{"id":"https://openalex.org/W2982537523","doi":"https://doi.org/10.1109/nextcomp.2019.8883624","title":"Detection of Genome Sequence Outliers Across Pan-Genomes","display_name":"Detection of Genome Sequence Outliers Across Pan-Genomes","publication_year":2019,"publication_date":"2019-09-01","ids":{"openalex":"https://openalex.org/W2982537523","doi":"https://doi.org/10.1109/nextcomp.2019.8883624","mag":"2982537523"},"language":"en","primary_location":{"id":"doi:10.1109/nextcomp.2019.8883624","is_oa":false,"landing_page_url":"https://doi.org/10.1109/nextcomp.2019.8883624","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 Conference on Next Generation Computing Applications (NextComp)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5061771901","display_name":"Lakshmi Sujeeun","orcid":"https://orcid.org/0000-0002-0030-2135"},"institutions":[{"id":"https://openalex.org/I69072986","display_name":"University of Mauritius","ror":"https://ror.org/05cyprz33","country_code":"MU","type":"education","lineage":["https://openalex.org/I69072986"]}],"countries":["MU"],"is_corresponding":true,"raw_author_name":"Lakshmi Sujeeun","raw_affiliation_strings":["Center for Biomedical and Biomaterials Research, University of Mauritius, Reduit, Mauritius"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical and Biomaterials Research, University of Mauritius, Reduit, Mauritius","institution_ids":["https://openalex.org/I69072986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007832378","display_name":"Shakuntala Baichoo","orcid":"https://orcid.org/0000-0002-9335-1939"},"institutions":[{"id":"https://openalex.org/I69072986","display_name":"University of Mauritius","ror":"https://ror.org/05cyprz33","country_code":"MU","type":"education","lineage":["https://openalex.org/I69072986"]}],"countries":["MU"],"is_corresponding":false,"raw_author_name":"Shakuntala Baichoo","raw_affiliation_strings":["Faculty of Information, Communication and Digital Technologies, University of Mauritius Reduit, Mauritius"],"affiliations":[{"raw_affiliation_string":"Faculty of Information, Communication and Digital Technologies, University of Mauritius Reduit, Mauritius","institution_ids":["https://openalex.org/I69072986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040931751","display_name":"Zahra Mungloo-Dilmohamud","orcid":"https://orcid.org/0000-0002-1751-5487"},"institutions":[{"id":"https://openalex.org/I69072986","display_name":"University of Mauritius","ror":"https://ror.org/05cyprz33","country_code":"MU","type":"education","lineage":["https://openalex.org/I69072986"]}],"countries":["MU"],"is_corresponding":false,"raw_author_name":"Zahra Mungloo-Dilmohamud","raw_affiliation_strings":["Faculty of Information, Communication and Digital Technologies, University of Mauritius Reduit, Mauritius"],"affiliations":[{"raw_affiliation_string":"Faculty of Information, Communication and Digital Technologies, University of Mauritius Reduit, Mauritius","institution_ids":["https://openalex.org/I69072986"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083351004","display_name":"Yasmina Jaufeerally\u2010Fakim","orcid":null},"institutions":[{"id":"https://openalex.org/I69072986","display_name":"University of Mauritius","ror":"https://ror.org/05cyprz33","country_code":"MU","type":"education","lineage":["https://openalex.org/I69072986"]}],"countries":["MU"],"is_corresponding":false,"raw_author_name":"Yasmina Jaufeerally-Fakim","raw_affiliation_strings":["Faculty of Agriculture, University of Mauritius, Reduit, Mauritius"],"affiliations":[{"raw_affiliation_string":"Faculty of Agriculture, University of Mauritius, Reduit, Mauritius","institution_ids":["https://openalex.org/I69072986"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5061771901"],"corresponding_institution_ids":["https://openalex.org/I69072986"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.19363011,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"184","issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11153","display_name":"Streptococcal Infections and Treatments","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11153","display_name":"Streptococcal Infections and Treatments","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9958999752998352,"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/T10195","display_name":"Antimicrobial Resistance in Staphylococcus","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.8506700992584229},{"id":"https://openalex.org/keywords/streptococcus-sanguinis","display_name":"Streptococcus sanguinis","score":0.7216668128967285},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6793222427368164},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.610133171081543},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.5265153646469116},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5105510950088501},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4932076334953308},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4700941741466522},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.46226632595062256},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4328669607639313},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.4298173189163208},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.421996533870697},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.05412024259567261}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8506700992584229},{"id":"https://openalex.org/C2777867728","wikidata":"https://www.wikidata.org/wiki/Q2033849","display_name":"Streptococcus sanguinis","level":4,"score":0.7216668128967285},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6793222427368164},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.610133171081543},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.5265153646469116},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5105510950088501},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4932076334953308},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4700941741466522},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.46226632595062256},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4328669607639313},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.4298173189163208},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.421996533870697},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.05412024259567261},{"id":"https://openalex.org/C58123911","wikidata":"https://www.wikidata.org/wiki/Q467410","display_name":"Biofilm","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/nextcomp.2019.8883624","is_oa":false,"landing_page_url":"https://doi.org/10.1109/nextcomp.2019.8883624","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 Conference on Next Generation Computing Applications (NextComp)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.4000000059604645}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1519815462","https://openalex.org/W1850890413","https://openalex.org/W1936788844","https://openalex.org/W1963459864","https://openalex.org/W1968298460","https://openalex.org/W1971377345","https://openalex.org/W1988973871","https://openalex.org/W2014064754","https://openalex.org/W2016005362","https://openalex.org/W2031487259","https://openalex.org/W2041267682","https://openalex.org/W2041716296","https://openalex.org/W2055615325","https://openalex.org/W2079327011","https://openalex.org/W2082819719","https://openalex.org/W2092979861","https://openalex.org/W2103279361","https://openalex.org/W2103412835","https://openalex.org/W2108035844","https://openalex.org/W2109982529","https://openalex.org/W2113824405","https://openalex.org/W2117207428","https://openalex.org/W2119999417","https://openalex.org/W2122673596","https://openalex.org/W2125591244","https://openalex.org/W2134375163","https://openalex.org/W2141735861","https://openalex.org/W2142678478","https://openalex.org/W2150550043","https://openalex.org/W2156133126","https://openalex.org/W2157180542","https://openalex.org/W2157267947","https://openalex.org/W2160932169","https://openalex.org/W2168147993","https://openalex.org/W2324632057","https://openalex.org/W2335901076","https://openalex.org/W2414506155","https://openalex.org/W2417071471","https://openalex.org/W2558724937","https://openalex.org/W2559088283","https://openalex.org/W2617471186","https://openalex.org/W2800301968","https://openalex.org/W2800417838","https://openalex.org/W2803776132","https://openalex.org/W2949102320","https://openalex.org/W6631042569"],"related_works":["https://openalex.org/W4401039366","https://openalex.org/W2099015554","https://openalex.org/W776456635","https://openalex.org/W4388195308","https://openalex.org/W2746495695","https://openalex.org/W4362559663","https://openalex.org/W2936106179","https://openalex.org/W2276390413","https://openalex.org/W2805885671","https://openalex.org/W602433794"],"abstract_inverted_index":{"Thousands":[0],"of":[1,4,17,28,47,57,67,87,109,125,143,169],"genomic":[2,95,117],"sequences":[3,72,118],"multiple":[5,35],"microbial":[6],"species":[7,104],"have":[8],"already":[9],"been":[10],"deciphered,":[11],"providing":[12],"us":[13],"with":[14,154,159],"extensive":[15],"vistas":[16],"variation":[18],"at":[19],"the":[20,53,58,134,166,170],"micro-":[21],"and":[22,97,115,184,203],"macro-evolutionary":[23],"levels.":[24],"Pan-genomes":[25],"denote":[26],"sets":[27],"all":[29],"unique":[30],"gene":[31,55,185],"families":[32],"found":[33],"in":[34,38,129,176,199],"related":[36,45],"genomes":[37],"a":[39,48,65,68,85,107,141,150,192,200],"given":[40,69],"taxon":[41,70],"-":[42],"for":[43,196],"instance":[44],"strains":[46,89],"bacterial":[49,103],"species,":[50],"thus":[51,164],"representing":[52,106],"entire":[54],"pool":[56],"taxon.":[59],"We":[60],"demonstrate":[61],"here":[62],"that":[63,101,133],"characterizing":[64],"pan-genome":[66,182,197],"using":[71],"generated":[73],"from":[74],"different":[75],"genome":[76,81,147],"projects":[77],"can":[78],"misguide":[79],"subsequent":[80],"comparison":[82],"studies":[83],"when":[84],"set":[86],"incorrect":[88],"is":[90],"selected":[91],"as":[92,121],"input.":[93],"Deploying":[94],"resources":[96],"tools,":[98],"we":[99],"report":[100],"seven":[102],"datasets,":[105],"total":[108],"249":[110],"strains,":[111,163],"contained":[112],"\"contaminating\"":[113],"data":[114],"11":[116],"were":[119],"identified":[120],"outliers.":[122],"The":[123],"example":[124],"Streptococcus":[126,145,155,161],"sanguinis":[127,146,162],"used":[128],"this":[130,177],"study":[131,178],"revealed":[132],"outlier":[135,167],"strain":[136,171],"ATCC":[137,172],"49296,":[138],"detected":[139],"among":[140],"dataset":[142],"23":[144],"sequences,":[148],"showed":[149],"much":[151],"closer":[152],"relationship":[153],"oralis":[156],"35037T":[157],"than":[158],"other":[160,209],"confirming":[165],"status":[168],"49296.":[173],"Results":[174],"provided":[175],"are":[179],"supported":[180],"by":[181],"trees":[183],"sequence-":[186],"based":[187],"phylogeny.":[188],"This":[189],"approach":[190],"provides":[191],"better":[193],"quality":[194],"control":[195],"analysis":[198],"rapid,":[201],"efficient":[202],"scalable":[204],"manner":[205],"including":[206],"application":[207],"to":[208],"taxa.":[210]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}