{"id":"https://openalex.org/W2148285441","doi":"https://doi.org/10.1109/bibmw.2011.6112529","title":"An approach to phylogenomic analysis of bacterial pathogens","display_name":"An approach to phylogenomic analysis of bacterial pathogens","publication_year":2011,"publication_date":"2011-11-01","ids":{"openalex":"https://openalex.org/W2148285441","doi":"https://doi.org/10.1109/bibmw.2011.6112529","mag":"2148285441"},"language":"en","primary_location":{"id":"doi:10.1109/bibmw.2011.6112529","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2011.6112529","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","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/A5069076714","display_name":"Leonid Zaslavsky","orcid":"https://orcid.org/0000-0001-5873-4873"},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"L. Zaslavsky","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000089880","display_name":"Vyacheslav Chetvernin","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"V. Chetvernin","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080745883","display_name":"Dmitry Dernovoy","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Dernovoy","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047765716","display_name":"B. Fedorov","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. Fedorov","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060126033","display_name":"William Klimke","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. Klimke","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106185389","display_name":"A. Souvorov","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Souvorov","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039267538","display_name":"I. Tolstoy","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"I. Tolstoy","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073454926","display_name":"Tatiana Tatusova","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Tatusova","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056652131","display_name":"David J. Lipman","orcid":"https://orcid.org/0009-0002-3443-2023"},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. J. Lipman","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5069076714"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12781555,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"981","last_page":"981"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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":0.980400025844574,"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"}},{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.9666000008583069,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/genome","display_name":"Genome","score":0.8186323642730713},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8184301853179932},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.7419470548629761},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7096834778785706},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.5528485774993896},{"id":"https://openalex.org/keywords/phylum","display_name":"Phylum","score":0.5478817820549011},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5218762159347534},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5213797688484192},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.47011080384254456},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"Phylogenomics","score":0.456832617521286},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.45076027512550354},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.4420424997806549},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4380732774734497},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4355277717113495},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.41617390513420105},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.4147224426269531},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.4123958945274353},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3343926668167114}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8186323642730713},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8184301853179932},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.7419470548629761},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7096834778785706},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.5528485774993896},{"id":"https://openalex.org/C91066513","wikidata":"https://www.wikidata.org/wiki/Q38348","display_name":"Phylum","level":3,"score":0.5478817820549011},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5218762159347534},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5213797688484192},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.47011080384254456},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.456832617521286},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.45076027512550354},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.4420424997806549},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4380732774734497},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4355277717113495},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.41617390513420105},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.4147224426269531},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.4123958945274353},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3343926668167114}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibmw.2011.6112529","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2011.6112529","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5899999737739563,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4236476334","https://openalex.org/W2057191541","https://openalex.org/W2171532415","https://openalex.org/W1992296962","https://openalex.org/W2125609055","https://openalex.org/W4309766482","https://openalex.org/W2011735044","https://openalex.org/W2370031212","https://openalex.org/W4322421693","https://openalex.org/W4382652642"],"abstract_inverted_index":{"From":[0],"the":[1,4,40,84,167,197,217,220,224],"beginning":[2],"of":[3,20,39,56,73,86,98,116,121,131,153,169,223,249],"microbial":[5],"genome":[6,22,106,117,136,162],"sequencing":[7,48,78],"era,":[8],"researchers":[9],"have":[10,175],"shown":[11],"a":[12,31,54,80,96,113,139,143,161,231,235],"commendable":[13],"commitment":[14],"to":[15,82,89,178],"phylogenetic":[16,132,158,214,247],"diversity.":[17],"The":[18,104],"completion":[19],"one":[21],"from":[23,192],"each":[24,242],"prokaryotic":[25],"division":[26],"or":[27],"phylum":[28,193],"is":[29,226,252],"still":[30],"frequently":[32],"articulated":[33],"community":[34],"goal.":[35],"However,":[36],"largely":[37],"because":[38],"interest":[41],"in":[42,47,109],"human":[43],"pathogens":[44],"and":[45,63,93,124,128,183,189,204,208],"advances":[46],"technologies,":[49],"there":[50],"are":[51],"also":[52],"now":[53],"number":[55],"very":[57,232],"closely":[58],"related":[59],"genomes":[60,191,251],"whose":[61],"organization":[62],"gene":[64],"content":[65],"can":[66,94,209],"be":[67,95,210,239],"directly":[68],"compared.":[69],"Studying":[70],"genetic":[71],"variability":[72],"pathogenic":[74],"bacteria":[75],"using":[76,160],"whole-genome":[77],"provides":[79,138],"way":[81],"understanding":[83],"mechanism":[85],"bacterial":[87,105,155],"adaptation":[88],"rapid":[90],"environmental":[91],"changes":[92],"source":[97],"useful":[99],"information":[100],"on":[101,135,166,187],"virulence":[102],"mechanisms.":[103],"datasets":[107],"available":[108],"public":[110],"archives":[111],"represent":[112],"large":[114],"collection":[115],"at":[118,230],"different":[119],"levels":[120],"sequence":[122],"quality":[123],"assembly.":[125],"A":[126],"fast":[127],"reliable":[129,205],"method":[130,225],"classification":[133],"based":[134,165],"sequences":[137],"necessary":[140],"foundation":[141],"for":[142,180,212,219],"more":[144],"detailed":[145],"comparative":[146],"analysis.":[147],"NCBI":[148],"has":[149],"developed":[150],"an":[151],"approach":[152],"grouping":[154],"organisms":[156],"into":[157],"clades":[159],"dissimilarity":[163],"measure":[164],"comparison":[168],"universally":[170],"conserved":[171],"markers.":[172],"Special":[173],"adjustments":[174],"been":[176],"made":[177],"compensate":[179],"data":[181],"inaccuracy":[182],"incompleteness.":[184],"Tests":[185],"performed":[186],"complete":[188],"draft":[190],"Proteobacteria":[194],"demonstrated":[195],"that":[196],"proposed":[198],"robust":[199],"genomic":[200],"distance":[201],"allows":[202],"stable":[203],"species-level":[206],"clustering":[207],"used":[211],"forming":[213],"clades.":[215],"Since":[216],"tradeoff":[218],"increased":[221],"robustness":[222],"its":[227],"limited":[228],"sensitivity":[229],"fine":[233],"level,":[234],"phylogenomic":[236],"refinement":[237],"could":[238],"done":[240],"within":[241],"constructed":[243],"clade":[244],"when":[245],"file-level":[246],"resolution":[248],"close":[250],"necessary.":[253]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
