{"id":"https://openalex.org/W149781492","doi":null,"title":"Phylodynamic Methods for Infectious Disease Epidemiology","display_name":"Phylodynamic Methods for Infectious Disease Epidemiology","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W149781492","mag":"149781492"},"language":"en","primary_location":{"id":"pmh:oai:dukespace.lib.duke.edu:10161/8701","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/10161/8701","pdf_url":null,"source":{"id":"https://openalex.org/S4306400687","display_name":"DukeSpace (Duke University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I170897317","host_organization_name":"Duke University","host_organization_lineage":["https://openalex.org/I170897317"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dissertation"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"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/A5058082988","display_name":"David A. Rasmussen","orcid":"https://orcid.org/0000-0001-9457-7561","observed_orcids":["https://orcid.org/0000-0001-9457-7561"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"David A. Rasmussen","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-9457-7561","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5058082988"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"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/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.8047000169754028,"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"}},"topics":[{"id":"https://openalex.org/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.8047000169754028,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.13840000331401825,"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/T11152","display_name":"Stochastic processes and statistical mechanics","score":0.00989999994635582,"subfield":{"id":"https://openalex.org/subfields/2610","display_name":"Mathematical Physics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylodynamics","display_name":"phylodynamics","score":0.9919999837875366},{"id":"https://openalex.org/keywords/coalescent-models","display_name":"coalescent models","score":0.8809999823570251},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.8190000057220459},{"id":"https://openalex.org/keywords/particle-filtering","display_name":"particle filter","score":0.9950000047683716},{"id":"https://openalex.org/keywords/host-population-structure","display_name":"host population structure","score":0.7149999737739563},{"id":"https://openalex.org/keywords/spatial-structure","display_name":"spatial structure","score":0.8349999785423279},{"id":"https://openalex.org/keywords/vector-borne-diseases","display_name":"vector-borne diseases","score":0.7110000252723694},{"id":"https://openalex.org/keywords/dengue-virus","display_name":"dengue virus","score":0.9020000100135803},{"id":"https://openalex.org/keywords/seasonal-variation","display_name":"seasonal variation","score":0.8339999914169312},{"id":"https://openalex.org/keywords/vector-dynamics","display_name":"vector dynamics","score":0.675000011920929},{"id":"https://openalex.org/keywords/hospitalization-data","display_name":"hospitalization data","score":0.7009999752044678}],"concepts":[{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.6818492412567139},{"id":"https://openalex.org/C107130276","wikidata":"https://www.wikidata.org/wiki/Q133805","display_name":"Epidemiology","level":2,"score":0.5782160758972168},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.48748779296875},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43994754552841187},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.43739446997642517},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.43447792530059814},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3535005748271942},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3421481251716614},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.3396419584751129},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.31418800354003906},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.24726980924606323},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.1011691689491272}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:dukespace.lib.duke.edu:10161/8701","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/10161/8701","pdf_url":null,"source":{"id":"https://openalex.org/S4306400687","display_name":"DukeSpace (Duke University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I170897317","host_organization_name":"Duke University","host_organization_lineage":["https://openalex.org/I170897317"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dissertation"},{"id":"mag:149781492","doi":null,"is_oa":false,"landing_page_url":"https://dukespace.lib.duke.edu/dspace/bitstream/10161/8701/1/Rasmussen_duke_0066D_12325.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":121,"referenced_works":["https://openalex.org/W172946292","https://openalex.org/W1483307070","https://openalex.org/W1501586228","https://openalex.org/W1546828436","https://openalex.org/W1596716429","https://openalex.org/W1606697907","https://openalex.org/W1768287364","https://openalex.org/W1793259860","https://openalex.org/W1830883013","https://openalex.org/W1874454247","https://openalex.org/W1915699870","https://openalex.org/W1939346899","https://openalex.org/W1963568208","https://openalex.org/W1965433670","https://openalex.org/W1966116088","https://openalex.org/W1967386494","https://openalex.org/W1968573859","https://openalex.org/W1970771372","https://openalex.org/W1973194618","https://openalex.org/W1975231997","https://openalex.org/W1978546114","https://openalex.org/W1979257831","https://openalex.org/W1979743121","https://openalex.org/W1993210385","https://openalex.org/W1995060260","https://openalex.org/W2001259823","https://openalex.org/W2004506270","https://openalex.org/W2007593785","https://openalex.org/W2011323609","https://openalex.org/W2012620166","https://openalex.org/W2016767093","https://openalex.org/W2018463841","https://openalex.org/W2023937195","https://openalex.org/W2035738809","https://openalex.org/W2041903808","https://openalex.org/W2043839667","https://openalex.org/W2044038393","https://openalex.org/W2048328788","https://openalex.org/W2052262596","https://openalex.org/W2053214735","https://openalex.org/W2055041101","https://openalex.org/W2055936398","https://openalex.org/W2065266611","https://openalex.org/W2065382983","https://openalex.org/W2066937690","https://openalex.org/W2068438963","https://openalex.org/W2071613821","https://openalex.org/W2071783541","https://openalex.org/W2073627497","https://openalex.org/W2074607858","https://openalex.org/W2078325486","https://openalex.org/W2081410257","https://openalex.org/W2081741802","https://openalex.org/W2082056205","https://openalex.org/W2092500478","https://openalex.org/W2092955687","https://openalex.org/W2098062910","https://openalex.org/W2098538101","https://openalex.org/W2098613108","https://openalex.org/W2099143009","https://openalex.org/W2099843292","https://openalex.org/W2102694845","https://openalex.org/W2103250575","https://openalex.org/W2103950304","https://openalex.org/W2107021548","https://openalex.org/W2107206185","https://openalex.org/W2108571548","https://openalex.org/W2110835349","https://openalex.org/W2112509042","https://openalex.org/W2113434524","https://openalex.org/W2115596355","https://openalex.org/W2118849557","https://openalex.org/W2119560885","https://openalex.org/W2121527356","https://openalex.org/W2121855838","https://openalex.org/W2121917753","https://openalex.org/W2122980269","https://openalex.org/W2126531452","https://openalex.org/W2127832030","https://openalex.org/W2128232522","https://openalex.org/W2129402715","https://openalex.org/W2130333286","https://openalex.org/W2130416410","https://openalex.org/W2133979592","https://openalex.org/W2139166200","https://openalex.org/W2140105153","https://openalex.org/W2140607780","https://openalex.org/W2141123747","https://openalex.org/W2141367465","https://openalex.org/W2142713959","https://openalex.org/W2142773663","https://openalex.org/W2146442942","https://openalex.org/W2148207513","https://openalex.org/W2150508312","https://openalex.org/W2150977550","https://openalex.org/W2151729750","https://openalex.org/W2152815500","https://openalex.org/W2153432740","https://openalex.org/W2153611488","https://openalex.org/W2154353570","https://openalex.org/W2156358357","https://openalex.org/W2156913396","https://openalex.org/W2159064890","https://openalex.org/W2160535947","https://openalex.org/W2161582762","https://openalex.org/W2162174872","https://openalex.org/W2162990662","https://openalex.org/W2163036286","https://openalex.org/W2163124559","https://openalex.org/W2163357043","https://openalex.org/W2166022262","https://openalex.org/W2167030304","https://openalex.org/W2167134550","https://openalex.org/W2167154952","https://openalex.org/W2169623461","https://openalex.org/W2170106032","https://openalex.org/W2171520681","https://openalex.org/W2171689424","https://openalex.org/W2176170147","https://openalex.org/W2180132705","https://openalex.org/W2319462502"],"related_works":["https://openalex.org/W7095960184","https://openalex.org/W7099670381","https://openalex.org/W7098386556","https://openalex.org/W1963568208","https://openalex.org/W2170932222","https://openalex.org/W3143253205","https://openalex.org/W2952663165","https://openalex.org/W7213476335","https://openalex.org/W2055041101","https://openalex.org/W2622640614"],"abstract_inverted_index":{"In":[0,254],"this":[1,100,138,267],"dissertation,":[2],"I":[3,97,135,200,210],"present":[4],"a":[5,34,52,168],"general":[6],"statistical":[7],"framework":[8,28,140,268],"for":[9],"phylodynamic":[10,214],"inference":[11,72,215],"that":[12,99,234],"can":[13,29,102,195,249,269],"be":[14,30,103,196,250],"used":[15,31,104,197],"to":[16,32,44,54,105,141,174,190,218,259],"estimate":[17,107,175],"epidemiological":[18,38,92,108,130],"parameters":[19,75,109],"and":[20,66,76,125,157,179,244,264,274],"reconstruct":[21,115,220],"disease":[22,117,283],"dynamics":[23,50,118,222,243,248],"from":[24,119,123,181,252],"pathogen":[25,53],"genealogies.":[26,253],"This":[27],"fit":[33],"broad":[35],"class":[36],"of":[37,51,73,110,129,145,160,171,204,223],"models,":[39,43,266],"including":[40,149],"nonlinear":[41],"stochastic":[42],"genealogies":[45,124],"by":[46,166,230,256],"relating":[47],"the":[48,91,193,202,221,279],"population":[49,147],"its":[55],"genealogy":[56],"using":[57,167],"coalescent":[58,232],"theory.":[59],"By":[60],"combining":[61],"Markov":[62],"chain":[63],"Monte":[64],"Carlo":[65],"particle":[67],"filtering":[68],"methods,":[69],"efficient":[70],"Bayesian":[71],"all":[74],"unobserved":[77],"latent":[78],"variables":[79],"is":[80,164],"possible":[81],"even":[82],"when":[83],"analytical":[84],"likelihood":[85],"expressions":[86],"are":[87],"not":[88],"available":[89],"under":[90],"model.":[93],"Through":[94],"extensive":[95],"simulations,":[96],"show":[98,211],"method":[101],"reliably":[106,219],"interest":[111],"as":[112,114],"well":[113],"past":[116],"genealogies,":[120],"or":[121,155],"jointly":[122],"other":[126],"common":[127],"sources":[128],"data":[131,184],"like":[132,240],"time":[133],"series.":[134],"then":[136],"extend":[137],"basic":[139],"include":[142,260],"different":[143,158],"types":[144],"host":[146],"structure,":[148,153,246],"models":[150,233],"with":[151],"spatial":[152,245],"multiple-hosts":[154],"vectors,":[156],"stages":[159],"infection.":[161],"The":[162],"later":[163],"demonstrated":[165],"multistage":[169],"model":[170],"HIV":[172,182],"infection":[173],"stage-specific":[176],"transmission":[177],"rates":[178],"incidence":[180],"sequence":[183],"collected":[185],"in":[186,207,226],"Detroit,":[187],"Michigan.":[188],"Finally,":[189],"demonstrate":[191],"how":[192,212],"approach":[194],"more":[198,261,271],"generally,":[199],"consider":[201],"case":[203],"dengue":[205,224],"virus":[206],"southern":[208],"Vietnam.":[209],"earlier":[213],"methods":[216],"fail":[217],"observed":[225],"hospitalization":[227],"data,":[228],"but":[229],"deriving":[231],"take":[235],"into":[236,278],"consideration":[237],"ecological":[238],"complexities":[239],"seasonality,":[241],"vector":[242],"accurate":[247,272],"reconstructed":[251],"sum,":[255],"extending":[257],"phylodynamics":[258],"ecologically":[262],"realistic":[263],"mechanistic":[265],"provide":[270],"estimates":[273],"give":[275],"deeper":[276],"insight":[277],"processes":[280],"driving":[281],"infectious":[282],"dynamics.":[284]},"counts_by_year":[],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2016-06-24T00:00:00"}
