{"id":"https://openalex.org/W2276690235","doi":"https://doi.org/10.1142/s0219720016400035","title":"GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome","display_name":"GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome","publication_year":2015,"publication_date":"2015-11-23","ids":{"openalex":"https://openalex.org/W2276690235","doi":"https://doi.org/10.1142/s0219720016400035","mag":"2276690235","pmid":"https://pubmed.ncbi.nlm.nih.gov/26907990"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720016400035","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720016400035","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5050387311","display_name":"Bingxin Lu","orcid":"https://orcid.org/0000-0002-0606-5150"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Bingxin Lu","raw_affiliation_strings":["Department of Computer Science, National University of Singapore, 13 Computing Drive, Singapore 117417, Republic of Singapore"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, 13 Computing Drive, Singapore 117417, Republic of Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037482622","display_name":"Wai Yie Leong","orcid":"https://orcid.org/0000-0002-5389-1121"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Hon Wai Leong","raw_affiliation_strings":["Department of Computer Science, National University of Singapore, 13 Computing Drive, Singapore 117417, Republic of Singapore"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, 13 Computing Drive, Singapore 117417, Republic of Singapore","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5050387311"],"corresponding_institution_ids":["https://openalex.org/I165932596"],"apc_list":null,"apc_paid":null,"fwci":1.3128,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.80580928,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"14","issue":"01","first_page":"1640003","last_page":"1640003"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9983999729156494,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.9958000183105469,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food 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/genome","display_name":"Genome","score":0.8891299962997437},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.7039487361907959},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.6024709343910217},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5669731497764587},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.520966649055481},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.47262808680534363},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3835858404636383},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3077881932258606},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19735711812973022}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8891299962997437},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.7039487361907959},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.6024709343910217},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5669731497764587},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.520966649055481},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.47262808680534363},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3835858404636383},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3077881932258606},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19735711812973022}],"mesh":[{"descriptor_ui":"D003353","descriptor_name":"Corynebacterium diphtheriae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003353","descriptor_name":"Corynebacterium diphtheriae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003353","descriptor_name":"Corynebacterium diphtheriae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011550","descriptor_name":"Pseudomonas aeruginosa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012485","descriptor_name":"Salmonella typhi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012485","descriptor_name":"Salmonella typhi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012485","descriptor_name":"Salmonella typhi","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044404","descriptor_name":"Genomic Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044404","descriptor_name":"Genomic Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044404","descriptor_name":"Genomic Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720016400035","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720016400035","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:26907990","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26907990","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 bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8700000047683716,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320698","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1571024744","https://openalex.org/W1964752634","https://openalex.org/W1967779392","https://openalex.org/W1968146772","https://openalex.org/W2021931962","https://openalex.org/W2042573466","https://openalex.org/W2073519406","https://openalex.org/W2074879055","https://openalex.org/W2086012088","https://openalex.org/W2097936772","https://openalex.org/W2105497548","https://openalex.org/W2108228587","https://openalex.org/W2113824405","https://openalex.org/W2114839482","https://openalex.org/W2124574960","https://openalex.org/W2129978006","https://openalex.org/W2139790819","https://openalex.org/W2145753399","https://openalex.org/W2151183612","https://openalex.org/W2151863305","https://openalex.org/W2165913026","https://openalex.org/W2172093365","https://openalex.org/W2492794003"],"related_works":["https://openalex.org/W2987420353","https://openalex.org/W2079327011","https://openalex.org/W2889029343","https://openalex.org/W1491897707","https://openalex.org/W2056973287","https://openalex.org/W2061340009","https://openalex.org/W3111025641","https://openalex.org/W3202542829","https://openalex.org/W1965562485","https://openalex.org/W2340204314"],"abstract_inverted_index":{"Genomic":[0],"islands":[1],"(GIs)":[2],"are":[3,17,24],"clusters":[4],"of":[5,58,84,104,140,162,192],"functionally":[6],"related":[7,69],"genes":[8,40],"acquired":[9],"by":[10],"lateral":[11],"genetic":[12],"transfer":[13],"(LGT),":[14],"and":[15,44],"they":[16,31],"present":[18],"in":[19,138,188,194],"many":[20],"bacterial":[21,28,87],"genomes.":[22,70,80,197],"GIs":[23,119],"extremely":[25],"important":[26],"for":[27,95,174,185],"research,":[29],"because":[30],"not":[32],"only":[33,121],"promote":[34],"genome":[35,124],"evolution":[36],"but":[37],"also":[38],"contain":[39],"that":[41],"enhance":[42],"adaption":[43],"enable":[45],"antibiotic":[46],"resistance.":[47],"Many":[48],"methods":[49,73,96],"have":[50],"been":[51],"proposed":[52],"to":[53,78,97,117,170],"predict":[54,118],"GI.":[55],"But":[56],"most":[57],"them":[59],"rely":[60],"on":[61,102,129,146],"either":[62],"annotations":[63],"or":[64],"comparisons":[65],"with":[66,156],"other":[67],"closely":[68],"Hence":[71],"these":[72],"cannot":[74],"be":[75],"easily":[76],"applied":[77],"new":[79],"As":[81],"the":[82,122],"number":[83],"newly":[85,195],"sequenced":[86,196],"genomes":[88],"rapidly":[89],"increases,":[90],"there":[91],"is":[92,127],"a":[93,105,113,181,189],"need":[94],"detect":[98],"GI":[99,193],"based":[100,128],"solely":[101],"sequences":[103],"single":[106],"genome.":[107,176],"In":[108,177],"this":[109],"paper,":[110],"we":[111],"propose":[112],"novel":[114],"method,":[115],"GI-SVM,":[116],"given":[120],"unannotated":[123],"sequence.":[125],"GI-SVM":[126,150,165,179],"one-class":[130],"support":[131],"vector":[132],"machine":[133],"(SVM),":[134],"utilizing":[135],"composition":[136],"bias":[137],"terms":[139],"k-mer":[141],"content.":[142],"From":[143],"our":[144],"evaluations":[145],"three":[147],"real":[148],"genomes,":[149],"can":[151],"achieve":[152],"higher":[153],"recall":[154],"compared":[155],"current":[157],"methods,":[158],"without":[159],"much":[160],"loss":[161],"precision.":[163],"Besides,":[164],"allows":[166],"flexible":[167],"parameter":[168],"tuning":[169],"get":[171],"optimal":[172],"results":[173],"each":[175],"short,":[178],"provides":[180],"more":[182],"sensitive":[183],"method":[184],"researchers":[186],"interested":[187],"first-pass":[190],"detection":[191]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
