{"id":"https://openalex.org/W2120764558","doi":null,"title":"Towards a new paradigm linking virus molecular evolution and pathogenesis: experimental design and phylodynamic inference.","display_name":"Towards a new paradigm linking virus molecular evolution and pathogenesis: experimental design and phylodynamic inference.","publication_year":2012,"publication_date":"2012-04-01","ids":{"openalex":"https://openalex.org/W2120764558","mag":"2120764558","pmid":"https://pubmed.ncbi.nlm.nih.gov/22707126"},"language":"en","primary_location":{"id":"pmid:22707126","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22707126","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,"listed_in":[],"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":"The new microbiologica","raw_type":"Journal Article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["pubmed"],"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/A5012396011","display_name":"Melissa M. Norstr\u00f6m","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Melissa M Norstr\u00f6m","raw_affiliation_strings":["Department of Laboratory Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Laboratory Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082445631","display_name":"Annika C. Karlsson","orcid":"https://orcid.org/0000-0002-2028-8393","observed_orcids":["https://orcid.org/0000-0002-2028-8393"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Annika C Karlsson","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5030387965","display_name":"Marco Salemi","orcid":"https://orcid.org/0000-0003-0136-2102","observed_orcids":["https://orcid.org/0000-0003-0136-2102"]},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marco Salemi","raw_affiliation_strings":["[University of Florida]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"[University of Florida]","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4399,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.58514539,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":87,"max":96},"biblio":{"volume":"35","issue":"2","first_page":"101","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9839000105857849,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9839000105857849,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.004100000020116568,"subfield":{"id":"https://openalex.org/subfields/2604","display_name":"Applied Mathematics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0038999998942017555,"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/phylodynamics","display_name":"phylodynamics","score":0.9959999918937683},{"id":"https://openalex.org/keywords/viral-pathogenesis","display_name":"viral pathogenesis","score":0.8460000157356262},{"id":"https://openalex.org/keywords/experimental-design","display_name":"experimental design","score":0.8259999752044678},{"id":"https://openalex.org/keywords/intra-host-viral-evolution","display_name":"intra-host viral evolution","score":0.8519999980926514},{"id":"https://openalex.org/keywords/population-dynamics","display_name":"population dynamics","score":0.6010000109672546},{"id":"https://openalex.org/keywords/infectious-disease-pandemics","display_name":"infectious disease pandemics","score":0.8240000009536743},{"id":"https://openalex.org/keywords/rna-viruses","display_name":"RNA viruses","score":0.8709999918937683},{"id":"https://openalex.org/keywords/retroviruses","display_name":"retroviruses","score":0.996999979019165},{"id":"https://openalex.org/keywords/epidemiological-data","display_name":"epidemiological data","score":0.6729999780654907}],"concepts":[{"id":"https://openalex.org/C21833749","wikidata":"https://www.wikidata.org/wiki/Q7189431","display_name":"Viral phylodynamics","level":4,"score":0.9528446197509766},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6461285948753357},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.6431496143341064},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5983770489692688},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5861895084381104},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5699620246887207},{"id":"https://openalex.org/C8769409","wikidata":"https://www.wikidata.org/wiki/Q2066554","display_name":"Viral evolution","level":4,"score":0.5419983863830566},{"id":"https://openalex.org/C166393388","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Molecular evolution","level":4,"score":0.4661824405193329},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4515775740146637},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.4322833716869354},{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.415763795375824},{"id":"https://openalex.org/C89623803","wikidata":"https://www.wikidata.org/wiki/Q12184","display_name":"Pandemic","level":5,"score":0.41291919350624084},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.2811640501022339},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23618367314338684},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.16787749528884888},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.1573563814163208},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.15670984983444214},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08173757791519165},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.08060118556022644},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014777","descriptor_name":"Virus Diseases","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"pmid:22707126","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22707126","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,"listed_in":[],"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":"The new microbiologica","raw_type":"Journal Article"},{"id":"mag:2120764558","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22707126","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,"listed_in":[],"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":null,"is_accepted":false,"is_published":false,"raw_source_name":"PubMed","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":86,"referenced_works":["https://openalex.org/W265112487","https://openalex.org/W569294424","https://openalex.org/W1493083214","https://openalex.org/W1530675242","https://openalex.org/W1534406401","https://openalex.org/W1545804207","https://openalex.org/W1588193375","https://openalex.org/W1692577869","https://openalex.org/W1962897568","https://openalex.org/W1964738454","https://openalex.org/W1968494119","https://openalex.org/W1969035202","https://openalex.org/W1970472356","https://openalex.org/W1972639541","https://openalex.org/W1973667633","https://openalex.org/W1974464383","https://openalex.org/W1978087960","https://openalex.org/W1978444265","https://openalex.org/W1980030331","https://openalex.org/W1982494640","https://openalex.org/W1987174734","https://openalex.org/W1992579646","https://openalex.org/W1993167804","https://openalex.org/W2001259823","https://openalex.org/W2002446259","https://openalex.org/W2002768536","https://openalex.org/W2005412543","https://openalex.org/W2006556166","https://openalex.org/W2008635309","https://openalex.org/W2009111710","https://openalex.org/W2009950794","https://openalex.org/W2016358361","https://openalex.org/W2020474114","https://openalex.org/W2020674176","https://openalex.org/W2030919551","https://openalex.org/W2031830783","https://openalex.org/W2038852567","https://openalex.org/W2039440086","https://openalex.org/W2039980955","https://openalex.org/W2041076979","https://openalex.org/W2041903808","https://openalex.org/W2052558548","https://openalex.org/W2053043249","https://openalex.org/W2063839249","https://openalex.org/W2065461553","https://openalex.org/W2069881886","https://openalex.org/W2083436647","https://openalex.org/W2084513007","https://openalex.org/W2084725601","https://openalex.org/W2087076382","https://openalex.org/W2088701712","https://openalex.org/W2092500478","https://openalex.org/W2094939159","https://openalex.org/W2097585709","https://openalex.org/W2100401777","https://openalex.org/W2103849916","https://openalex.org/W2104917264","https://openalex.org/W2106549255","https://openalex.org/W2108457462","https://openalex.org/W2108504053","https://openalex.org/W2116453268","https://openalex.org/W2120622846","https://openalex.org/W2121009566","https://openalex.org/W2126515754","https://openalex.org/W2129141072","https://openalex.org/W2129607320","https://openalex.org/W2130333286","https://openalex.org/W2140607780","https://openalex.org/W2140689424","https://openalex.org/W2142657851","https://openalex.org/W2142773663","https://openalex.org/W2144413761","https://openalex.org/W2148314976","https://openalex.org/W2148686896","https://openalex.org/W2152365654","https://openalex.org/W2153432740","https://openalex.org/W2153878586","https://openalex.org/W2154283429","https://openalex.org/W2155998147","https://openalex.org/W2156084908","https://openalex.org/W2162990662","https://openalex.org/W2163357043","https://openalex.org/W2164582219","https://openalex.org/W2167740275","https://openalex.org/W2277485793","https://openalex.org/W2482546709"],"related_works":["https://openalex.org/W7046235756","https://openalex.org/W2604907813","https://openalex.org/W2622640614","https://openalex.org/W2546714107","https://openalex.org/W7047490860","https://openalex.org/W7148658967","https://openalex.org/W2142773663","https://openalex.org/W2886854192","https://openalex.org/W3187962553","https://openalex.org/W149781492"],"abstract_inverted_index":{"Phylogenetic":[0],"analysis":[1],"has":[2,23,66],"become":[3],"a":[4,13],"powerful":[5],"tool":[6],"for":[7],"the":[8,17,28,45,54,69,84,92,97,146],"investigation":[9],"of":[10,30,36,59,71,83,94,99,140,164,169],"evolution":[11,136],"at":[12],"molecular":[14],"level.":[15],"During":[16],"last":[18],"three":[19],"decades,":[20],"statistical":[21],"phylogenetics":[22],"increasingly":[24],"been":[25],"applied":[26],"to":[27,127,137,157,160],"study":[29,70],"microbial":[31],"pathogens.":[32],"The":[33],"new":[34,166],"field":[35],"phylodynamics":[37],"was":[38],"formally":[39],"introduced":[40],"in":[41,76,87,96,102],"2004":[42],"and":[43,49,56,80,120,152],"encompasses":[44],"interaction":[46],"between":[47,148],"evolutionary":[48],"ecological":[50],"processes":[51],"that":[52,124],"shape":[53],"spatiotemporal":[55],"phylogenetic":[57],"patterns":[58],"infectious":[60,141],"disease":[61,142],"dynamics.":[62],"This":[63,114],"novel":[64],"framework":[65],"significantly":[67],"enhanced":[68],"measurable":[72],"evolving":[73],"pathogen":[74],"populations,":[75],"particular":[77],"RNA":[78],"viruses":[79],"retroviruses.":[81],"One":[82],"major":[85],"challenges":[86],"phylodynamic":[88,130,153],"studies,":[89],"however,":[90],"is":[91],"generation":[93],"data":[95,121],"form":[98],"dense":[100],"coverage":[101],"sequence":[103],"sampling":[104],"coupled":[105],"with":[106],"high":[107],"quality":[108],"epidemiological":[109],"and/or":[110],"accurate":[111],"clinical":[112],"information.":[113],"review":[115],"focuses":[116],"specifically":[117],"on":[118],"experimental":[119,150],"assembling":[122],"strategies":[123],"are":[125],"required":[126],"test":[128],"multi-level":[129],"hypotheses,":[131],"ranging":[132],"from":[133],"intra-host":[134],"viral":[135],"population":[138],"dynamics":[139],"pandemics.":[143],"Ultimately,":[144],"bridging":[145],"gap":[147],"rational":[149],"design":[151],"inference":[154],"will":[155],"prove":[156],"be":[158],"essential":[159],"take":[161],"full":[162],"advantage":[163],"this":[165],"exciting":[167],"area":[168],"research.":[170]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
