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Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.
Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC. Gire SK, et al. Among authors: Gladden AD. Science. 2014 Sep 12;345(6202):1369-72. doi: 10.1126/science.1259657. Epub 2014 Aug 28. Science. 2014. PMID: 25214632 Free PMC article.
Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.
Andersen KG, Shapiro BJ, Matranga CB, Sealfon R, Lin AE, Moses LM, Folarin OA, Goba A, Odia I, Ehiane PE, Momoh M, England EM, Winnicki S, Branco LM, Gire SK, Phelan E, Tariyal R, Tewhey R, Omoniwa O, Fullah M, Fonnie R, Fonnie M, Kanneh L, Jalloh S, Gbakie M, Saffa S, Karbo K, Gladden AD, Qu J, Stremlau M, Nekoui M, Finucane HK, Tabrizi S, Vitti JJ, Birren B, Fitzgerald M, McCowan C, Ireland A, Berlin AM, Bochicchio J, Tazon-Vega B, Lennon NJ, Ryan EM, Bjornson Z, Milner DA Jr, Lukens AK, Broodie N, Rowland M, Heinrich M, Akdag M, Schieffelin JS, Levy D, Akpan H, Bausch DG, Rubins K, McCormick JB, Lander ES, Günther S, Hensley L, Okogbenin S; Viral Hemorrhagic Fever Consortium, Schaffner SF, Okokhere PO, Khan SH, Grant DS, Akpede GO, Asogun DA, Gnirke A, Levin JZ, Happi CT, Garry RF, Sabeti PC. Andersen KG, et al. Among authors: Gladden AD. Cell. 2015 Aug 13;162(4):738-50. doi: 10.1016/j.cell.2015.07.020. Cell. 2015. PMID: 26276630 Free PMC article.
Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.
Matranga CB, Andersen KG, Winnicki S, Busby M, Gladden AD, Tewhey R, Stremlau M, Berlin A, Gire SK, England E, Moses LM, Mikkelsen TS, Odia I, Ehiane PE, Folarin O, Goba A, Kahn SH, Grant DS, Honko A, Hensley L, Happi C, Garry RF, Malboeuf CM, Birren BW, Gnirke A, Levin JZ, Sabeti PC. Matranga CB, et al. Among authors: Gladden AD. Genome Biol. 2014;15(11):519. doi: 10.1186/PREACCEPT-1698056557139770. Genome Biol. 2014. PMID: 25403361 Free PMC article.
Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.
Tully DC, Ogilvie CB, Batorsky RE, Bean DJ, Power KA, Ghebremichael M, Bedard HE, Gladden AD, Seese AM, Amero MA, Lane K, McGrath G, Bazner SB, Tinsley J, Lennon NJ, Henn MR, Brumme ZL, Norris PJ, Rosenberg ES, Mayer KH, Jessen H, Kosakovsky Pond SL, Walker BD, Altfeld M, Carlson JM, Allen TM. Tully DC, et al. Among authors: Gladden AD. PLoS Pathog. 2016 May 10;12(5):e1005619. doi: 10.1371/journal.ppat.1005619. eCollection 2016 May. PLoS Pathog. 2016. PMID: 27163788 Free PMC article.
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.
Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Günthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM. Henn MR, et al. Among authors: Gladden AD. PLoS Pathog. 2012;8(3):e1002529. doi: 10.1371/journal.ppat.1002529. Epub 2012 Mar 8. PLoS Pathog. 2012. PMID: 22412369 Free PMC article.
Immune-driven recombination and loss of control after HIV superinfection.
Streeck H, Li B, Poon AF, Schneidewind A, Gladden AD, Power KA, Daskalakis D, Bazner S, Zuniga R, Brander C, Rosenberg ES, Frost SD, Altfeld M, Allen TM. Streeck H, et al. Among authors: Gladden AD. J Exp Med. 2008 Aug 4;205(8):1789-96. doi: 10.1084/jem.20080281. Epub 2008 Jul 14. J Exp Med. 2008. PMID: 18625749 Free PMC article.
Rapid evolution of HIV-1 to functional CD8⁺ T cell responses in humanized BLT mice.
Dudek TE, No DC, Seung E, Vrbanac VD, Fadda L, Bhoumik P, Boutwell CL, Power KA, Gladden AD, Battis L, Mellors EF, Tivey TR, Gao X, Altfeld M, Luster AD, Tager AM, Allen TM. Dudek TE, et al. Among authors: Gladden AD. Sci Transl Med. 2012 Jul 18;4(143):143ra98. doi: 10.1126/scitranslmed.3003984. Sci Transl Med. 2012. PMID: 22814851 Free PMC article.
Compensatory mutations restore the replication defects caused by cytotoxic T lymphocyte escape mutations in hepatitis C virus polymerase.
Oniangue-Ndza C, Kuntzen T, Kemper M, Berical A, Wang YE, Neumann-Haefelin C, Foote PK, Hills-Evans K, Reyor LL, Kane K, Gladden AD, Bloom AK, Power KA, Thimme R, Lauer GM, Henn MR, Kim AY, Allen TM. Oniangue-Ndza C, et al. Among authors: Gladden AD. J Virol. 2011 Nov;85(22):11883-90. doi: 10.1128/JVI.00779-11. Epub 2011 Aug 31. J Virol. 2011. PMID: 21880756 Free PMC article.
Protective HLA class I alleles that restrict acute-phase CD8+ T-cell responses are associated with viral escape mutations located in highly conserved regions of human immunodeficiency virus type 1.
Wang YE, Li B, Carlson JM, Streeck H, Gladden AD, Goodman R, Schneidewind A, Power KA, Toth I, Frahm N, Alter G, Brander C, Carrington M, Walker BD, Altfeld M, Heckerman D, Allen TM. Wang YE, et al. Among authors: Gladden AD. J Virol. 2009 Feb;83(4):1845-55. doi: 10.1128/JVI.01061-08. Epub 2008 Nov 26. J Virol. 2009. PMID: 19036810 Free PMC article.
Transmission and long-term stability of compensated CD8 escape mutations.
Schneidewind A, Brumme ZL, Brumme CJ, Power KA, Reyor LL, O'Sullivan K, Gladden A, Hempel U, Kuntzen T, Wang YE, Oniangue-Ndza C, Jessen H, Markowitz M, Rosenberg ES, Sékaly RP, Kelleher AD, Walker BD, Allen TM. Schneidewind A, et al. J Virol. 2009 Apr;83(8):3993-7. doi: 10.1128/JVI.01108-08. Epub 2008 Dec 17. J Virol. 2009. PMID: 19091871 Free PMC article.
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