{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:17:49Z","timestamp":1761488269598},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,6,16]],"date-time":"2009-06-16T00:00:00Z","timestamp":1245110400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2009,12]]},"DOI":"10.1186\/1752-0509-3-62","type":"journal-article","created":{"date-parts":[[2009,6,16]],"date-time":"2009-06-16T18:13:32Z","timestamp":1245176012000},"source":"Crossref","is-referenced-by-count":3,"title":["Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains"],"prefix":"10.1186","volume":"3","author":[{"given":"Patricia","family":"Buendia","sequence":"first","affiliation":[]},{"given":"Giri","family":"Narasimhan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,6,16]]},"reference":[{"key":"330_CR1","doi-asserted-by":"publisher","first-page":"2993","DOI":"10.1093\/bioinformatics\/btm413","volume":"23","author":"P Buendia","year":"2007","unstructured":"Buendia P, Narasimhan G: Sliding MinPD: Building evolutionary networks of serial samples via a recombination detection approach. Bioinformatics. 2007, 23: 2993-3000. 10.1093\/bioinformatics\/btm413","journal-title":"Bioinformatics"},{"key":"330_CR2","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1038\/nrg1246","volume":"5","author":"A Rambaut","year":"2004","unstructured":"Rambaut A, Posada D, Crandall KA, Holmes EC: The causes and consequences of HIV evolution. Nat Rev Genet. 2004, 5: 52-61. 10.1038\/nrg1246","journal-title":"Nat Rev Genet"},{"key":"330_CR3","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1136\/bmj.329.7458.121","volume":"329","author":"JP Ruger","year":"2004","unstructured":"Ruger JP: Combating HIV\/AIDS in developing countries. Br Med J. 2004, 329: 121-122. 10.1136\/bmj.329.7458.121.","journal-title":"Br Med J"},{"key":"330_CR4","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1093\/infdis\/169.5.968","volume":"169","author":"DD Richman","year":"1994","unstructured":"Richman DD, Bozzette SA: The impact of the syncytium-inducing phenotype of human immunodeficiency virus on disease progression. J Infect Dis. 1994, 169: 968-974.","journal-title":"J Infect Dis"},{"key":"330_CR5","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1097\/01.qai.0000152835.17747.47","volume":"38","author":"P Delobel","year":"2005","unstructured":"Delobel P, Sandres-Saune K, Cazabat M, Pasquier C, Marchou B, Massip P, Izopet J: R5 to X4 switch of the predominant HIV-1 population in cellular reservoirs during effective highly active antiretroviral therapy. J Acquir Immune Defic Syndr. 2005, 38: 382-392. 10.1097\/01.qai.0000152835.17747.47","journal-title":"J Acquir Immune Defic Syndr"},{"key":"330_CR6","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1007\/s00239-001-0034-9","volume":"54","author":"D Posada","year":"2002","unstructured":"Posada D, Crandall KA: The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol. 2002, 54: 396-402.","journal-title":"J Mol Evol"},{"key":"330_CR7","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1093\/genetics\/156.2.879","volume":"156","author":"M Schierup","year":"2000","unstructured":"Schierup M, Hein J: Consequences of recombination on traditional phylogenetic analysis. Genetics. 2000, 156: 879-891.","journal-title":"Genetics"},{"key":"330_CR8","first-page":"231","volume":"187","author":"MH Schierup","year":"2003","unstructured":"Schierup MH, Forsberg R: Recombination and phylogeneticanalysis of HIV-1. Book Recombination and phylogenetic analysis of HIV-1 (Editor ed.^eds.), City. 2003, 187: 231-245.","journal-title":"Book Recombination and phylogenetic analysis of HIV-1 (Editor ed.^eds.), City"},{"key":"330_CR9","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1093\/bioinformatics\/16.4.395","volume":"16","author":"A Rambaut","year":"2000","unstructured":"Rambaut A: Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics. 2000, 16: 395-399. 10.1093\/bioinformatics\/16.4.395","journal-title":"Bioinformatics"},{"key":"330_CR10","doi-asserted-by":"publisher","first-page":"1807","DOI":"10.1093\/oxfordjournals.molbev.a026281","volume":"17","author":"A Drummond","year":"2000","unstructured":"Drummond A, Rodrigo AG: Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA (sUPGMA). Mol Biol Evol. 2000, 17: 1807-1815.","journal-title":"Mol Biol Evol"},{"key":"330_CR11","unstructured":"BEAST v1.0. http:\/\/beast.bio.ed.ac.uk\/"},{"key":"330_CR12","first-page":"595","volume-title":"Pacific Symposium on Biocomputing; Hawaii","author":"F Ren","year":"2001","unstructured":"Ren F, Ogishima S, Tanaka H: A new algorithm for analysis of within-host HIV-1 evolution. Pacific Symposium on Biocomputing; Hawaii. 2001, 595-605."},{"issue":"2","key":"330_CR13","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1273\/cbij.1.73","volume":"1","author":"S Ogishima","year":"2001","unstructured":"Ogishima S, Ren F, Tanaka H: Reconstruction and analysis of within-host longitudinal HIV-1 evolution by a distance-based sequential-linking algorithm. Chem-Bio Informatics Journal. 2001, 1 (2): 73-83. 10.1273\/cbij.1.73.","journal-title":"Chem-Bio Informatics Journal"},{"key":"330_CR14","first-page":"110","volume-title":"Proc IEEE Comput Sys Bioinform Conf; Stanford, CA","author":"P Buendia","year":"2004","unstructured":"Buendia P, Narasimhan G: MinPD: Distance-based Phylogenetic Analysis and Recombination Detection of Serially-Sampled HIV Quasispecies. Proc IEEE Comput Sys Bioinform Conf; Stanford, CA. 2004, 110-119."},{"key":"330_CR15","first-page":"163","volume-title":"Principles of Virology","author":"SJ Flint","year":"2000","unstructured":"Flint SJ, Enquist LW, Krug RM: Genome Replication and mRNA production by RNA Viruses. Principles of Virology. 2000, 163-196. Washington: ASM Press"},{"key":"330_CR16","volume-title":"Ph.D. Dissertation","author":"P Buendia","year":"2006","unstructured":"Buendia P: Phylogenetic Analysis of Within-Host Serially-Sampled Viral Data. Ph.D. Dissertation. 2006, Florida International University, College of Engineering and Computing"},{"key":"330_CR17","doi-asserted-by":"publisher","first-page":"2472","DOI":"10.1128\/JVI.80.5.2472-2482.2006","volume":"80","author":"C Charpentier","year":"2006","unstructured":"Charpentier C, Nora T, Tenaillon O, Clavel F, Hance AJ: Extensive Recombination among Human Immunodeficiency Virus Type 1 Quasispecies Makes an Important Contribution to Viral Diversity in Individual Patients. J Virol. 2006, 80: 2472-2482. 10.1128\/JVI.80.5.2472-2482.2006","journal-title":"J Virol"},{"key":"330_CR18","doi-asserted-by":"publisher","first-page":"1573","DOI":"10.1534\/genetics.103.023382","volume":"167","author":"D Shriner","year":"2004","unstructured":"Shriner D, Rodrigo AG, Nickle DC, Mullins JI: Pervasive Genomic Recombination of HIV-1 in Vivo. Genetics. 2004, 167: 1573-1583. 10.1534\/genetics.103.023382","journal-title":"Genetics"},{"key":"330_CR19","doi-asserted-by":"publisher","first-page":"7620","DOI":"10.1128\/JVI.00083-07","volume":"81","author":"T Nora","year":"2007","unstructured":"Nora T, Charpentier C, Tenaillon O, Hoede C, Clavel F, Hance AJ: Extensive recombination between HIV-1 quasispecies makes an important contribution to viral diversity in individual patients. J Virol. 2007, 81: 7620-7628. 10.1128\/JVI.00083-07","journal-title":"J Virol"},{"key":"330_CR20","doi-asserted-by":"publisher","first-page":"476","DOI":"10.1016\/j.meegid.2007.02.001","volume":"7","author":"A Carvajal-Rodr\u00edguez","year":"2007","unstructured":"Carvajal-Rodr\u00edguez A, Crandall KA, Posada D: Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy. Infect Genet Evol. 2007, 7: 476-483. 10.1016\/j.meegid.2007.02.001","journal-title":"Infect Genet Evol"},{"key":"330_CR21","doi-asserted-by":"crossref","first-page":"10489","DOI":"10.1128\/JVI.73.12.10489-10502.1999","volume":"73","author":"R Shankarappa","year":"1999","unstructured":"Shankarappa R, Margolick RB, Gange SJ, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, Huang X-L, Mullins JI: Consistent viral evolutionary changes associated with the progression of HIV-1 infection. J Virol. 1999, 73: 10489-10502.","journal-title":"J Virol"},{"key":"330_CR22","doi-asserted-by":"publisher","first-page":"4835","DOI":"10.1073\/pnas.89.11.4835","volume":"89","author":"EC Holmes","year":"1992","unstructured":"Holmes EC, Zhang LQ, Simmonds P, Ludlam CA, Brown AJ: Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc Natl Acad Sci USA. 1992, 89: 4835-4839. 10.1073\/pnas.89.11.4835","journal-title":"Proc Natl Acad Sci USA"},{"key":"330_CR23","doi-asserted-by":"publisher","first-page":"11715","DOI":"10.1128\/JVI.76.22.11715-11720.2002","volume":"76","author":"HA Ross","year":"2002","unstructured":"Ross HA, Rodrigo AG: Immune-mediated positive selection drives Human Immunodeficiency Virus Type 1 molecular variation and predicts disease duration. J Virol. 2002, 76: 11715-11720. 10.1128\/JVI.76.22.11715-11720.2002","journal-title":"J Virol"},{"key":"330_CR24","doi-asserted-by":"publisher","first-page":"13757","DOI":"10.1073\/pnas.241370698","volume":"98","author":"D Posada","year":"2001","unstructured":"Posada D, Crandall KA: Evaluation of methods for detecting recombination from DNA sequences: computer simulations. National Academy of Science of the United States of America. 2001, 98: 13757-13762. 10.1073\/pnas.241370698.","journal-title":"National Academy of Science of the United States of America"},{"key":"330_CR25","first-page":"807","volume-title":"International Conference on Computational Science (IWBRA); Reading, UK","author":"P Buendia","year":"2006","unstructured":"Buendia P, Collins T, Narasimhan G: Reconstructing Ancestor-Descendant Lineages from Serially-Sampled Data: A Comparison Study. International Conference on Computational Science (IWBRA); Reading, UK. 2006, 807-814."},{"key":"330_CR26","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1086\/317641","volume":"183","author":"H Imamichi","year":"2001","unstructured":"Imamichi H, Crandall K, Natarajan V, Jiang M, Dewar R, Berg S, Gaddam A, Bosche M, Metcalf J, Davey RJ, Lane H: Human immunodeficiency virus type 1 quasispecies that rebound after discontinuation of highly active antiretroviral therapy are similar to the viral quasi species present before initiation of therapy. J Infect Dis. 2001, 183: 36-50. 10.1086\/317641","journal-title":"J Infect Dis"},{"key":"330_CR27","doi-asserted-by":"publisher","first-page":"3879","DOI":"10.1073\/pnas.0800050105","volume":"105","author":"S Palmer","year":"2008","unstructured":"Palmer S, Maldarelli F, Wiegand A, Bernstein B, Hanna GJ, Brun SC, Kempf DJ, Mellors JW, Coffin JM, King MS: Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy. Proc Natl Acad Sci USA. 2008, 105: 3879-3884. 10.1073\/pnas.0800050105","journal-title":"Proc Natl Acad Sci USA"},{"key":"330_CR28","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1038\/scientificamerican0793-42","volume":"269","author":"M Eigen","year":"1993","unstructured":"Eigen M: Viral Quasispecies. Sci Am. 1993, 269: 42-49.","journal-title":"Sci Am"},{"key":"330_CR29","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.tree.2004.10.009","volume":"20","author":"DJ Wilson","year":"2005","unstructured":"Wilson DJ, Falush D, McVean G: Germs, genomes and genealogies. Trends Ecol Evol. 2005, 20: 39-45. 10.1016\/j.tree.2004.10.009","journal-title":"Trends Ecol Evol"},{"key":"330_CR30","doi-asserted-by":"publisher","first-page":"4140","DOI":"10.1128\/JVI.79.7.4140-4149.2005","volume":"79","author":"J Chen","year":"2005","unstructured":"Chen J, Dang Q, Unutmaz D, Pathak VK, Maldarelli F, Powell D, Hu WS: Mechanisms of Nonrandom Human Immunodeficiency Virus Type 1 Infection and Double Infection: Preference in Virus Entry Is Important but Is Not the Sole Factor. J Virol. 2005, 79: 4140-4149. 10.1128\/JVI.79.7.4140-4149.2005","journal-title":"J Virol"},{"key":"330_CR31","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1073\/pnas.0307636100","volume":"101","author":"Q Dang","year":"2004","unstructured":"Dang Q, Chen J, Unutmaz D, Coffin JM, Pathak VK, P D, KewalRamani VN, Maldarelli F, Hu WS: Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways. Proc Natl Acad Sci USA. 2004, 101: 632-637. 10.1073\/pnas.0307636100","journal-title":"Proc Natl Acad Sci USA"},{"key":"330_CR32","doi-asserted-by":"publisher","first-page":"4204","DOI":"10.1073\/pnas.0306764101","volume":"101","author":"DN Levy","year":"2004","unstructured":"Levy DN, Aldrovandi GM, Kutsch O, Shaw GM: Dynamics of HIV-1 recombination in its natural target cells. Proc Natl Acad Sci USA. 2004, 101: 4204-4209. 10.1073\/pnas.0306764101","journal-title":"Proc Natl Acad Sci USA"},{"key":"330_CR33","doi-asserted-by":"publisher","first-page":"6441","DOI":"10.1128\/JVI.00591-06","volume":"80","author":"JR Bailey","year":"2006","unstructured":"Bailey JR, Sedaghat AR, Kieffer T, Brennan T, Lee PK, Wind-Rotolo M, Haggerty CM, Kamireddi AR, Liu Y, Lee J, et al.: Residual Human Immunodeficiency Virus Type 1 Viremia in Some Patients on Antiretroviral Therapy Is Dominated by a Small Number of Invariant Clones Rarely Found in Circulating CD4+ T Cells. J Virol. 2006, 80: 6441-6457. 10.1128\/JVI.00591-06","journal-title":"J Virol"},{"key":"330_CR34","doi-asserted-by":"publisher","first-page":"9625","DOI":"10.1128\/JVI.79.15.9625-9634.2005","volume":"79","author":"NH Tobin","year":"2005","unstructured":"Tobin NH, Learn GH, Holte SE, Wang Y, Melvin AJ, McKernan JL, Pawluk DM, Mohan KM, Lewis PF, Mullins JI, Frenkel LM: Evidence that Low-Level Viremias during Effective Highly Active Antiretroviral Therapy Result from Two Processes: Expression of Archival Virus and Replication of Virus. J Virol. 2005, 79: 9625-9634. 10.1128\/JVI.79.15.9625-9634.2005","journal-title":"J Virol"},{"key":"330_CR35","doi-asserted-by":"publisher","first-page":"2481","DOI":"10.1098\/rspb.2007.0413","volume":"31","author":"D Wodarz","year":"2007","unstructured":"Wodarz D, Levy DN: Human immunodeficiency virus evolution towards reduced replicative fitness in vivo and the development of AIDS. Proc Biol Sci. 2007, 31: 2481-2490. 10.1098\/rspb.2007.0413.","journal-title":"Proc Biol Sci"},{"key":"330_CR36","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1017\/S0016672303006128","volume":"81","author":"D Shriner","year":"2003","unstructured":"Shriner D, Nickle DC, Jensen MA, Mullins JI: Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genetics Research. 2003, 81: 115-121. 10.1017\/S0016672303006128","journal-title":"Genetics Research"},{"key":"330_CR37","doi-asserted-by":"publisher","first-page":"1411","DOI":"10.1534\/genetics.105.044917","volume":"172","author":"DJ Wilson","year":"2006","unstructured":"Wilson DJ, McVean G: Estimating diversifying selection and functional constraint in the presence of recombination. Genetics. 2006, 172: 1411-1425. 10.1534\/genetics.105.044917","journal-title":"Genetics"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-3-62.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1752-0509-3-62\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-3-62.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,7]],"date-time":"2021-10-07T12:08:08Z","timestamp":1633608488000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-3-62"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,6,16]]},"references-count":37,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["330"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-3-62","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,6,16]]},"article-number":"62"}}