{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,1,20]],"date-time":"2025-01-20T17:10:46Z","timestamp":1737393046454,"version":"3.33.0"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Traditional phylogenetic methods assume tree-like evolutionary models and are likely to perform poorly when provided with sequence data from fast-evolving, recombining viruses. Furthermore, these methods assume that all the sequence data are from contemporaneous taxa, which is not valid for serially-sampled data. A more general approach is proposed here, referred to as the Sliding MinPD method, that reconstructs evolutionary networks for serially-sampled sequences in the presence of recombination.<\/jats:p><jats:p>Results: Sliding MinPD combines distance-based phylogenetic methods with automated recombination detection based on the best-known sliding window approaches to reconstruct serial evolutionary networks. Its performance was evaluated through comprehensive simulation studies and was also applied to a set of serially-sampled HIV sequences from a single patient. The resulting network organizations reveal unique patterns of viral evolution and may help explain the emergence of disease-associated mutants and drug-resistant strains with implications for patient prognosis and treatment strategies.<\/jats:p><jats:p>Availability: From website http:\/\/biorg.cis.fiu.edu\/SlidingMinPD<\/jats:p><jats:p>Contact: \u00a0giri@cis.fiu.edu<\/jats:p><jats:p>Supplementary information: \u00a0http:\/\/biorg.cis.fiu.edu\/SlidingMinPD<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm413","type":"journal-article","created":{"date-parts":[[2007,8,24]],"date-time":"2007-08-24T00:50:47Z","timestamp":1187916647000},"page":"2993-3000","source":"Crossref","is-referenced-by-count":8,"title":["Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach"],"prefix":"10.1093","volume":"23","author":[{"given":"Patricia","family":"Buendia","sequence":"first","affiliation":[{"name":"Bioinformatics Research Group (BioRG), School of Computing and Information Science, Florida International University, Miami, FL 33199, USA"}]},{"given":"Giri","family":"Narasimhan","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Group (BioRG), School of Computing and Information Science, Florida International University, Miami, FL 33199, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,8,23]]},"reference":[{"key":"2023041208261018200_","doi-asserted-by":"crossref","DOI":"10.1109\/CSB.2004.1332423","article-title":"MinPD: distance-based phylogenetic analysis and recombination detection of serially-sampled HIV quasispecies","volume-title":"Proceedings of the IEEE Computational Systems Bioinformatics Conference","author":"Buendia","year":"2004"},{"key":"2023041208261018200_","doi-asserted-by":"crossref","first-page":"2313","DOI":"10.1093\/bioinformatics\/btl387","article-title":"Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network","volume":"22","author":"Buendia","year":"2006","journal-title":"Bioinformatics"},{"key":"2023041208261018200_","article-title":"Searching for recombinant donors in a phylogenetic network of serial samples","author":"Buendia","year":"2007","journal-title":"To appear in International Symposium on Bioinformatics Research and Applications (ISBRA)"},{"key":"2023041208261018200_","doi-asserted-by":"crossref","first-page":"10958","DOI":"10.1073\/pnas.96.20.10958","article-title":"Latent reservoirs of HIV: obstacles to the eradication of virus","volume":"96","author":"Chun","year":"1999","journal-title":"Proc. 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