{"id":"https://openalex.org/W2790921906","doi":"https://doi.org/10.1093/bioinformatics/bty095","title":"Improved genomic island predictions with IslandPath-DIMOB","display_name":"Improved genomic island predictions with IslandPath-DIMOB","publication_year":2018,"publication_date":"2018-02-22","ids":{"openalex":"https://openalex.org/W2790921906","doi":"https://doi.org/10.1093/bioinformatics/bty095","mag":"2790921906","pmid":"https://pubmed.ncbi.nlm.nih.gov/29905770"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2161/25098008/bty095.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2161/25098008/bty095.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051395377","display_name":"Claire Bertelli","orcid":"https://orcid.org/0000-0003-0550-8981"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Claire Bertelli","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050197558","display_name":"Fiona S. L. Brinkman","orcid":"https://orcid.org/0000-0002-0584-4099"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Fiona S L Brinkman","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5050197558"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.7781,"has_fulltext":false,"cited_by_count":224,"citation_normalized_percentile":{"value":0.96289329,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"34","issue":"13","first_page":"2161","last_page":"2167"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.33649998903274536,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.33649998903274536,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.12999999523162842,"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/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":0.05909999832510948,"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/computer-science","display_name":"Computer science","score":0.5092819929122925},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4496765434741974},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3127191960811615}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5092819929122925},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4496765434741974},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3127191960811615}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2161/25098008/bty095.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29905770","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29905770","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},{"id":"pmh:oai:pubmedcentral.nih.gov:6022643","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6022643","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2161/25098008/bty095.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7164556442","display_name":null,"funder_award_id":"P300PA_164673","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G8195779656","display_name":"IslandComPlot - enabling large scale comparison of bacterial genomic islands to investigate infectious disease outbreaks and Pseudomonas aeruginosa evolution","funder_award_id":"164673","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1553112231","https://openalex.org/W1819081776","https://openalex.org/W1849979647","https://openalex.org/W1927124817","https://openalex.org/W1956137100","https://openalex.org/W1964752634","https://openalex.org/W1967779392","https://openalex.org/W1968146772","https://openalex.org/W2029034654","https://openalex.org/W2054275184","https://openalex.org/W2088258525","https://openalex.org/W2089310071","https://openalex.org/W2108473040","https://openalex.org/W2115095549","https://openalex.org/W2120817193","https://openalex.org/W2121621283","https://openalex.org/W2129978006","https://openalex.org/W2133683841","https://openalex.org/W2138122982","https://openalex.org/W2145753399","https://openalex.org/W2151183612","https://openalex.org/W2158847524","https://openalex.org/W2166787839","https://openalex.org/W2224056471","https://openalex.org/W2228304976","https://openalex.org/W2305704688","https://openalex.org/W2307372947","https://openalex.org/W2342192228","https://openalex.org/W2380785990","https://openalex.org/W2565952559","https://openalex.org/W2610656577","https://openalex.org/W6657682888","https://openalex.org/W6698165869"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189"],"abstract_inverted_index":{"Motivation:":[0],"Genomic":[1],"islands":[2],"(GIs)":[3],"are":[4,27,244],"clusters":[5],"of":[6,8,28,51,71,106,115,174,204,213],"genes":[7,44],"probable":[9],"horizontal":[10],"origin":[11],"that":[12],"play":[13],"a":[14,77,125,134],"major":[15,119],"role":[16],"in":[17,38,82,155,210],"bacterial":[18],"and":[19,23,31,45,102,117,152,157,216,220,232],"archaeal":[20],"genome":[21],"evolution":[22],"microbial":[24,72,211],"adaptability.":[25],"They":[26],"high":[29,181],"medical":[30],"industrial":[32,217],"interest,":[33],"due":[34],"to":[35,97,142],"their":[36,207],"enrichment":[37],"virulence":[39],"factors,":[40],"some":[41],"antimicrobial":[42],"resistance":[43],"adaptive":[46],"metabolic":[47],"pathways.":[48],"The":[49,113,184],"development":[50],"more":[52,201],"sensitive":[53],"but":[54],"precise":[55],"prediction":[56,80,169],"tools,":[57],"using":[58,124],"either":[59],"sequence":[60,99],"composition-based":[61],"methods":[62,170],"or":[63],"comparative":[64,131],"genomics,":[65,132],"is":[66,224],"needed":[67],"as":[68,233],"large-scale":[69],"analyses":[70],"genomes":[73],"increase.":[74],"Results:":[75],"IslandPath-DIMOB,":[76],"leading":[78],"GI":[79,127],"tool":[81],"the":[83,94,103,143,162,175,228,238],"IslandViewer":[84,229],"webserver,":[85],"has":[86,121,161],"now":[87],"been":[88,122],"significantly":[89],"improved":[90],"by":[91,130],"modifying":[92],"both":[93],"decision":[95],"algorithm":[96],"determine":[98],"composition":[100],"biases,":[101],"underlying":[104],"database":[105],"HMM":[107],"profiles":[108],"for":[109],"associated":[110],"mobility":[111],"genes.":[112],"accuracy":[114],"IslandPath-DIMOB":[116,148,160,197,222],"other":[118],"software":[120,235],"assessed":[123],"reference":[126],"dataset":[128,137],"predicted":[129],"plus":[133],"manually":[135],"curated":[136],"from":[138],"literature":[139],"review.":[140],"Compared":[141],"previous":[144],"version":[145],"(v0.2.0),":[146],"this":[147],"v1.0.0":[149,198,223],"achieves":[150],"11.7%":[151],"5.3%":[153],"increase":[154],"recall":[156,177,189],"precision,":[158],"respectively.":[159],"highest":[163,176],"Matthews":[164],"correlation":[165],"coefficient":[166],"among":[167],"individual":[168],"tested,":[171],"combining":[172],"one":[173],"measures":[178],"(46.9%)":[179],"at":[180,246],"precision":[182,193],"(87.4%).":[183],"only":[185],"method":[186],"with":[187],"higher":[188],"had":[190],"notably":[191],"lower":[192],"(55.1%).":[194],"This":[195],"new":[196],"will":[199],"facilitate":[200],"accurate":[202],"studies":[203],"GIs,":[205],"including":[206],"key":[208],"roles":[209],"adaptability":[212],"medical,":[214],"environmental":[215],"interest.":[218],"Availability":[219],"implementation:":[221],"freely":[225],"available":[226,245],"through":[227],"webserver":[230],"{{http://www.pathogenomics.sfu.ca/islandviewer/}}":[231],"standalone":[234],"{{https://github.com/brinkmanlab/islandpath/}}":[236],"under":[237],"GNU-GPLv3.":[239],"Supplementary":[240,242],"information:":[241],"data":[243],"Bioinformatics":[247],"online.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":22},{"year":2025,"cited_by_count":49},{"year":2024,"cited_by_count":48},{"year":2023,"cited_by_count":26},{"year":2022,"cited_by_count":31},{"year":2021,"cited_by_count":26},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":3}],"updated_date":"2026-07-17T09:13:05.818461","created_date":"2025-10-10T00:00:00"}