{"id":"https://openalex.org/W2949210352","doi":"https://doi.org/10.1093/bioinformatics/bty921","title":"FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences","display_name":"FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences","publication_year":2018,"publication_date":"2018-11-01","ids":{"openalex":"https://openalex.org/W2949210352","doi":"https://doi.org/10.1093/bioinformatics/bty921","mag":"2949210352","pmid":"https://pubmed.ncbi.nlm.nih.gov/30395173"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty921","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty921","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1852/31617987/bty921.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1852/31617987/bty921.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008998282","display_name":"Niema Moshiri","orcid":"https://orcid.org/0000-0003-2209-8128"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Niema Moshiri","raw_affiliation_strings":["Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000526097","display_name":"Manon Ragonnet\u2010Cronin","orcid":"https://orcid.org/0000-0002-4879-2209"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manon Ragonnet-Cronin","raw_affiliation_strings":["Department of Medicine, UC San Diego, La Jolla, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, UC San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069232831","display_name":"Joel O. Wertheim","orcid":"https://orcid.org/0000-0003-4882-5856"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joel O Wertheim","raw_affiliation_strings":["Department of Medicine, UC San Diego, La Jolla, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, UC San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087959579","display_name":"Siavash Mirarab","orcid":"https://orcid.org/0000-0001-5410-1518"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Siavash Mirarab","raw_affiliation_strings":["Department of Electrical and Computer Engineering, UC San Diego, La Jolla, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, UC San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5087959579"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.2669,"has_fulltext":false,"cited_by_count":66,"citation_normalized_percentile":{"value":0.92733645,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"35","issue":"11","first_page":"1852","last_page":"1861"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.31299999356269836,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.31299999356269836,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.10080000013113022,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.07209999859333038,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7665385007858276},{"id":"https://openalex.org/keywords/transmission","display_name":"Transmission (telecommunications)","score":0.6969617009162903},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.5230435132980347},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5226563811302185},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5121593475341797},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5078979134559631},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.416924387216568},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40667834877967834},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3852691650390625},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.3720793128013611},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13939592242240906}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7665385007858276},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.6969617009162903},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.5230435132980347},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5226563811302185},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5121593475341797},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5078979134559631},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.416924387216568},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40667834877967834},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3852691650390625},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.3720793128013611},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13939592242240906},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D006801","descriptor_name":"Humans","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty921","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty921","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1852/31617987/bty921.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30395173","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30395173","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,"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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt9m44c9fb","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/9m44c9fb","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 35, iss 11","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6931354","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6931354","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty921","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty921","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1852/31617987/bty921.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8399999737739563,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2569555022","display_name":null,"funder_award_id":"P30 AI027767","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3010116066","display_name":null,"funder_award_id":"K01 AI110181","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3338472867","display_name":null,"funder_award_id":"ACI-1053575","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3639457605","display_name":null,"funder_award_id":"1098048","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6520098237","display_name":null,"funder_award_id":"MR/R015600/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G6851572038","display_name":null,"funder_award_id":"R01 AI135992","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G7574901604","display_name":null,"funder_award_id":"ID15-SD-052 to J.O.W.","funder_id":"https://openalex.org/F4320308298","funder_display_name":"California HIV/AIDS Research Program"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320308298","display_name":"California HIV/AIDS Research Program","ror":"https://ror.org/00pjdza24"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949210352.pdf"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W1525734744","https://openalex.org/W1593676244","https://openalex.org/W1832577619","https://openalex.org/W1923320973","https://openalex.org/W1969180491","https://openalex.org/W1981476804","https://openalex.org/W1983610133","https://openalex.org/W1985249225","https://openalex.org/W2002470750","https://openalex.org/W2005751699","https://openalex.org/W2008620264","https://openalex.org/W2010981336","https://openalex.org/W2012749243","https://openalex.org/W2026628477","https://openalex.org/W2029973096","https://openalex.org/W2031611770","https://openalex.org/W2053214735","https://openalex.org/W2060425093","https://openalex.org/W2060788622","https://openalex.org/W2064766914","https://openalex.org/W2065461553","https://openalex.org/W2080723129","https://openalex.org/W2087120817","https://openalex.org/W2101267973","https://openalex.org/W2102424972","https://openalex.org/W2104713832","https://openalex.org/W2105243066","https://openalex.org/W2112090702","https://openalex.org/W2119284380","https://openalex.org/W2123009189","https://openalex.org/W2124790653","https://openalex.org/W2125359798","https://openalex.org/W2125464221","https://openalex.org/W2126371317","https://openalex.org/W2127048411","https://openalex.org/W2127832030","https://openalex.org/W2132022337","https://openalex.org/W2133979592","https://openalex.org/W2139736670","https://openalex.org/W2143718171","https://openalex.org/W2144775551","https://openalex.org/W2146950091","https://openalex.org/W2148870302","https://openalex.org/W2149445861","https://openalex.org/W2150646850","https://openalex.org/W2151831732","https://openalex.org/W2152505869","https://openalex.org/W2157539385","https://openalex.org/W2160226661","https://openalex.org/W2164582219","https://openalex.org/W2295400169","https://openalex.org/W2318310546","https://openalex.org/W2344940607","https://openalex.org/W2415238254","https://openalex.org/W2528483098","https://openalex.org/W2549654384","https://openalex.org/W2571541240","https://openalex.org/W2610626809","https://openalex.org/W2614081736","https://openalex.org/W2757222109","https://openalex.org/W2764031498","https://openalex.org/W2770277364","https://openalex.org/W2793085614","https://openalex.org/W2884242568","https://openalex.org/W2886693548","https://openalex.org/W2951126701","https://openalex.org/W2964052890","https://openalex.org/W3100315707","https://openalex.org/W3102641634","https://openalex.org/W4232687841","https://openalex.org/W6679191575","https://openalex.org/W6681367416","https://openalex.org/W6785874604"],"related_works":["https://openalex.org/W4365211920","https://openalex.org/W3014948380","https://openalex.org/W4380551139","https://openalex.org/W4317695495","https://openalex.org/W4395044357","https://openalex.org/W4287117424","https://openalex.org/W4387506531","https://openalex.org/W2087346071","https://openalex.org/W2967848559","https://openalex.org/W4299831724"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"ability":[2],"to":[3,36,55,61,102,114,117,123,152,170],"simulate":[4,153],"epidemics":[5,88],"as":[6,138],"a":[7,80,99,139,206],"function":[8],"of":[9,134,160,174],"model":[10,101,130],"parameters":[11],"allows":[12],"insights":[13],"that":[14,89,142],"are":[15,90,219],"unobtainable":[16],"from":[17],"real":[18],"datasets.":[19,163],"Further,":[20],"reconstructing":[21],"transmission":[22,42,106,186],"networks":[23],"for":[24,73,83,87],"fast-evolving":[25,93],"viruses":[26],"like":[27,95],"Human":[28],"Immunodeficiency":[29],"Virus":[30],"(HIV)":[31],"may":[32],"have":[33,46],"the":[34,118,128,158,161,167,172,175],"potential":[35],"greatly":[37],"enhance":[38],"epidemic":[39],"intervention,":[40],"but":[41],"network":[43,187],"reconstruction":[44,188],"methods":[45,189],"been":[47],"inadequately":[48],"studied,":[49],"largely":[50],"because":[51],"it":[52],"is":[53,121,136,201],"difficult":[54],"obtain":[56],"'truth'":[57],"sets":[58],"on":[59,179,212],"which":[60,135],"test":[62],"them":[63],"and":[64,76,110,113,156,190,205],"properly":[65],"measure":[66],"their":[67,191],"performance.":[68],"RESULTS:":[69],"We":[70,149,164,182],"introduce":[71],"FrAmework":[72],"VIral":[74],"Transmission":[75],"Evolution":[77],"Simulation":[78],"(FAVITES),":[79],"robust":[81],"framework":[82],"simulating":[84],"realistic":[85],"datasets":[86,155],"caused":[91],"by":[92,126],"pathogens":[94],"HIV.":[96],"FAVITES":[97,120,151,200],"creates":[98],"generative":[100,129],"produce":[103],"contact":[104],"networks,":[105,107],"phylogenetic":[108],"trees":[109],"sequence":[111],"datasets,":[112],"add":[115],"error":[116],"data.":[119],"designed":[122],"be":[124,144,210],"extensible":[125],"dividing":[127],"into":[131],"modules,":[132],"each":[133],"expressed":[137],"fixed":[140],"API":[141],"can":[143,209],"implemented":[145],"using":[146],"various":[147],"models.":[148],"use":[150,166],"HIV":[154],"study":[157,171,184],"realism":[159],"simulated":[162,168],"then":[165],"data":[169,218],"impact":[173],"increased":[176],"treatment":[177],"efforts":[178],"epidemiological":[180],"outcomes.":[181],"also":[183],"two":[185],"effectiveness":[192],"in":[193],"detecting":[194],"fast-growing":[195],"clusters.":[196],"AVAILABILITY":[197],"AND":[198],"IMPLEMENTATION:":[199],"available":[202,220],"at":[203,221],"https://github.com/niemasd/FAVITES,":[204],"Docker":[207],"image":[208],"found":[211],"DockerHub":[213],"(https://hub.docker.com/r/niemasd/favites).":[214],"SUPPLEMENTARY":[215],"INFORMATION:":[216],"Supplementary":[217],"Bioinformatics":[222],"online.":[223]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":2}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
