{"id":"https://openalex.org/W2746228932","doi":"https://doi.org/10.1145/3107411.3108214","title":"Dynamic Phylogenetic Inference for Sequence-based Typing Data","display_name":"Dynamic Phylogenetic Inference for Sequence-based Typing Data","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2746228932","doi":"https://doi.org/10.1145/3107411.3108214","mag":"2746228932"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3108214","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108214","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/10400.21/13316","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110540557","display_name":"Alexandre P. Francisco","orcid":"https://orcid.org/0000-0003-4852-1641"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Alexandre P. Francisco","raw_affiliation_strings":["University of Lisbon, Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"University of Lisbon, Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034448156","display_name":"Marta Nascimento","orcid":null},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Marta Nascimento","raw_affiliation_strings":["University of Lisbon, Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"University of Lisbon, Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041077284","display_name":"C\u00e1tia Vaz","orcid":"https://orcid.org/0000-0001-6074-3074"},"institutions":[{"id":"https://openalex.org/I203847022","display_name":"Instituto Polit\u00e9cnico de Lisboa","ror":"https://ror.org/04ea70f07","country_code":"PT","type":"education","lineage":["https://openalex.org/I203847022"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"C\u00e1tia Vaz","raw_affiliation_strings":["Polythenic Institute of Lisbon, Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"Polythenic Institute of Lisbon, Lisboa, Portugal","institution_ids":["https://openalex.org/I203847022"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5110540557"],"corresponding_institution_ids":["https://openalex.org/I141596103"],"apc_list":null,"apc_paid":null,"fwci":0.1123,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.51127537,"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":"604","last_page":"604"},"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9534000158309937,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9440000057220459,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7706931829452515},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6091770529747009},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5535140037536621},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4888409972190857},{"id":"https://openalex.org/keywords/typing","display_name":"Typing","score":0.4636788070201874},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.46363967657089233},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33493945002555847},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11201679706573486}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7706931829452515},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6091770529747009},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5535140037536621},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4888409972190857},{"id":"https://openalex.org/C2781209916","wikidata":"https://www.wikidata.org/wiki/Q3215756","display_name":"Typing","level":2,"score":0.4636788070201874},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.46363967657089233},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33493945002555847},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11201679706573486},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C28490314","wikidata":"https://www.wikidata.org/wiki/Q189436","display_name":"Speech recognition","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/3107411.3108214","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108214","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:repositorio.ipl.pt:10400.21/13316","is_oa":true,"landing_page_url":"http://hdl.handle.net/10400.21/13316","pdf_url":null,"source":{"id":"https://openalex.org/S4306400762","display_name":"Reposit\u00f3rio Cient\u00edfico do Instituto Polit\u00e9cnico de Lisboa (Instituto Polit\u00e9cnico de Lisboa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I203847022","host_organization_name":"Instituto Polit\u00e9cnico de Lisboa","host_organization_lineage":["https://openalex.org/I203847022"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conference object"},{"id":"pmh:oai:repositorio.ipl.pt:10400.21/9813","is_oa":true,"landing_page_url":"http://hdl.handle.net/10400.21/9813","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conference object"}],"best_oa_location":{"id":"pmh:oai:repositorio.ipl.pt:10400.21/13316","is_oa":true,"landing_page_url":"http://hdl.handle.net/10400.21/13316","pdf_url":null,"source":{"id":"https://openalex.org/S4306400762","display_name":"Reposit\u00f3rio Cient\u00edfico do Instituto Polit\u00e9cnico de Lisboa (Instituto Polit\u00e9cnico de Lisboa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I203847022","host_organization_name":"Instituto Polit\u00e9cnico de Lisboa","host_organization_lineage":["https://openalex.org/I203847022"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conference object"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2582522631","display_name":null,"funder_award_id":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G5658732297","display_name":null,"funder_award_id":"TUBITACK/0004/2014","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6647558509","display_name":null,"funder_award_id":"UID/CEC/500021/2013","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7984092497","display_name":null,"funder_award_id":"SAICTPAC/0021/2015","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W1584328577","https://openalex.org/W1999417916","https://openalex.org/W2330229417","https://openalex.org/W2342204193","https://openalex.org/W2400243543","https://openalex.org/W4299924427"],"related_works":["https://openalex.org/W3176169626","https://openalex.org/W1606200072","https://openalex.org/W4312203868","https://openalex.org/W2069013776","https://openalex.org/W2057351134","https://openalex.org/W1979674660","https://openalex.org/W2038264393","https://openalex.org/W2059637021","https://openalex.org/W1981020211","https://openalex.org/W2013429256"],"abstract_inverted_index":{"Typing":[0],"methods":[1],"are":[2],"widely":[3],"used":[4],"in":[5,28],"the":[6,16,31,39,42,62,109],"surveillance":[7],"of":[8,15,19,33,57,87,118],"infectious":[9],"diseases,":[10],"outbreaks":[11],"investigation":[12],"and":[13,48,103],"studies":[14],"natural":[17],"history":[18],"an":[20],"infection.":[21],"And":[22],"their":[23],"use":[24],"is":[25,46,97],"becoming":[26],"standard,":[27],"particular":[29],"with":[30],"introduction":[32],"High":[34],"Throughput":[35],"Sequencing":[36],"(HTS).":[37],"On":[38],"other":[40],"hand,":[41],"data":[43,73,102],"being":[44],"generated":[45],"massive":[47],"many":[49],"algorithms":[50,66],"have":[51],"been":[52],"proposed":[53],"for":[54],"phylogenetic":[55],"analysis":[56],"typing":[58],"data,":[59],"such":[60],"as":[61],"goeBURST":[63,88],"algorithm.":[64,89],"These":[65],"must":[67],"however":[68],"be":[69],"run":[70],"whenever":[71],"new":[72,95,101],"becomes":[74],"available":[75],"starting":[76],"from":[77],"scratch.":[78],"We":[79],"address":[80],"this":[81,94],"issue":[82],"proposing":[83],"a":[84],"dynamic":[85],"version":[86,96],"Experimental":[90],"results":[91],"show":[92],"that":[93],"efficient":[98],"on":[99],"integrating":[100],"updating":[104],"inferred":[105],"evolutionary":[106],"patterns,":[107],"improving":[108],"update":[110],"running":[111],"time":[112],"by":[113],"at":[114],"least":[115],"one":[116],"order":[117],"magnitude.":[119]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
