{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T20:55:07Z","timestamp":1743108907630,"version":"3.40.3"},"publisher-location":"Cham","reference-count":61,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030651534"},{"type":"electronic","value":"9783030651541"}],"license":[{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020]]},"DOI":"10.1007\/978-3-030-65154-1_3","type":"book-chapter","created":{"date-parts":[[2021,1,4]],"date-time":"2021-01-04T19:06:19Z","timestamp":1609787179000},"page":"34-50","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Towards a Phylogenetic Measure to Quantify HIV Incidence"],"prefix":"10.1007","author":[{"given":"Pieter","family":"Libin","sequence":"first","affiliation":[]},{"given":"Nassim","family":"Versbraegen","sequence":"additional","affiliation":[]},{"given":"Ana B.","family":"Abecasis","sequence":"additional","affiliation":[]},{"given":"Perpetua","family":"Gomes","sequence":"additional","affiliation":[]},{"given":"Tom","family":"Lenaerts","sequence":"additional","affiliation":[]},{"given":"Ann","family":"Now\u00e9","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,1,5]]},"reference":[{"key":"3_CR1","unstructured":"UNAIDS. Fact sheet - latest global and regional statistics on the status of the aids epidemic, July 2017"},{"issue":"6","key":"3_CR2","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1007\/s10461-008-9519-5","volume":"13","author":"LB Hightow-Weidman","year":"2009","unstructured":"Hightow-Weidman, L.B., Golin, C.E., Green, K., Shaw, E.N.P., MacDonald, P.D.M., Leone, P.A.: Identifying people with acute HIV infection: demographic features, risk factors, and use of health care among individuals with AHI in North Carolina. AIDS Behav. 13(6), 1075\u20131083 (2009)","journal-title":"AIDS Behav."},{"key":"3_CR3","doi-asserted-by":"crossref","unstructured":"Burton, G.F., Keele, B.F., Estes, J.D., Thacker, T.C., Gartner, S.: Follicular dendritic cell contributions to HIV pathogenesis. In: Seminars in Immunology, vol. 14, pp. 275\u2013284. Elsevier (2002)","DOI":"10.1016\/S1044-5323(02)00060-X"},{"key":"3_CR4","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1016\/j.coviro.2017.12.001","volume":"28","author":"K Theys","year":"2018","unstructured":"Theys, K., Libin, P., Pineda-Pena, A.-C., Nowe, A., Vandamme, A.-M., Abecasis, A.B.: The impact of HIV-1 within-host evolution on transmission dynamics. Curr. Opin. Virol. 28, 92\u2013101 (2018)","journal-title":"Curr. Opin. Virol."},{"issue":"1","key":"3_CR5","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1097\/QAI.0b013e3181c98fa8","volume":"54","author":"EM Begier","year":"2010","unstructured":"Begier, E.M., et al.: Undiagnosed HIV infection among New York City jail entrants, 2006: results of a blinded serosurvey. JAIDS J. Acquir. Immune Defic. Syndr. 54(1), 93\u2013101 (2010)","journal-title":"JAIDS J. Acquir. Immune Defic. Syndr."},{"issue":"5","key":"3_CR6","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1097\/EDE.0000000000000324","volume":"26","author":"A van Sighem","year":"2015","unstructured":"van Sighem, A., et al.: Estimating HIV incidence, time to diagnosis, and the undiagnosed HIV epidemic using routine surveillance data. Epidemiology 26(5), 653 (2015)","journal-title":"Epidemiology"},{"issue":"7","key":"3_CR7","doi-asserted-by":"publisher","first-page":"1131","DOI":"10.1097\/QAD.0000000000001034","volume":"30","author":"A Mammone","year":"2016","unstructured":"Mammone, A., et al.: How many people are living with undiagnosed HIV infection? an estimate for Italy, based on surveillance data. AIDS 30(7), 1131 (2016)","journal-title":"AIDS"},{"issue":"6","key":"3_CR8","doi-asserted-by":"publisher","first-page":"801","DOI":"10.4103\/0971-5916.92627","volume":"134","author":"M Vajpayee","year":"2011","unstructured":"Vajpayee, M., Mohan, T.: Current practices in laboratory monitoring of HIV infection. Indian J. Med. Res. 134(6), 801 (2011)","journal-title":"Indian J. Med. Res."},{"issue":"1","key":"3_CR9","doi-asserted-by":"publisher","first-page":"e1002803","DOI":"10.1371\/journal.pcbi.1002803","volume":"9","author":"M Sunn\u00e5ker","year":"2013","unstructured":"Sunn\u00e5ker, M., Busetto, A.G., Numminen, E., Corander, J., Foll, M., Dessimoz, C.: Approximate bayesian computation. PLoS Comput. Biology 9(1), e1002803 (2013)","journal-title":"PLoS Comput. Biology"},{"key":"3_CR10","unstructured":"Ridley, M.: Evolution. John Wiley & Sons Incorporated (2009)"},{"issue":"1","key":"3_CR11","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1146\/annurev.en.10.010165.000525","volume":"10","author":"W Hennig","year":"1965","unstructured":"Hennig, W.: Phylogenetic systematics. Ann. Rev. Entomol. 10(1), 97\u2013116 (1965)","journal-title":"Ann. Rev. Entomol."},{"key":"3_CR12","volume-title":"The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing","author":"M Salemi","year":"2009","unstructured":"Salemi, M., Lemey, P., Vandamme, A.-M.: The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. Cambridge University Press, Cambridge (2009)"},{"key":"3_CR13","volume-title":"Inferring Phylogenies","author":"J Felsenstein","year":"2004","unstructured":"Felsenstein, J.: Inferring Phylogenies, vol. 2. Sinauer associates Sunderland, MA (2004)"},{"issue":"5","key":"3_CR14","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1145\/1183907.1183909","volume":"53","author":"B Chor","year":"2006","unstructured":"Chor, B., Tuller, T.: Finding a maximum likelihood tree is hard. J. ACM (JACM) 53(5), 722\u2013744 (2006)","journal-title":"J. ACM (JACM)"},{"issue":"1","key":"3_CR15","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1109\/TCBB.2006.4","volume":"3","author":"S Roch","year":"2006","unstructured":"Roch, S.: A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. IEEE\/ACM Trans. Comput. Biol. Bioinform. (TCBB) 3(1), 92 (2006)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform. (TCBB)"},{"key":"3_CR16","doi-asserted-by":"crossref","unstructured":"Freed, E.O.: HIV-1 replication. Somatic Cell Mol. Genet. 26(1\u20136), 13\u201333 (2001)","DOI":"10.1023\/A:1021070512287"},{"issue":"6173","key":"3_CR17","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1038\/333504a0","volume":"333","author":"R Gallo","year":"1988","unstructured":"Gallo, R., Wong-Staal, F., Montagnier, L., Haseltine, W.A., Yoshida, M.: HIV\/HTLV gene nomenclature. Nature 333(6173), 504\u2013504 (1988)","journal-title":"Nature"},{"key":"3_CR18","unstructured":"Kindt, T.J., Goldsby, R.A., Osborne, B.A., Kuby, J.: Kuby immunology. Macmillan (2007)"},{"issue":"1","key":"3_CR19","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1038\/nrg1246","volume":"5","author":"A Rambaut","year":"2004","unstructured":"Rambaut, A., Posada, D., Crandall, K.A., Holmes, E.C.: The causes and consequences of HIV evolution. Nature reviews. Genetics 5(1), 52 (2004)","journal-title":"Nature reviews. Genetics"},{"issue":"4","key":"3_CR20","doi-asserted-by":"publisher","first-page":"1244","DOI":"10.1172\/JCI34706","volume":"118","author":"MS Cohen","year":"2008","unstructured":"Cohen, M.S., Hellmann, N., Levy, J.A., DeCock, K., Lange, J.: The spread, treatment, and prevention of HIV-1: evolution of a global pandemic. J. Clin. Inv. 118(4), 1244 (2008)","journal-title":"J. Clin. Inv."},{"issue":"7","key":"3_CR21","doi-asserted-by":"publisher","first-page":"654","DOI":"10.7326\/0003-4819-124-7-199604010-00006","volume":"124","author":"AS Fauci","year":"1996","unstructured":"Fauci, A.S., Pantaleo, G., Stanley, S., Weissman, D.: Immunopathogenic mechanisms of HIV infection. Ann. Internal Medi. 124(7), 654\u2013663 (1996)","journal-title":"Ann. Internal Medi."},{"issue":"3","key":"3_CR22","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1016\/S0272-2712(02)00015-X","volume":"22","author":"MR Ferguson","year":"2002","unstructured":"Ferguson, M.R., Rojo, D.R., von Lindern, J.J., O\u2019Brien, W.A.: HIV-1 replication cycle. Clin. Lab. Med. 22(3), 611\u2013635 (2002)","journal-title":"Clin. Lab. Med."},{"issue":"3","key":"3_CR23","first-page":"125","volume":"8","author":"P Lemey","year":"2006","unstructured":"Lemey, P., Rambaut, A., Pybus, O.G.: HIV evolutionary dynamics within and among hosts. AIDs Rev. 8(3), 125\u2013140 (2006)","journal-title":"AIDs Rev."},{"issue":"4","key":"3_CR24","first-page":"313","volume":"5","author":"W-H Li","year":"1988","unstructured":"Li, W.-H., Tanimura, M., Sharp, P.M.: Rates and dates of divergence between AIDS virus nucleotide sequences. Mol. Biol. Evol. 5(4), 313\u2013330 (1988)","journal-title":"Mol. Biol. Evol."},{"issue":"6510","key":"3_CR25","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1038\/373117a0","volume":"373","author":"X Wei","year":"1995","unstructured":"Wei, X., et al.: Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373(6510), 117\u2013122 (1995)","journal-title":"Nature"},{"issue":"6510","key":"3_CR26","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/373123a0","volume":"373","author":"DD Ho","year":"1995","unstructured":"Ho, D.D., Neumann, A.U., Perelson, A.S., Chen, W., Leonard, J.M., Markowitz, M.: Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373(6510), 123\u2013126 (1995)","journal-title":"Nature"},{"issue":"2","key":"3_CR27","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1017\/S1464793101005668","volume":"76","author":"EC Holmes","year":"2001","unstructured":"Holmes, E.C.: On the origin and evolution of the human immunodeficiency virus (HIV). Biol. Rev. 76(2), 239\u2013254 (2001)","journal-title":"Biol. Rev."},{"issue":"5453","key":"3_CR28","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1126\/science.287.5453.607","volume":"287","author":"BH Hahn","year":"2000","unstructured":"Hahn, B.H., Shaw, G.M., De, K.M., Sharp, P.M., et al.: AIDS as a zoonosis: scientific and public health implications. Science 287(5453), 607\u2013614 (2000)","journal-title":"Science"},{"issue":"1","key":"3_CR29","doi-asserted-by":"publisher","first-page":"006841","DOI":"10.1101\/cshperspect.a006841","volume":"1","author":"PM Sharp","year":"2011","unstructured":"Sharp, P.M., Hahn, B.H.: Origins of HIV and the AIDS pandemic. Cold Spring Harbor Perspect. Med. 1(1), 006841 (2011)","journal-title":"Cold Spring Harbor Perspect. Med."},{"issue":"12","key":"3_CR30","doi-asserted-by":"publisher","first-page":"588","DOI":"10.1016\/j.tim.2008.09.003","volume":"16","author":"TI de Silva","year":"2008","unstructured":"de Silva, T.I., Cotten, M., Rowland-Jones, S.L.: HIV-2: the forgotten AIDS virus. Trends Microbiol. 16(12), 588\u2013595 (2008)","journal-title":"Trends Microbiol."},{"issue":"9637","key":"3_CR31","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1016\/S0140-6736(08)60884-3","volume":"372","author":"MH Merson","year":"2008","unstructured":"Merson, M.H., O\u2019Malley, J., Serwadda, D., Apisuk, C.: The history and challenge of HIV prevention. Lancet 372(9637), 475\u2013488 (2008)","journal-title":"Lancet"},{"issue":"4","key":"3_CR32","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1097\/00002030-199704000-00013","volume":"11","author":"M Peeters","year":"1997","unstructured":"Peeters, M., Gueye, A., Mboup, S., Bibollet-Ruche, F., Ekaza, E., Mulanga, C., Ouedrago, R., Gandji, R., Mpele, P., Dibanga, G., et al.: Geographical distribution of HIV-1 group O viruses in Africa. Aids 11(4), 493\u2013498 (1997)","journal-title":"Aids"},{"issue":"1","key":"3_CR33","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1089\/aid.2009.0178","volume":"26","author":"A Vallari","year":"2010","unstructured":"Vallari, A., et al.: Four new HIV-1 group N isolates from cameroon: prevalence continues to be low. AIDS Res. Hum. Retroviruses 26(1), 109\u2013115 (2010)","journal-title":"AIDS Res. Hum. Retroviruses"},{"issue":"3","key":"3_CR34","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1128\/JVI.02005-10","volume":"85","author":"A Vallari","year":"2011","unstructured":"Vallari, A., Holzmayer, V., Harris, B., Yamaguchi, J., Ngansop, C., Makamche, F., Mbanya, D., Kaptu\u00e9, L., Ndembi, N., G\u00fcrtler, L., et al.: Confirmation of putative HIV-1 group P in Cameroon. J. Virol. 85(3), 1403\u20131407 (2011)","journal-title":"J. Virol."},{"key":"3_CR35","doi-asserted-by":"crossref","unstructured":"Goudsmit, J.: Viral sex: The nature of AIDS. Oxford University Press on Demand (1997)","DOI":"10.1093\/oso\/9780195097283.001.0001"},{"issue":"19","key":"3_CR36","doi-asserted-by":"publisher","first-page":"10209","DOI":"10.1128\/JVI.00872-07","volume":"81","author":"L Buonaguro","year":"2007","unstructured":"Buonaguro, L., Tornesello, M.L., Buonaguro, F.M.: Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications. J. Virol. 81(19), 10209\u201310219 (2007)","journal-title":"J. Virol."},{"issue":"15","key":"3_CR37","doi-asserted-by":"publisher","first-page":"1590","DOI":"10.1056\/NEJMra0706737","volume":"358","author":"BS Taylor","year":"2008","unstructured":"Taylor, B.S., Sobieszczyk, M.E., McCutchan, F.E., Hammer, S.M.: The challenge of HIV-1 subtype diversity. New Engl. J. Med. 358(15), 1590\u20131602 (2008)","journal-title":"New Engl. J. Med."},{"issue":"19","key":"3_CR38","doi-asserted-by":"publisher","first-page":"12515","DOI":"10.1128\/JVI.79.19.12515-12527.2005","volume":"79","author":"ML Santiago","year":"2005","unstructured":"Santiago, M.L., et al.: Simian immunodeficiency virus infection in free-ranging sooty mangabeys (Cercocebus atys atys) from the Tai Forest, Cote d\u2019Ivoire: implications for the origin of epidemic human immunodeficiency virus type 2. J. Virol. 79(19), 12515\u201312527 (2005)","journal-title":"J. Virol."},{"issue":"8","key":"3_CR39","doi-asserted-by":"publisher","first-page":"1177","DOI":"10.1086\/512682","volume":"195","author":"JM Baeten","year":"2007","unstructured":"Baeten, J.M., et al.: HIV-1 subtype D infection is associated with faster disease progression than subtype A in spite of similar plasma HIV-1 loads. J. Infect. Dis. 195(8), 1177\u20131180 (2007)","journal-title":"J. Infect. Dis."},{"key":"3_CR40","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.meegid.2013.04.032","volume":"19","author":"A-C Pineda-Pe\u00f1a","year":"2013","unstructured":"Pineda-Pe\u00f1a, A.-C., et al.: Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. Infect. Genet. Evol. 19, 337\u2013348 (2013)","journal-title":"Infect. Genet. Evol."},{"key":"3_CR41","unstructured":"Libin, P., Versbraegen, N., Cuypers, L., Theys, K., Now\u00e9, A.: An automated maximum likelihood method for classifying virus sequences (2016)"},{"key":"3_CR42","series-title":"Lecture Notes in Mathematics","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1007\/978-3-540-78911-6_2","volume-title":"Mathematical Epidemiology","author":"F Brauer","year":"2008","unstructured":"Brauer, F.: Compartmental models in epidemiology. Mathematical Epidemiology. LNM, vol. 1945, pp. 19\u201379. Springer, Heidelberg (2008). https:\/\/doi.org\/10.1007\/978-3-540-78911-6_2"},{"key":"3_CR43","unstructured":"Stacy, S., Black, A., Bedford, T.: Using the coalescent framework to detect missed infections in phylogenetic trees (2016)"},{"issue":"3","key":"3_CR44","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1016\/0304-4149(82)90011-4","volume":"13","author":"JFC Kingman","year":"1982","unstructured":"Kingman, J.F.C.: The coalescent. Stochastic processes and their applications 13(3), 235\u2013248 (1982)","journal-title":"Stochastic processes and their applications"},{"key":"3_CR45","unstructured":"Diniz, A.: Portugal infe\u00e7\u00e3o VIH, SIDA e tuberculose em n\u00fameros, 2015. Portugal Infe\u00e7\u00e3o VIH, SIDA e Tuberculose em n\u00fameros, 2015, pp. 5\u201370 (2015)"},{"issue":"1","key":"3_CR46","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1742-4690-10-7","volume":"10","author":"AB Abecasis","year":"2013","unstructured":"Abecasis, A.B., et al.: HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in europe suggest highly compartmentalized epidemics. Retrovirology 10(1), 7 (2013)","journal-title":"Retrovirology"},{"issue":"11","key":"3_CR47","doi-asserted-by":"publisher","first-page":"1477","DOI":"10.1093\/bioinformatics\/btt162","volume":"29","author":"P Libin","year":"2013","unstructured":"Libin, P., et al.: RegaDB: community-driven data management and analysis for infectious diseases. Bioinformatics 29(11), 1477\u20131480 (2013)","journal-title":"Bioinformatics"},{"key":"3_CR48","doi-asserted-by":"crossref","unstructured":"Pineda-Pe\u00f1a, A.-C., et al.: Automated subtyping of HIV-1 genetic sequences for clinical andsurveillance purposes: performance evaluation of the new rega version 3 andseven other tools. Infection, Genetics Evol. 19, 337\u2013348 (2013)","DOI":"10.1016\/j.meegid.2013.04.032"},{"key":"3_CR49","doi-asserted-by":"crossref","unstructured":"Carlos, L., et al.: A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res. 37(suppl\\_2), W634\u2013W642 (2009)","DOI":"10.1093\/nar\/gkp455"},{"issue":"14","key":"3_CR50","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","volume":"30","author":"K Katoh","year":"2002","unstructured":"Katoh, K., Misawa, K., Kuma, K., Miyata, T.: MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res. 30(14), 3059\u20133066 (2002)","journal-title":"Nucleic Acids Res."},{"issue":"9","key":"3_CR51","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis, A.: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9), 1312\u20131313 (2014)","journal-title":"Bioinformatics"},{"issue":"9","key":"3_CR52","doi-asserted-by":"publisher","first-page":"2483","DOI":"10.1093\/molbev\/msv123","volume":"32","author":"AFY Poon","year":"2015","unstructured":"Poon, A.F.Y.: Phylodynamic inference with kernel ABC and its application to HIV epidemiology. Mol. Biol. Evol. 32(9), 2483\u20132495 (2015)","journal-title":"Mol. Biol. Evol."},{"key":"3_CR53","unstructured":"Libin, P., Hernalsteen, L., Theys, K., Gomes, P., Abecasis, A., Nowe, A.: Bayesian inference of set-point viral load transmission models. In: 30th Benelux Conference on Artificial Intelligence, pp. 107\u2013121 (2018)"},{"issue":"11","key":"3_CR54","doi-asserted-by":"publisher","first-page":"e78122","DOI":"10.1371\/journal.pone.0078122","volume":"8","author":"AFY Poon","year":"2013","unstructured":"Poon, A.F.Y., Walker, L.W., Murray, H., McCloskey, R.M., Harrigan, P.R., Liang, R.H.: Mapping the shapes of phylogenetic trees from human and zoonotic RNA viruses. PLoS One 8(11), e78122 (2013)","journal-title":"PLoS One"},{"issue":"4","key":"3_CR55","doi-asserted-by":"publisher","first-page":"e1003570","DOI":"10.1371\/journal.pcbi.1003570","volume":"10","author":"DA Rasmussen","year":"2014","unstructured":"Rasmussen, D.A., Volz, E.M., Koelle, K.: Phylodynamic inference for structured epidemiological models. PLoS Comput. Biolo. 10(4), e1003570 (2014)","journal-title":"PLoS Comput. Biolo."},{"issue":"1","key":"3_CR56","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1534\/genetics.111.134627","volume":"190","author":"EM Volz","year":"2012","unstructured":"Volz, E.M.: Complex population dynamics and the coalescent under neutrality. Genetics 190(1), 187\u2013201 (2012)","journal-title":"Genetics"},{"key":"3_CR57","unstructured":"Volz, E.M.: Estimating HIV transmission rates with rcolgem (2014). Accessed Aug 2017"},{"key":"3_CR58","unstructured":"Volz, E.M.: Simulating genealogies with an epidemiological coalescent model using rcolgem (2015). Accessed Aug 2017"},{"key":"3_CR59","doi-asserted-by":"crossref","unstructured":"Ratmann, O., et al.: Phylogenetic tools for generalized HIV-1 epidemics: findings from the PANGEA-HIV methods comparison. Mol. Biol. Evol. 34(1), 185\u2013203 (2017)","DOI":"10.1093\/molbev\/msw217"},{"issue":"24","key":"3_CR60","doi-asserted-by":"publisher","first-page":"3993","DOI":"10.1093\/bioinformatics\/btx535","volume":"33","author":"P Libin","year":"2017","unstructured":"Libin, P., et al.: PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context. Bioinformatics 33(24), 3993\u20133995 (2017)","journal-title":"Bioinformatics"},{"issue":"2","key":"3_CR61","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1002\/tax.572002","volume":"57","author":"TF Stuessy","year":"2008","unstructured":"Stuessy, T.F., K\u00f6nig, C.: Patrocladistic classification. Taxon 57(2), 594\u2013601 (2008)","journal-title":"Taxon"}],"container-title":["Communications in Computer and Information Science","Artificial Intelligence and Machine Learning"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-65154-1_3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T19:21:09Z","timestamp":1724181669000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-65154-1_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020]]},"ISBN":["9783030651534","9783030651541"],"references-count":61,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-65154-1_3","relation":{},"ISSN":["1865-0929","1865-0937"],"issn-type":[{"type":"print","value":"1865-0929"},{"type":"electronic","value":"1865-0937"}],"subject":[],"published":{"date-parts":[[2020]]},"assertion":[{"value":"5 January 2021","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"BNAIC","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Benelux Conference on Artificial Intelligence","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Brussels","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Belgium","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2019","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"6 November 2019","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"8 November 2019","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"bnaic2019","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/bnaic19.brussels","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"50","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"11","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"22% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"2.76","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3.4","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"No","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"Peer review information is presented for joint conferences BENELEARN 2019 and BNAIC 2019","order":10,"name":"additional_info_on_review_process","label":"Additional Info on Review Process","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}