982510384","https://openalex.org/W3003422837","https://openalex.org/W3007485829","https://openalex.org/W3010330848","https://openalex.org/W3032564623","https://openalex.org/W3105107487","https://openalex.org/W3105202247","https://openalex.org/W3114013865","https://openalex.org/W3136092383","https://openalex.org/W3139017962","https://openalex.org/W4245053291","https://openalex.org/W6646303671","https://openalex.org/W6769662530"],"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/W3052741125","https://openalex.org/W2667943050"],"abstract_inverted_index":{"CRISPR/Cas9":[0,26,118],"is":[1,28,41,87,92,121,130],"a":[2,88,106,134,143],"powerful":[3],"genome-editing":[4],"technology":[5],"that":[6,91,120],"has":[7],"been":[8,57],"widely":[9],"applied":[10],"in":[11,47,116,178],"targeted":[12],"gene":[13,16,48,185],"repair":[14],"and":[15,38,81,96,125,140,155,174,196],"expression":[17],"regulation.":[18],"One":[19],"of":[20,31,66,114,151,203],"the":[21,25,29,63,117,149,163,169,183,192],"main":[22],"challenges":[23],"for":[24,98,127,162],"system":[27,119],"occurrence":[30],"unexpected":[32],"cleavage":[33],"at":[34,71],"some":[35],"sites":[36],"(off-targets)":[37],"predicting":[39,191],"them":[40],"necessary":[42],"due":[43],"to":[44,61,94,110,123,147],"its":[45],"relevance":[46],"editing":[49],"research.":[50],"Very":[51],"few":[52],"deep":[53],"learning":[54,83],"models":[55],"have":[56],"developed":[58],"so":[59],"far":[60],"predict":[62,111,148],"off-target":[64,112,156,184,197],"propensity":[65],"single":[67],"guide":[68],"RNA":[69],"(sgRNA)":[70],"specific":[72],"DNA":[73,159],"fragments":[74],"by":[75,132,141,190],"using":[76,142],"artificial":[77],"feature":[78],"extract":[79],"operations":[80],"machine":[82],"techniques;":[84],"however,":[85],"this":[86,101],"convoluted":[89],"process":[90],"difficult":[93],"understand":[95,124],"implement":[97],"researchers.":[99,128],"In":[100],"research":[102],"work,":[103],"we":[104],"introduce":[105],"novel":[107],"graph-based":[108],"approach":[109],"efficacy":[113],"sgRNA":[115,154,195],"easy":[122],"replicate":[126],"This":[129],"achieved":[131],"creating":[133],"graph":[135],"with":[136,199],"sequences":[137,164,198],"as":[138],"nodes":[139],"link":[144,188],"prediction":[145],"method":[146],"presence":[150],"links":[152,193],"between":[153,194],"inducing":[157],"target":[158],"sequences.":[160,170],"Features":[161],"are":[165],"extracted":[166],"from":[167],"within":[168],"We":[171],"used":[172],"HEK293":[173],"K562":[175],"t":[176],"datasets":[177],"our":[179],"experiments.":[180],"GCN":[181],"predicted":[182],"knockouts":[186],"(using":[187],"prediction)":[189],"an":[200],"auROC":[201],"value":[202],"0.987.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
