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Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. Mavian C, et al. Among authors: pond sk. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12522-12523. doi: 10.1073/pnas.2007295117. Epub 2020 May 7. Proc Natl Acad Sci U S A. 2020. PMID: 32381734 Free PMC article. No abstract available.
The replication-competent HIV-1 latent reservoir is primarily established near the time of therapy initiation.
Abrahams MR, Joseph SB, Garrett N, Tyers L, Moeser M, Archin N, Council OD, Matten D, Zhou S, Doolabh D, Anthony C, Goonetilleke N, Karim SA, Margolis DM, Pond SK, Williamson C, Swanstrom R. Abrahams MR, et al. Among authors: pond sk. Sci Transl Med. 2019 Oct 9;11(513):eaaw5589. doi: 10.1126/scitranslmed.aaw5589. Sci Transl Med. 2019. PMID: 31597754 Free PMC article.
A first look at ARFome: dual-coding genes in mammalian genomes.
Chung WY, Wadhawan S, Szklarczyk R, Pond SK, Nekrutenko A. Chung WY, et al. Among authors: pond sk. PLoS Comput Biol. 2007 May;3(5):e91. doi: 10.1371/journal.pcbi.0030091. PLoS Comput Biol. 2007. PMID: 17511511 Free PMC article.
Characterizing HIV transmission networks across the United States.
Aldous JL, Pond SK, Poon A, Jain S, Qin H, Kahn JS, Kitahata M, Rodriguez B, Dennis AM, Boswell SL, Haubrich R, Smith DM. Aldous JL, et al. Among authors: pond sk. Clin Infect Dis. 2012 Oct;55(8):1135-43. doi: 10.1093/cid/cis612. Epub 2012 Jul 10. Clin Infect Dis. 2012. PMID: 22784872 Free PMC article.
Comparison of methods to detect HIV dual infection.
Pacold M, Smith D, Little S, Cheng PM, Jordan P, Ignacio C, Richman D, Pond SK. Pacold M, et al. Among authors: pond sk. AIDS Res Hum Retroviruses. 2010 Dec;26(12):1291-8. doi: 10.1089/aid.2010.0042. Epub 2010 Oct 18. AIDS Res Hum Retroviruses. 2010. PMID: 20954840 Free PMC article.
The relatedness of HIV epidemics in the United States-Mexico border region.
Mehta SR, Delport W, Brouwer KC, Espitia S, Patterson T, Pond SK, Strathdee SA, Smith DM. Mehta SR, et al. Among authors: pond sk. AIDS Res Hum Retroviruses. 2010 Dec;26(12):1273-7. doi: 10.1089/aid.2010.0021. Epub 2010 Oct 26. AIDS Res Hum Retroviruses. 2010. PMID: 20977301 Free PMC article.
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