{"id":"https://openalex.org/W4387250751","doi":"https://doi.org/10.1109/cibcb56990.2023.10264900","title":"Bacterial phenotype prediction based on methylation site profiles","display_name":"Bacterial phenotype prediction based on methylation site profiles","publication_year":2023,"publication_date":"2023-08-29","ids":{"openalex":"https://openalex.org/W4387250751","doi":"https://doi.org/10.1109/cibcb56990.2023.10264900"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb56990.2023.10264900","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/cibcb56990.2023.10264900","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","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/A5036770431","display_name":"Mark\u00e9ta Nykr\u00fdnov\u00e1","orcid":"https://orcid.org/0000-0002-0205-6935"},"institutions":[{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Marketa Nykrynova","raw_affiliation_strings":["Brno University of Technology,Department of Biomedical Engineering,Brno,Czechia","Department of Biomedical Engineering, Brno University of Technology, Brno, Czechia"],"affiliations":[{"raw_affiliation_string":"Brno University of Technology,Department of Biomedical Engineering,Brno,Czechia","institution_ids":["https://openalex.org/I60587646"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Brno University of Technology, Brno, Czechia","institution_ids":["https://openalex.org/I60587646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021543198","display_name":"Mat\u011bj Bezd\u00ed\u010dek","orcid":"https://orcid.org/0000-0002-5833-8325"},"institutions":[{"id":"https://openalex.org/I4210102302","display_name":"University Hospital Brno","ror":"https://ror.org/00qq1fp34","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210102302"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Matej Bezdicek","raw_affiliation_strings":["University Hospital Brno,Department of Internal Medicine - Haematology and Oncology,Brno,Czechia","Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czechia"],"affiliations":[{"raw_affiliation_string":"University Hospital Brno,Department of Internal Medicine - Haematology and Oncology,Brno,Czechia","institution_ids":["https://openalex.org/I4210102302"]},{"raw_affiliation_string":"Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czechia","institution_ids":["https://openalex.org/I4210102302"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014908038","display_name":"Martina Lengerov\u00e1","orcid":"https://orcid.org/0000-0001-8739-9998"},"institutions":[{"id":"https://openalex.org/I4210102302","display_name":"University Hospital Brno","ror":"https://ror.org/00qq1fp34","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210102302"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Martina Lengerova","raw_affiliation_strings":["University Hospital Brno,Department of Internal Medicine - Haematology and Oncology,Brno,Czechia","Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czechia"],"affiliations":[{"raw_affiliation_string":"University Hospital Brno,Department of Internal Medicine - Haematology and Oncology,Brno,Czechia","institution_ids":["https://openalex.org/I4210102302"]},{"raw_affiliation_string":"Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czechia","institution_ids":["https://openalex.org/I4210102302"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049637180","display_name":"Helena \u0160kutkov\u00e1","orcid":"https://orcid.org/0000-0003-4562-2746"},"institutions":[{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Helena Skutkova","raw_affiliation_strings":["Brno University of Technology,Department of Biomedical Engineering,Brno,Czechia","Department of Biomedical Engineering, Brno University of Technology, Brno, Czechia"],"affiliations":[{"raw_affiliation_string":"Brno University of Technology,Department of Biomedical Engineering,Brno,Czechia","institution_ids":["https://openalex.org/I60587646"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Brno University of Technology, Brno, Czechia","institution_ids":["https://openalex.org/I60587646"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5036770431"],"corresponding_institution_ids":["https://openalex.org/I60587646"],"apc_list":null,"apc_paid":null,"fwci":0.1592,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.59603953,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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":0.9987999796867371,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9887999892234802,"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":0.9843000173568726,"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/biology","display_name":"Biology","score":0.6408683061599731},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6173164248466492},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6108296513557434},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5988254547119141},{"id":"https://openalex.org/keywords/intergenic-region","display_name":"Intergenic region","score":0.5879031419754028},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.5752273201942444},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.5627930164337158},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5194008350372314},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.488706111907959},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.45757389068603516},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.4375265836715698},{"id":"https://openalex.org/keywords/dna-sequencer","display_name":"DNA sequencer","score":0.43737146258354187},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.4216839373111725},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3585048317909241},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.23083949089050293}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6408683061599731},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6173164248466492},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6108296513557434},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5988254547119141},{"id":"https://openalex.org/C195139083","wikidata":"https://www.wikidata.org/wiki/Q3463539","display_name":"Intergenic region","level":4,"score":0.5879031419754028},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5752273201942444},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.5627930164337158},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5194008350372314},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.488706111907959},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.45757389068603516},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4375265836715698},{"id":"https://openalex.org/C70712619","wikidata":"https://www.wikidata.org/wiki/Q908889","display_name":"DNA sequencer","level":4,"score":0.43737146258354187},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.4216839373111725},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3585048317909241},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.23083949089050293},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb56990.2023.10264900","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/cibcb56990.2023.10264900","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1974883084","https://openalex.org/W2024848067","https://openalex.org/W2065461553","https://openalex.org/W2121703775","https://openalex.org/W2134861388","https://openalex.org/W2134977238","https://openalex.org/W2168069435","https://openalex.org/W2231664225","https://openalex.org/W2270848678","https://openalex.org/W2346680365","https://openalex.org/W2548672526","https://openalex.org/W2591330300","https://openalex.org/W2735521454","https://openalex.org/W2771499133","https://openalex.org/W2891078715","https://openalex.org/W2900423390","https://openalex.org/W2914786907","https://openalex.org/W2951434717","https://openalex.org/W2963689420","https://openalex.org/W2990088567","https://openalex.org/W2995813047","https://openalex.org/W3010221984","https://openalex.org/W3081894105","https://openalex.org/W3131630024","https://openalex.org/W3134082414","https://openalex.org/W3136952346","https://openalex.org/W3151608695","https://openalex.org/W3170621487","https://openalex.org/W3173258969","https://openalex.org/W3175842380","https://openalex.org/W3193789503","https://openalex.org/W4205809000","https://openalex.org/W4206039299"],"related_works":["https://openalex.org/W2982006786","https://openalex.org/W2181443374","https://openalex.org/W2263329608","https://openalex.org/W1987280265","https://openalex.org/W2391967221","https://openalex.org/W2088759376","https://openalex.org/W1617115804","https://openalex.org/W2118769983","https://openalex.org/W2340744449","https://openalex.org/W2106267607"],"abstract_inverted_index":{"Methylated":[0],"site":[1,86,130],"mapping":[2,91],"in":[3,11,101,132,158],"the":[4,13,93,122,126,141,165],"DNA":[5,24,84],"sequences":[6],"plays":[7],"a":[8,51,62,79,117,133],"key":[9],"role":[10],"understanding":[12],"physiology":[14],"and":[15,19,160],"pathology":[16],"of":[17,64,113,125,135,143],"cells":[18],"organisms.":[20],"Thanks":[21],"to":[22,68,92,97,116],"third-generation":[23],"sequencers,":[25],"these":[26],"epigenetic":[27],"modifications":[28],"can":[29,46,168],"be":[30,47,169],"detected":[31],"already":[32],"when":[33],"reading":[34],"genetic":[35],"information.":[36],"Therefore,":[37],"not":[38],"only":[39],"genotypic":[40],"classification":[41,71],"but":[42],"also":[43],"phenotypic":[44],"specifications":[45],"determined":[48],"based":[49],"on":[50],"single":[52,118],"sequencing":[53,89],"run.":[54],"However,":[55],"for":[56,73,82,140],"phenotyping":[57],"purposes,":[58],"there":[59],"is":[60],"still":[61],"lack":[63],"effective":[65],"standardized":[66],"tools":[67],"design":[69],"uniform":[70],"schemes":[72],"different":[74],"laboratories.":[75],"Here,":[76],"we":[77],"present":[78],"simple":[80],"tool":[81],"comparing":[83],"methylation":[85],"profiles,":[87],"utilizing":[88],"reads":[90,109],"reference":[94],"genome":[95,99],"similar":[96],"core":[98],"analysis":[100],"bacterial":[102,136,174],"genotyping.":[103],"The":[104],"proposed":[105],"pipeline":[106],"maps":[107],"sequence":[108,166],"with":[110],"marked":[111],"positions":[112,131],"methylated":[114,129,145,156],"bases":[115],"representative":[119],"reference.":[120],"Thus":[121],"output":[123],"consists":[124],"uniformly":[127],"aligned":[128],"set":[134],"genomes.":[137],"This":[138],"allows":[139],"evaluation":[142],"common":[144],"sites":[146,157],"across":[147],"all":[148],"genomes,":[149],"i.e.,,core":[150],"methylome\u201d,":[151],"as":[152,154,177],"well":[153],"unique":[155],"gene":[159],"intergenic":[161],"regions.":[162],"Thus,":[163],"determining":[164],"type":[167],"further":[170],"refined":[171],"by":[172],"predicting":[173],"behaviour":[175],"such":[176],"antibiotic":[178],"resistance":[179],"or":[180],"virulence.":[181]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2025-12-22T23:10:17.713674","created_date":"2025-10-10T00:00:00"}
