Bailey AL, Lauck M, Sibley SD, Friedrich TC, Kuhn JH, Freimer NB, Jasinska AJ, Phillips-Conroy JE, Jolly CJ, Marx PA, Apetrei C, Rogers J, Goldberg TL, O’Connor DH. 2016. Zoonotic Potential of Simian Arteriviruses. J Virol 90:630. PMC4702702.

Arias JF, Colomer-Lluch M, von Bredow B, Greene JM, MacDonald J, O’Connor DH, Serra-Moreno R, Evans DT. 2016. Tetherin Antagonism by HIV-1 Group M Nef Proteins. J Virol

Yu SQ, Cai Y, Lyons C, Johnson RF, Postnikova E, Mazur S, Johnson JC, Radoshitzky SR, Bailey AL, Lauck M, Goldberg TL, O’Connor DH, Jahrling PB, Friedrich TC, Kuhn JH. 2016. Specific Detection of Two Divergent Simian Arteriviruses Using RNAscope In Situ Hybridization. PLoS One 11:e0151313. PMC4786270.

Kuhn JH, Lauck M, Bailey AL, Shchetinin AM, Vishnevskaya TV, Bao Y, Ng TF, LeBreton M, Schneider BS, Gillis A, Tamoufe U, Diffo Jle D, Takuo JM, Kondov NO, Coffey LL, Wolfe ND, Delwart E, Clawson AN, Postnikova E, Bollinger L, Lackemeyer MG, Radoshitzky SR, Palacios G, Wada J, Shevtsova ZV, Jahrling PB, Lapin BA, Deriabin PG, Dunowska M, Alkhovsky SV, Rogers J, Friedrich TC, O’Connor DH, Goldberg TL. 2016. Reorganization and expansion of the nidoviral family Arteriviridae. Arch Virol 161:755.

Kallas EG, O’Connor DH. 2016. Real-Time Sharing of Zika Virus Data in an Interconnected World. JAMA Pediatr 170:633.

Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M, Daringer NM, Bosch I, Dudley DM, O’Connor DH, Gehrke L, Collins JJ. 2016. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell 165:1255.

Simons ND, Ruiz-Lopez MJ, Chapman CA, Goldberg TL, Karl JA, Wiseman RW, Bohn PS, O’Connor DH, Ting N. 2016. Rapid Identification of Major Histocompatibility Complex Class I Haplotypes Using Deep Sequencing in an Endangered Old World Monkey. Conserv Genet Resour 8:23. PMC4863455.

Bennett AJ, Sibley SD, Lauck M, Weny G, Hyeroba D, Tumukunde A, Friedrich TC, O’Connor DH, Johnson CA, Rothman JM, Goldberg TL. 2016. Naturally Circulating Hepatitis A Virus in Olive Baboons, Uganda. Emerg Infect Dis 22:1308. PMC4918173.

O’Connor DH, Osorio JE, Tanuri A, Kallas EG. 2016. Forging Collaborative Relationships in Brazil: From AIDS to ZIKV. Cell 166:2.

Wahl-Jensen V, Johnson JC, Lauck M, Weinfurter JT, Moncla LH, Weiler AM, Charlier O, Rojas O, Byrum R, Ragland DR, Huzella L, Zommer E, Cohen M, Bernbaum JG, Cai Y, Sanford HB, Mazur S, Johnson RF, Qin J, Palacios GF, Bailey AL, Jahrling PB, Goldberg TL, O’Connor DH, Friedrich TC, Kuhn JH. 2016. Divergent Simian Arteriviruses Cause Simian Hemorrhagic Fever of Differing Severities in Macaques. MBio 7:e02009. PMC4791849.

Lee LM, Wallace RS, Clyde VL, Gendron-Fitzpatrick A, Sibley SD, Stuchin M, Lauck M, O’Connor DH, Nakao M, Lavikainen A, Hoberg EP, Goldberg TL. 2016. Definitive Hosts of Versteria Tapeworms (Cestoda: Taeniidae) Causing Fatal Infection in North America. Emerg Infect Dis 22:707. PMC4806962.

Bailey AL, Lauck M, Ghai RR, Nelson CW, Heimbruch K, Hughes AL, Goldberg TL, Kuhn JH, Jasinska AJ, Freimer NB, Apetrei C, O’Connor DH. 2016. Arteriviruses, Pegiviruses, and Lentiviruses Are Common among Wild African Monkeys. J Virol 90:6724. PMC4944300.

Dudley DM, Aliota MT, Mohr EL, Weiler AM, Lehrer-Brey G, Weisgrau KL, Mohns MS, Breitbach ME, Rasheed MN, Newman CM, Gellerup DD, Moncla LH, Post J, Schultz-Darken N, Schotzko ML, Hayes JM, Eudailey JA, Moody MA, Permar SR, O’Connor SL, Rakasz EG, Simmons HA, Capuano S, Golos TG, Osorio JE, Friedrich TC, O’Connor DH. 2016. A rhesus macaque model of Asian-lineage Zika virus infection. Nat Commun 7:12204. PMC4931337.

Ayala VI, Trivett MT, Coren LV, Jain S, Bohn PS, Wiseman RW, O’Connor DH, Ohlen C, Ott DE. 2016. A novel SIV gag-specific CD4(+)T-cell clone suppresses SIVmac239 replication in CD4(+)T cells revealing the interplay between antiviral effector cells and their infected targets. Virology 493:100. PMC4860118.

Ladner JT, Wiley MR, Beitzel B, Auguste AJ, Dupuis AP, Lindquist ME, Sibley SD, Kota KP, Fetterer D, Eastwood G, Kimmel D, Prieto K, Guzman H, Aliota MT, Reyes D, Brueggemann EE, St John L, Hyeroba D, Lauck M, Friedrich TC, O’Connor DH, Gestole MC, Cazares LH, Popov VL, Castro-Llanos F, Kochel TJ, Kenny T, White B, Ward MD, Loaiza JR, Goldberg TL, Weaver SC, Kramer LD, Tesh RB, Palacios G. 2016. A Multicomponent Animal Virus Isolated from Mosquitoes. Cell Host Microbe 20:357. PMC5025392.

Mothe BR, Lindestam Arlehamn CS, Dow C, Dillon MB, Wiseman RW, Bohn P, Karl J, Golden NA, Gilpin T, Foreman TW, Rodgers MA, Mehra S, Scriba TJ, Flynn JL, Kaushal D, O’Connor DH, Sette A. 2015. The TB-specific CD4(+) T cell immune repertoire in both cynomolgus and rhesus macaques largely overlap with humans. Tuberculosis (Edinb) 95:722. PMC4773292.

Warren WC, Jasinska AJ, Garcia-Perez R, Svardal H, Tomlinson C, Rocchi M, Archidiacono N, Capozzi O, Minx P, Montague MJ, Kyung K, Hillier LW, Kremitzki M, Graves T, Chiang C, Hughes J, Tran N, Huang Y, Ramensky V, Choi OW, Jung YJ, Schmitt CA, Juretic N, Wasserscheid J, Turner TR, Wiseman RW, Tuscher JJ, Karl JA, Schmitz JE, Zahn R, O’Connor DH, Redmond E, Nisbett A, Jacquelin B, Muller-Trutwin MC, Brenchley JM, Dione M, Antonio M, Schroth GP, Kaplan JR, Jorgensen MJ, Thomas GW, Hahn MW, Raney BJ, Aken B, Nag R, Schmitz J, Churakov G, Noll A, Stanyon R, Webb D, Thibaud-Nissen F, Nordborg M, Marques-Bonet T, Dewar K, Weinstock GM, Wilson RK, Freimer NB. 2015. The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Res 25:1921. PMC4665013.

Cai Y, Postnikova EN, Bernbaum JG, Yu SQ, Mazur S, Deiuliis NM, Radoshitzky SR, Lackemeyer MG, McCluskey A, Robinson PJ, Haucke V, Wahl-Jensen V, Bailey AL, Lauck M, Friedrich TC, O’Connor DH, Goldberg TL, Jahrling PB, Kuhn JH. 2015. Simian hemorrhagic fever virus cell entry is dependent on CD163 and uses a clathrin-mediated endocytosis-like pathway. J Virol 89:844. PMC4301170.

Heimbruch KE, Karl JA, Wiseman RW, Dudley DM, Johnson Z, Kaur A, O’Connor DH. 2015. Novel MHC class I full-length allele and haplotype characterization in sooty mangabeys. Immunogenetics 67:437. PMC4498956.

Westbrook CJ, Karl JA, Wiseman RW, Mate S, Koroleva G, Garcia K, Sanchez-Lockhart M, O’Connor DH, Palacios G. 2015. No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing. Hum Immunol 76:891.

Bialas KM, Tanaka T, Tran D, Varner V, Cisneros De La Rosa E, Chiuppesi F, Wussow F, Kattenhorn L, Macri S, Kunz EL, Estroff JA, Kirchherr J, Yue Y, Fan Q, Lauck M, O’Connor DH, Hall AH, Xavier A, Diamond DJ, Barry PA, Kaur A, Permar SR. 2015. Maternal CD4+ T cells protect against severe congenital cytomegalovirus disease in a novel nonhuman primate model of placental cytomegalovirus transmission. Proc Natl Acad Sci U S A 112:13645. PMC4640765.

Correll M, Bailey AL, Sarikaya A, O’Connor DH, Gleicher M. 2015. LayerCake: a tool for the visual comparison of viral deep sequencing data. Bioinformatics 31:3522. PMC4626748.

Lauck M, Alkhovsky SV, Bao Y, Bailey AL, Shevtsova ZV, Shchetinin AM, Vishnevskaya TV, Lackemeyer MG, Postnikova E, Mazur S, Wada J, Radoshitzky SR, Friedrich TC, Lapin BA, Deriabin PG, Jahrling PB, Goldberg TL, O’Connor DH, Kuhn JH. 2015. Historical Outbreaks of Simian Hemorrhagic Fever in Captive Macaques Were Caused by Distinct Arteriviruses. J Virol 89:8082. PMC4505640.

Lauck M, Yu SQ, Cai Y, Hensley LE, Chiu CY, O’Connor DH, Kuhn JH. 2015. Genome Sequence of Bivens Arm Virus, a Tibrovirus Belonging to the Species Tibrogargan virus (Mononegavirales: Rhabdoviridae). Genome Announc 3PMC4394750.

Lauck M, Bailey AL, Andersen KG, Goldberg TL, Sabeti PC, O’Connor DH. 2015. GB virus C coinfections in west African Ebola patients. J Virol 89:2425. PMC4338908.

Mohns MS, Greene JM, Cain BT, Pham NH, Gostick E, Price DA, O’Connor DH. 2015. Expansion of Simian Immunodeficiency Virus (SIV)-Specific CD8 T Cell Lines from SIV-Naive Mauritian Cynomolgus Macaques for Adoptive Transfer. J Virol 89:9748. PMC4577914.

Breed MW, Elser SE, Torben W, Jordan AP, Aye PP, Midkiff C, Schiro F, Sugimoto C, Alvarez-Hernandez X, Blair RV, Somasunderam A, Utay NS, Kuroda MJ, Pahar B, Wiseman RW, O’Connor DH, LaBranche CC, Montefiori DC, Marsh M, Li Y, Piatak MJ, Lifson JD, Keele BF, Fultz PN, Lackner AA, Hoxie JA. 2015. Elite Control, Gut CD4 T Cell Sparing, and Enhanced Mucosal T Cell Responses in Macaca nemestrina Infected by a Simian Immunodeficiency Virus Lacking a gp41 Trafficking Motif. J Virol 89:10156. PMC4580161.

Bailey AL, Lauck M, Mohns M, Peterson EJ, Beheler K, Brunner KG, Crosno K, Mejia A, Mutschler J, Gehrke M, Greene J, Ericsen AJ, Weiler A, Lehrer-Brey G, Friedrich TC, Sibley SD, Kallas EG, Capuano S, Rogers J, Goldberg TL, Simmons HA, O’Connor DH. 2015. Durable sequence stability and bone marrow tropism in a macaque model of human pegivirus infection. Sci Transl Med 7:305ra144. PMC4605385.

Wang Z, Metcalf B, Kasheta M, Kasala-Hallinan C, Tran D, Johnson RP, Else JG, Karl J, O’Connor D, Apetrei C, Kaur A. 2015. Characterization of MHC class I alleles in sooty mangabeys as a tool for evaluating cellular immunity in natural hosts of SIV infection. Immunogenetics 67:447. PMC4536953.

Ericsen AJ, Starrett GJ, Greene JM, Lauck M, Raveendran M, Deiros DR, Mohns MS, Vince N, Cain BT, Pham NH, Weinfurter JT, Bailey AL, Budde ML, Wiseman RW, Gibbs R, Muzny D, Friedrich TC, Rogers J, O’Connor DH. 2014. Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication. Genome Biol 15:478. PMC4223156.

Bailey AL, Lauck M, Sibley SD, Pecotte J, Rice K, Weny G, Tumukunde A, Hyeroba D, Greene J, Correll M, Gleicher M, Friedrich TC, Jahrling PB, Kuhn JH, Goldberg TL, Rogers J, O’Connor DH. 2014. Two novel simian arteriviruses in captive and wild baboons (Papio spp.). J Virol 88:13231. PMC4249091.

Burwitz BJ, Wu HL, Reed JS, Hammond KB, Newman LP, Bimber BN, Nimiyongskul FA, Leon EJ, Maness NJ, Friedrich TC, Yokoyama M, Sato H, Matano T, O’Connor DH, Sacha JB. 2014. Tertiary mutations stabilize CD8+ T lymphocyte escape-associated compensatory mutations following transmission of simian immunodeficiency virus. J Virol 88:3598. PMC3957937.

Karl JA, Heimbruch KE, Vriezen CE, Mironczuk CJ, Dudley DM, Wiseman RW, O’Connor DH. 2014. Survey of major histocompatibility complex class II diversity in pig-tailed macaques. Immunogenetics 66:613. PMC4198495.

Greene JM, Weiler AM, Reynolds MR, Cain BT, Pham NH, Ericsen AJ, Peterson EJ, Crosno K, Brunner K, Friedrich TC, O’Connor DH. 2014. Rapid, repeated, low-dose challenges with SIVmac239 infect animals in a condensed challenge window. Retrovirology 11:66. PMC4149191.

Gooneratne SL, Alinejad-Rokny H, Ebrahimi D, Bohn PS, Wiseman RW, O’Connor DH, Davenport MP, Kent SJ. 2014. Linking pig-tailed macaque major histocompatibility complex class I haplotypes and cytotoxic T lymphocyte escape mutations in simian immunodeficiency virus infection. J Virol 88:14310. PMC4249162.

Schafer JL, Colantonio AD, Neidermyer WJ, Dudley DM, Connole M, O’Connor DH, Evans DT. 2014. KIR3DL01 recognition of Bw4 ligands in the rhesus macaque: maintenance of Bw4 specificity since the divergence of apes and Old World monkeys. J Immunol 192:1907. PMC4162532.

Bailey AL, Lauck M, Weiler A, Sibley SD, Dinis JM, Bergman Z, Nelson CW, Correll M, Gleicher M, Hyeroba D, Tumukunde A, Weny G, Chapman C, Kuhn JH, Hughes AL, Friedrich TC, Goldberg TL, O’Connor DH. 2014. High genetic diversity and adaptive potential of two simian hemorrhagic fever viruses in a wild primate population. PLoS One 9:e90714. PMC3961216.

Lauck M, Palacios G, Wiley MR, L Y, Fang Y, Lackemeyer MG, Cai Y, Bailey AL, Postnikova E, Radoshitzky SR, Johnson RF, Alkhovsky SV, Deriabin PG, Friedrich TC, Goldberg TL, Jahrling PB, O’Connor DH, Kuhn JH. 2014. Genome Sequences of Simian Hemorrhagic Fever Virus Variant NIH LVR42-0/M6941 Isolates (Arteriviridae: Arterivirus). Genome Announc 2PMC4192379.

Dudley DM, Karl JA, Creager HM, Bohn PS, Wiseman RW, O’Connor DH. 2014. Full-length novel MHC class I allele discovery by next-generation sequencing: two platforms are better than one. Immunogenetics 66:15. PMC3910708.

Goldberg TL, Gendron-Fitzpatrick A, Deering KM, Wallace RS, Clyde VL, Lauck M, Rosen GE, Bennett AJ, Greiner EC, O’Connor DH. 2014. Fatal metacestode infection in Bornean orangutan caused by unknown Versteria species. Emerg Infect Dis 20:109. PMC3884733.

Lauck M, Switzer WM, Sibley SD, Hyeroba D, Tumukunde A, Weny G, Shankar A, Greene JM, Ericsen AJ, Zheng H, Ting N, Chapman CA, Friedrich TC, Goldberg TL, O’Connor DH. 2014. Discovery and full genome characterization of a new SIV lineage infecting red-tailed guenons (Cercopithecus ascanius schmidti) in Kibale National Park, Uganda. Retrovirology 11:55. PMC4226943.

Sibley SD, Lauck M, Bailey AL, Hyeroba D, Tumukunde A, Weny G, Chapman CA, O’Connor DH, Goldberg TL, Friedrich TC. 2014. Discovery and characterization of distinct simian pegiviruses in three wild African Old World monkey species. PLoS One 9:e98569. PMC4053331.

Dudley DM, Bailey AL, Mehta SH, Hughes AL, Kirk GD, Westergaard RP, O’Connor DH. 2014. Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq. Retrovirology 11:122. PMC4302432.

Silveira EL, Fogg MH, Leskowitz RM, Ertl HC, Wiseman RW, O’Connor DH, Lieberman P, Wang F, Villinger F. 2013. Therapeutic vaccination against the rhesus lymphocryptovirus EBNA-1 homologue, rhEBNA-1, elicits T cell responses to novel epitopes in rhesus macaques. J Virol 87:13904. PMC3838282.

Cain BT, Pham NH, Budde ML, Greene JM, Weinfurter JT, Scarlotta M, Harris M, Chin E, O’Connor SL, Friedrich TC, O’Connor DH. 2013. T cell response specificity and magnitude against SIVmac239 are not concordant in major histocompatibility complex-matched animals. Retrovirology 10:116. PMC3874790.

Wilker PR, Dinis JM, Starrett G, Imai M, Hatta M, Nelson CW, O’Connor DH, Hughes AL, Neumann G, Kawaoka Y, Friedrich TC. 2013. Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses. Nat Commun 4:2636. PMC3845350.

Karl JA, Bohn PS, Wiseman RW, Nimityongskul FA, Lank SM, Starrett GJ, O’Connor DH. 2013. Major histocompatibility complex class I haplotype diversity in Chinese rhesus macaques. G3 (Bethesda) 3:1195. PMC3704247.

Wiseman RW, Karl JA, Bohn PS, Nimityongskul FA, Starrett GJ, O’Connor DH. 2013. Haplessly hoping: macaque major histocompatibility complex made easy. ILAR J 54:196. PMC3814398.

Lauck M, Sibley SD, Hyeroba D, Tumukunde A, Weny G, Chapman CA, Ting N, Switzer WM, Kuhn JH, Friedrich TC, O’Connor DH, Goldberg TL. 2013. Exceptional simian hemorrhagic fever virus diversity in a wild African primate community. J Virol 87:688. PMC3536393.

Lauck M, Switzer WM, Sibley SD, Hyeroba D, Tumukunde A, Weny G, Taylor B, Shankar A, Ting N, Chapman CA, Friedrich TC, Goldberg TL, O’Connor DH. 2013. Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda. Retrovirology 10:107. PMC4016034.

Ghai RR, Sibley SD, Lauck M, Dinis JM, Bailey AL, Chapman CA, Omeja P, Friedrich TC, O’Connor DH, Goldberg TL. 2013. Deep sequencing identifies two genotypes and high viral genetic diversity of human pegivirus (GB virus C) in rural Ugandan patients. J Gen Virol 94:2670. PMC3836497.

Del Prete GQ, Scarlotta M, Newman L, Reid C, Parodi LM, Roser JD, Oswald K, Marx PA, Miller CJ, Desrosiers RC, Barouch DH, Pal R, Piatak MJ, Chertova E, Giavedoni LD, O’Connor DH, Lifson JD, Keele BF. 2013. Comparative characterization of transfection- and infection-derived simian immunodeficiency virus challenge stocks for in vivo nonhuman primate studies. J Virol 87:4584. PMC3624367.

Thurber MI, Ghai RR, Hyeroba D, Weny G, Tumukunde A, Chapman CA, Wiseman RW, Dinis J, Steeil J, Greiner EC, Friedrich TC, O’Connor DH, Goldberg TL. 2013. Co-infection and cross-species transmission of divergent Hepatocystis lineages in a wild African primate community. Int J Parasitol 43:613. PMC3676718.

Greene JM, Lhost JJ, Hines PJ, Scarlotta M, Harris M, Burwitz BJ, Budde ML, Dudley DM, Pham N, Cain B, Mac Nair CE, Weiker MK, O’Connor SL, Friedrich TC, O’Connor DH. 2013. Adoptive transfer of lymphocytes isolated from simian immunodeficiency virus SIVmac239Deltanef-vaccinated macaques does not affect acute-phase viral loads but may reduce chronic-phase viral loads in major histocompatibility complex-matched recipients. J Virol 87:7382. PMC3700297.

Walsh AD, Bimber BN, Das A, Piaskowski SM, Rakasz EG, Bean AT, Mudd PA, Ericsen AJ, Wilson NA, Hughes AL, O’Connor DH, Maness NJ. 2013. Acute phase CD8+ T lymphocytes against alternate reading frame epitopes select for rapid viral escape during SIV infection. PLoS One 8:e61383. PMC3645990.

Lauck M, Sibley SD, Lara J, Purdy MA, Khudyakov Y, Hyeroba D, Tumukunde A, Weny G, Switzer WM, Chapman CA, Hughes AL, Friedrich TC, O’Connor DH, Goldberg TL. 2013. A novel hepacivirus with an unusually long and intrinsically disordered NS5A protein in a wild Old World primate. J Virol 87:8971. PMC3754081.

Lank SM, Golbach BA, Creager HM, Wiseman RW, Keskin DB, Reinherz EL, Brusic V, O’Connor DH. 2012. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing. BMC Genomics 13:378. PMC3575390.

Budde ML, Greene JM, Chin EN, Ericsen AJ, Scarlotta M, Cain BT, Pham NH, Becker EA, Harris M, Weinfurter JT, O’Connor SL, Piatak MJ, Lifson JD, Gostick E, Price DA, Friedrich TC, O’Connor DH. 2012. Specific CD8+ T cell responses correlate with control of simian immunodeficiency virus replication in Mauritian cynomolgus macaques. J Virol 86:7596. PMC3416303.

Hughes AL, Becker EA, Lauck M, Karl JA, Braasch AT, O’Connor DH, O’Connor SL. 2012. SIV genome-wide pyrosequencing provides a comprehensive and unbiased view of variation within and outside CD8 T lymphocyte epitopes. PLoS One 7:e47818. PMC3480401.

de Groot NG, Otting N, Robinson J, Blancher A, Lafont BA, Marsh SG, O’Connor DH, Shiina T, Walter L, Watkins DI, Bontrop RE. 2012. Nomenclature report on the major histocompatibility complex genes and alleles of Great Ape, Old and New World monkey species. Immunogenetics 64:615. PMC3396756.

Dudley DM, Chin EN, Bimber BN, Sanabani SS, Tarosso LF, Costa PR, Sauer MM, Kallas EG, O’Connor DH. 2012. Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance. PLoS One 7:e36494. PMC3344889.

Rout N, Greene J, Yue S, O’Connor D, Johnson RP, Else JG, Exley MA, Kaur A. 2012. Loss of effector and anti-inflammatory natural killer T lymphocyte function in pathogenic simian immunodeficiency virus infection. PLoS Pathog 8:e1002928. PMC3447755.

Johnson ZP, Eady RD, Ahmad SF, Agravat S, Morris T, Else J, Lank SM, Wiseman RW, O’Connor DH, Penedo MC, Larsen CP, Kean LS. 2012. Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets. Immunogenetics 64:329. PMC3514553.

Rasmussen RA, Siddappa NB, Lakhashe SK, Watkins J, Villinger F, Ibegbu C, Florese RH, Robert-Guroff M, Montefiori DC, Forthal DN, O’Connor D, Ruprecht RM. 2012. High-level, lasting antiviral immunity induced by a bimodal AIDS vaccine and boosted by live-virus exposure: prevention of viremia. AIDS 26:149. PMC3767758.

Lang Kuhs KA, Ginsberg AA, Yan J, Wiseman RW, Khan AS, Sardesai NY, O’Connor DH, Weiner DB. 2012. Hepatitis C virus NS3/NS4A DNA vaccine induces multiepitope T cell responses in rhesus macaques mimicking human immune responses [corrected]. Mol Ther 20:669. PMC3293616.

McLaren PJ, Ripke S, Pelak K, Weintrob AC, Patsopoulos NA, Jia X, Erlich RL, Lennon NJ, Kadie CM, Heckerman D, Gupta N, Haas DW, Deeks SG, Pereyra F, Walker BD, de Bakker PI. 2012. Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans. Hum Mol Genet 21:4334. PMC3441117.

Greene JM, Chin EN, Budde ML, Lhost JJ, Hines PJ, Burwitz BJ, Broman KW, Nelson JE, Friedrich TC, O’Connor DH. 2012. Ex vivo SIV-specific CD8 T cell responses in heterozygous animals are primarily directed against peptides presented by a single MHC haplotype. PLoS One 7:e43690. PMC3425510.

Mudd PA, Ericsen AJ, Burwitz BJ, Wilson NA, O’Connor DH, Hughes AL, Watkins DI. 2012. Escape from CD8(+) T cell responses in Mamu-B*00801(+) macaques differentiates progressors from elite controllers. J Immunol 188:3364. PMC3883130.

O’Connor SL, Becker EA, Weinfurter JT, Chin EN, Budde ML, Gostick E, Correll M, Gleicher M, Hughes AL, Price DA, Friedrich TC, O’Connor DH. 2012. Conditional CD8+ T cell escape during acute simian immunodeficiency virus infection. J Virol 86:605. PMC3255930.

Lauck M, Alvarado-Mora MV, Becker EA, Bhattacharya D, Striker R, Hughes AL, Carrilho FJ, O’Connor DH, Pinho JR. 2012. Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing. J Virol 86:3952. PMC3302523.

Dietrich EA, Brennan G, Ferguson B, Wiseman RW, O’Connor D, Hu SL. 2011. Variable prevalence and functional diversity of the antiretroviral restriction factor TRIMCyp in Macaca fascicularis. J Virol 85:9956. PMC3196437.

Budde ML, Lhost JJ, Burwitz BJ, Becker EA, Burns CM, O’Connor SL, Karl JA, Wiseman RW, Bimber BN, Zhang GL, Hildebrand W, Brusic V, O’Connor DH. 2011. Transcriptionally abundant major histocompatibility complex class I alleles are fundamental to nonhuman primate simian immunodeficiency virus-specific CD8+ T cell responses. J Virol 85:3250. PMC3067831.

Reed JS, Sidney J, Piaskowski SM, Glidden CE, Leon EJ, Burwitz BJ, Kolar HL, Eernisse CM, Furlott JR, Maness NJ, Walsh AD, Rudersdorf RA, Bardet W, McMurtrey CP, O’Connor DH, Hildebrand WH, Sette A, Watkins DI, Wilson NA. 2011. The role of MHC class I allele Mamu-A*07 during SIV(mac)239 infection. Immunogenetics 63:789. PMC3706270.

Burwitz BJ, Ende Z, Sudolcan B, Reynolds MR, Greene JM, Bimber BN, Almeida JR, Kurniawan M, Venturi V, Gostick E, Wiseman RW, Douek DC, Price DA, O’Connor DH. 2011. Simian immunodeficiency virus SIVmac239Deltanef vaccination elicits different Tat28-35SL8-specific CD8+ T-cell clonotypes compared to a DNA prime/adenovirus type 5 boost regimen in rhesus macaques. J Virol 85:3683. PMC3067854.

Fernandez CS, Reece JC, Saepuloh U, De Rose R, Ishkandriati D, O’Connor DH, Wiseman RW, Kent SJ. 2011. Screening and confirmatory testing of MHC class I alleles in pig-tailed macaques. Immunogenetics 63:511.

Burwitz BJ, Sacha JB, Reed JS, Newman LP, Norante FA, Bimber BN, Wilson NA, Watkins DI, O’Connor DH. 2011. Pyrosequencing reveals restricted patterns of CD8+ T cell escape-associated compensatory mutations in simian immunodeficiency virus. J Virol 85:13088. PMC3233179.

Lauck M, Hyeroba D, Tumukunde A, Weny G, Lank SM, Chapman CA, O’Connor DH, Friedrich TC, Goldberg TL. 2011. Novel, divergent simian hemorrhagic fever viruses in a wild Ugandan red colobus monkey discovered using direct pyrosequencing. PLoS One 6:e19056. PMC3081318.

Belisle SE, Yin J, Shedlock DJ, Dai A, Yan J, Hirao L, Kutzler MA, Lewis MG, Andersen H, Lank SM, Karl JA, O’Connor DH, Khan A, Sardesai N, Chang J, Aicher L, Palermo RE, Weiner DB, Katze MG, Boyer J. 2011. Long-term programming of antigen-specific immunity from gene expression signatures in the PBMC of rhesus macaques immunized with an SIV DNA vaccine. PLoS One 6:e19681. PMC3119060.

Colantonio AD, Bimber BN, Neidermyer WJJ, Reeves RK, Alter G, Altfeld M, Johnson RP, Carrington M, O’Connor DH, Evans DT. 2011. KIR polymorphisms modulate peptide-dependent binding to an MHC class I ligand with a Bw6 motif. PLoS Pathog 7:e1001316. PMC3053351.

Vojnov L, Martins MA, Almeida JR, Ende Z, Rakasz EG, Reynolds MR, Leon EJ, Weisgrau KL, Burwitz BJ, Folkvord JM, de Santana MG, Neves PC, Connick E, Skinner PJ, Gostick E, O’Connor DH, Wilson NA, Bonaldo MC, Galler R, Price DA, Douek DC, Watkins DI. 2011. GagCM9-specific CD8+ T cells expressing limited public TCR clonotypes do not suppress SIV replication in vivo. PLoS One 6:e23515. PMC3162554.

Keskin DB, Reinhold B, Lee SY, Zhang G, Lank S, O’Connor DH, Berkowitz RS, Brusic V, Kim SJ, Reinherz EL. 2011. Direct identification of an HPV-16 tumor antigen from cervical cancer biopsy specimens. Front Immunol 2:75. PMC3342284.

Greene JM, Wiseman RW, Lank SM, Bimber BN, Karl JA, Burwitz BJ, Lhost JJ, Hawkins OE, Kunstman KJ, Broman KW, Wolinsky SM, Hildebrand WH, O’Connor DH. 2011. Differential MHC class I expression in distinct leukocyte subsets. BMC Immunol 12:39. PMC3155488.

Nadazdin O, Boskovic S, Wee SL, Sogawa H, Koyama I, Colvin RB, Smith RN, Tocco G, O’Connor DH, Karl JA, Madsen JC, Sachs DH, Kawai T, Cosimi AB, Benichou G. 2011. Contributions of direct and indirect alloresponses to chronic rejection of kidney allografts in nonhuman primates. J Immunol 187:4589. PMC3197941.

Moreland AJ, Guethlein LA, Reeves RK, Broman KW, Johnson RP, Parham P, O’Connor DH, Bimber BN. 2011. Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques. BMC Genomics 12:295. PMC3125267.

Creager HM, Becker EA, Sandman KK, Karl JA, Lank SM, Bimber BN, Wiseman RW, Hughes AL, O’Connor SL, O’Connor DH. 2011. Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques. Immunogenetics 63:611. PMC3156323.

Bimber BN, Dudley DM, Lauck M, Becker EA, Chin EN, Lank SM, Grunenwald HL, Caruccio NC, Maffitt M, Wilson NA, Reed JS, Sosman JM, Tarosso LF, Sanabani S, Kallas EG, Hughes AL, O’Connor DH. 2010. Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. J Virol 84:12087. PMC2977871.

Bolton DL, Minang JT, Trivett MT, Song K, Tuscher JJ, Li Y, Piatak MJ, O’Connor D, Lifson JD, Roederer M, Ohlen C. 2010. Trafficking, persistence, and activation state of adoptively transferred allogeneic and autologous Simian Immunodeficiency Virus-specific CD8(+) T cell clones during acute and chronic infection of rhesus macaques. J Immunol 184:303. PMC2797565.

Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Ripke S, Brumme CJ, Pulit SL, Carrington M, Kadie CM, Carlson JM, Heckerman D, Graham RR, Plenge RM, Deeks SG, Gianniny L, Crawford G, Sullivan J, Gonzalez E, Davies L, Camargo A, Moore JM, Beattie N, Gupta S, Crenshaw A, Burtt NP, Guiducci C, Gupta N, Gao X, Qi Y, Yuki Y, Piechocka-Trocha A, Cutrell E, Rosenberg R, Moss KL, Lemay P, O’Leary J, Schaefer T, Verma P, Toth I, Block B, Baker B, Rothchild A, Lian J, Proudfoot J, Alvino DM, Vine S, Addo MM, Allen TM, Altfeld M, Henn MR, Le Gall S, Streeck H, Haas DW, Kuritzkes DR, Robbins GK, Shafer RW, Gulick RM, Shikuma CM, Haubrich R, Riddler S, Sax PE, Daar ES, Ribaudo HJ, Agan B, Agarwal S, Ahern RL, Allen BL, Altidor S, Altschuler EL, Ambardar S, Anastos K, Anderson B, Anderson V, Andrady U, Antoniskis D, Bangsberg D, Barbaro D, Barrie W, Bartczak J, Barton S, Basden P, Basgoz N, Bazner S, Bellos NC, Benson AM, Berger J, Bernard NF, Bernard AM, Birch C, Bodner SJ, Bolan RK, Boudreaux ET, Bradley M, Braun JF, Brndjar JE, Brown SJ, Brown K, Brown ST, Burack J, Bush LM, Cafaro V, Campbell O, Campbell J, Carlson RH, Carmichael JK, Casey KK, Cavacuiti C, Celestin G, Chambers ST, Chez N, Chirch LM, Cimoch PJ, Cohen D, Cohn LE, Conway B, Cooper DA, Cornelson B, Cox DT, Cristofano MV, Cuchural GJ, Czartoski JL, Dahman JM, Daly JS, Davis BT, Davis K, Davod SM, DeJesus E, Dietz CA, Dunham E, Dunn ME, Ellerin TB, Eron JJ, Fangman JJ, Farel CE, Ferlazzo H, Fidler S, Fleenor-Ford A, Frankel R, Freedberg KA, French NK, Fuchs JD, Fuller JD, Gaberman J, Gallant JE, Gandhi RT, Garcia E, Garmon D, Gathe JCJ, Gaultier CR, Gebre W, Gilman FD, Gilson I, Goepfert PA, Gottlieb MS, Goulston C, Groger RK, Gurley TD, Haber S, Hardwicke R, Hardy WD, Harrigan PR, Hawkins TN, Heath S, Hecht FM, Henry WK, Hladek M, Hoffman RP, Horton JM, Hsu RK, Huhn GD, Hunt P, Hupert MJ, Illeman ML, Jaeger H, Jellinger RM, John M, Johnson JA, Johnson KL, Johnson H, Johnson K, Joly J, Jordan WC, Kauffman CA, Khanlou H, Killian RK, Kim AY, Kim DD, Kinder CA, Kirchner JT, Kogelman L, Kojic EM, Korthuis PT, Kurisu W, Kwon DS, LaMar M, Lampiris H, Lanzafame M, Lederman MM, Lee DM, Lee JM, Lee MJ, Lee ET, Lemoine J, Levy JA, Llibre JM, Liguori MA, Little SJ, Liu AY, Lopez AJ, Loutfy MR, Loy D, Mohammed DY, Man A, Mansour MK, Marconi VC, Markowitz M, Marques R, Martin JN, Martin HLJ, Mayer KH, McElrath MJ, McGhee TA, McGovern BH, McGowan K, McIntyre D, Mcleod GX, Menezes P, Mesa G, Metroka CE, Meyer-Olson D, Miller AO, Montgomery K, Mounzer KC, Nagami EH, Nagin I, Nahass RG, Nelson MO, Nielsen C, Norene DL, O’Connor DH, Ojikutu BO, Okulicz J, Oladehin OO, Oldfield EC, Olender SA, Ostrowski M, Owen WFJ, Pae E, Parsonnet J, Pavlatos AM, Perlmutter AM, Pierce MN, Pincus JM, Pisani L, Price LJ, Proia L, Prokesch RC, Pujet HC, Ramgopal M, Rathod A, Rausch M, Ravishankar J, Rhame FS, Richards CS, Richman DD, Rodes B, Rodriguez M, Rose RC, Rosenberg ES, Rosenthal D, Ross PE, Rubin DS, Rumbaugh E, Saenz L, Salvaggio MR, Sanchez WC, Sanjana VM, Santiago S, Schmidt W, Schuitemaker H, Sestak PM, Shalit P, Shay W, Shirvani VN, Silebi VI, Sizemore JMJ, Skolnik PR, Sokol-Anderson M, Sosman JM, Stabile P, Stapleton JT, Starrett S, Stein F, Stellbrink HJ, Sterman FL, Stone VE, Stone DR, Tambussi G, Taplitz RA, Tedaldi EM, Telenti A, Theisen W, Torres R, Tosiello L, Tremblay C, Tribble MA, Trinh PD, Tsao A, Ueda P, Vaccaro A, Valadas E, Vanig TJ, Vecino I, Vega VM, Veikley W, Wade BH, Walworth C, Wanidworanun C, Ward DJ, Warner DA, Weber RD, Webster D, Weis S, Wheeler DA, White DJ, Wilkins E, Winston A, Wlodaver CG, van’t Wout A, Wright DP, Yang OO, Yurdin DL, Zabukovic BW, Zachary KC, Zeeman B, Zhao M. 2010. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 330:1551. PMC3235490.

Nadazdin O, Boskovic S, Murakami T, O’Connor DH, Wiseman RW, Karl JA, Tuscher JJ, Sachs DH, Madsen JC, Tocco G, Kawai T, Cosimi AB, Benichou G. 2010. Phenotype, distribution and alloreactive properties of memory T cells from cynomolgus monkeys. Am J Transplant 10:1375. PMC2893326.

O’Connor SL, Lhost JJ, Becker EA, Detmer AM, Johnson RC, Macnair CE, Wiseman RW, Karl JA, Greene JM, Burwitz BJ, Bimber BN, Lank SM, Tuscher JJ, Mee ET, Rose NJ, Desrosiers RC, Hughes AL, Friedrich TC, Carrington M, O’Connor DH. 2010. MHC heterozygote advantage in simian immunodeficiency virus-infected Mauritian cynomolgus macaques. Sci Transl Med 2:22ra18. PMC2865159.

Berman DM, Willman MA, Han D, Kleiner G, Kenyon NM, Cabrera O, Karl JA, Wiseman RW, O’Connor DH, Bartholomew AM, Kenyon NS. 2010. Mesenchymal stem cells enhance allogeneic islet engraftment in nonhuman primates. Diabetes 59:2558. PMC3279532.

Budde ML, Lhost JJ, Dudley DM, Rakasz EG, O’Connor DH. 2010. Integrin alpha4beta7 is downregulated on the surfaces of simian immunodeficiency virus SIVmac239-infected cells. J Virol 84:6344. PMC2903238.

Cafaro A, Bellino S, Titti F, Maggiorella MT, Sernicola L, Wiseman RW, Venzon D, Karl JA, O’Connor D, Monini P, Robert-Guroff M, Ensoli B. 2010. Impact of viral dose and major histocompatibility complex class IB haplotype on viral outcome in mauritian cynomolgus monkeys vaccinated with Tat upon challenge with simian/human immunodeficiency virus SHIV89.6P. J Virol 84:8953. PMC2919029.

Greene JM, Lhost JJ, Burwitz BJ, Budde ML, Macnair CE, Weiker MK, Gostick E, Friedrich TC, Broman KW, Price DA, O’Connor SL, O’Connor DH. 2010. Extralymphoid CD8+ T cells resident in tissue from simian immunodeficiency virus SIVmac239{Delta}nef-vaccinated macaques suppress SIVmac239 replication ex vivo. J Virol 84:3362. PMC2838091.

Casimiro DR, Cox K, Tang A, Sykes KJ, Feng M, Wang F, Bett A, Schleif WA, Liang X, Flynn J, Tobery TW, Wilson K, Finnefrock A, Huang L, Vitelli S, Lin J, Patel D, Davies ME, Heidecker GJ, Freed DC, Dubey S, O’Connor DH, Watkins DI, Zhang ZQ, Shiver JW. 2010. Efficacy of multivalent adenovirus-based vaccine against simian immunodeficiency virus challenge. J Virol 84:2996. PMC2826028.

Hughes AL, O’Connor S, Dudley DM, Burwitz BJ, Bimber BN, O’Connor D. 2010. Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus. Infect Genet Evol 10:555. PMC2863052.

Budde ML, Wiseman RW, Karl JA, Hanczaruk B, Simen BB, O’Connor DH. 2010. Characterization of Mauritian cynomolgus macaque major histocompatibility complex class I haplotypes by high-resolution pyrosequencing. Immunogenetics 62:773. PMC3077881.

Yamada S, Hatta M, Staker BL, Watanabe S, Imai M, Shinya K, Sakai-Tagawa Y, Ito M, Ozawa M, Watanabe T, Sakabe S, Li C, Kim JH, Myler PJ, Phan I, Raymond A, Smith E, Stacy R, Nidom CA, Lank SM, Wiseman RW, Bimber BN, O’Connor DH, Neumann G, Stewart LJ, Kawaoka Y. 2010. Biological and structural characterization of a host-adapting amino acid in influenza virus. PLoS Pathog 6:e1001034. PMC2916879.

Lank SM, Wiseman RW, Dudley DM, O’Connor DH. 2010. A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping. Hum Immunol 71:1011. PMC3191540.

Bimber BN, Burwitz BJ, O’Connor S, Detmer A, Gostick E, Lank SM, Price DA, Hughes A, O’Connor D. 2009. Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques. J Virol 83:8247. PMC2715741.

Kanthaswamy S, Capitanio JP, Dubay CJ, Ferguson B, Folks T, Ha JC, Hotchkiss CE, Johnson ZP, Katze MG, Kean LS, Kubisch HM, Lank S, Lyons LA, Miller GM, Nylander J, O’Connor DH, Palermo RE, Smith DG, Vallender EJ, Wiseman RW, Rogers J. 2009. Resources for genetic management and genomics research on non-human primates at the National Primate Research Centers (NPRCs). J Med Primatol 38 Suppl 1:17.

Burwitz BJ, Greene JM, O’Connor DH. 2009. Pirate primates in uncharted waters: lymphocyte transfers in unrelated, MHC-matched macaques. Curr HIV Res 7:51. PMC4509675.

Bimber BN, Chugh P, Giorgi EE, Kim B, Almudevar AL, Dewhurst S, O’Connor DH, Lee HY. 2009. Nef gene evolution from a single transmitted strain in acute SIV infection. Retrovirology 6:57. PMC2701916.

Mee ET, Badhan A, Karl JA, Wiseman RW, Cutler K, Knapp LA, Almond N, O’Connor DH, Rose NJ. 2009. MHC haplotype frequencies in a UK breeding colony of Mauritian cynomolgus macaques mirror those found in a distinct population from the same geographic origin. J Med Primatol 38:1. PMC4509677.

Burwitz BJ, Pendley CJ, Greene JM, Detmer AM, Lhost JJ, Karl JA, Piaskowski SM, Rudersdorf RA, Wallace LT, Bimber BN, Loffredo JT, Cox DG, Bardet W, Hildebrand W, Wiseman RW, O’Connor SL, O’Connor DH. 2009. Mauritian cynomolgus macaques share two exceptionally common major histocompatibility complex class I alleles that restrict simian immunodeficiency virus-specific CD8+ T cells. J Virol 83:6011. PMC2687399.

Wiseman RW, Karl JA, Bimber BN, O’Leary CE, Lank SM, Tuscher JJ, Detmer AM, Bouffard P, Levenkova N, Turcotte CL, Szekeres EJ, Wright C, Harkins T, O’Connor DH. 2009. Major histocompatibility complex genotyping with massively parallel pyrosequencing. Nat Med 15:1322. PMC2824247.

Valentine LE, Loffredo JT, Bean AT, Leon EJ, MacNair CE, Beal DR, Piaskowski SM, Klimentidis YC, Lank SM, Wiseman RW, Weinfurter JT, May GE, Rakasz EG, Wilson NA, Friedrich TC, O’Connor DH, Allison DB, Watkins DI. 2009. Infection with “escaped” virus variants impairs control of simian immunodeficiency virus SIVmac239 replication in Mamu-B*08-positive macaques. J Virol 83:11514. PMC2772717.

O’Leary CE, Wiseman RW, Karl JA, Bimber BN, Lank SM, Tuscher JJ, O’Connor DH. 2009. Identification of novel MHC class I sequences in pig-tailed macaques by amplicon pyrosequencing and full-length cDNA cloning and sequencing. Immunogenetics 61:689. PMC2813950.

Karl JA, Wiseman RW, O’Connor DH. 2009. Cost-effective sequence-based nonhuman primate MHC class I genotyping from RNA. Methods 49:11. PMC2732760.

Campbell KJ, Detmer AM, Karl JA, Wiseman RW, Blasky AJ, Hughes AL, Bimber BN, O’Connor SL, O’Connor DH. 2009. Characterization of 47 MHC class I sequences in Filipino cynomolgus macaques. Immunogenetics 61:177. PMC2666003.

Blasky AJ, Karl JA, Wiseman RW, Read DS, O’Connor DH. 2008. Rapid high-resolution MHC class I genotyping of Chinese rhesus macaques by capillary reference strand-mediated conformational analysis. Immunogenetics 60:575. PMC2561256.

Pendley CJ, Becker EA, Karl JA, Blasky AJ, Wiseman RW, Hughes AL, O’Connor SL, O’Connor DH. 2008. MHC class I characterization of Indonesian cynomolgus macaques. Immunogenetics 60:339. PMC2612123.

Bimber B, O’Connor DH. 2008. KIRigami: the case for studying NK cell receptors in SIV+ macaques. Immunol Res 40:235.

Karl JA, Wiseman RW, Campbell KJ, Blasky AJ, Hughes AL, Ferguson B, Read DS, O’Connor DH. 2008. Identification of MHC class I sequences in Chinese-origin rhesus macaques. Immunogenetics 60:37. PMC2830873.

Bimber BN, Moreland AJ, Wiseman RW, Hughes AL, O’Connor DH. 2008. Complete characterization of killer Ig-like receptor (KIR) haplotypes in Mauritian cynomolgus macaques: novel insights into nonhuman primate KIR gene content and organization. J Immunol 181:6301. PMC2832209.

Florese RH, Wiseman RW, Venzon D, Karl JA, Demberg T, Larsen K, Flanary L, Kalyanaraman VS, Pal R, Titti F, Patterson LJ, Heath MJ, O’Connor DH, Cafaro A, Ensoli B, Robert-Guroff M. 2008. Comparative study of Tat vaccine regimens in Mauritian cynomolgus and Indian rhesus macaques: influence of Mauritian MHC haplotypes on susceptibility/resistance to SHIV(89.6P) infection. Vaccine 26:3312. PMC2577850.

Greene JM, Burwitz BJ, Blasky AJ, Mattila TL, Hong JJ, Rakasz EG, Wiseman RW, Hasenkrug KJ, Skinner PJ, O’Connor SL, O’Connor DH. 2008. Allogeneic lymphocytes persist and traffic in feral MHC-matched mauritian cynomolgus macaques. PLoS One 3:e2384. PMC2408966.

Wiseman RW, Wojcechowskyj JA, Greene JM, Blasky AJ, Gopon T, Soma T, Friedrich TC, O’Connor SL, O’Connor DH. 2007. Simian immunodeficiency virus SIVmac239 infection of major histocompatibility complex-identical cynomolgus macaques from Mauritius. J Virol 81:349. PMC1797269.

Wojcechowskyj JA, Yant LJ, Wiseman RW, O’Connor SL, O’Connor DH. 2007. Control of simian immunodeficiency virus SIVmac239 is not predicted by inheritance of Mamu-B*17-containing haplotypes. J Virol 81:406. PMC1797263.

O’Connor SL, Blasky AJ, Pendley CJ, Becker EA, Wiseman RW, Karl JA, Hughes AL, O’Connor DH. 2007. Comprehensive characterization of MHC class II haplotypes in Mauritian cynomolgus macaques. Immunogenetics 59:449. PMC2836927.

Wilson NA, Reed J, Napoe GS, Piaskowski S, Szymanski A, Furlott J, Gonzalez EJ, Yant LJ, Maness NJ, May GE, Soma T, Reynolds MR, Rakasz E, Rudersdorf R, McDermott AB, O’Connor DH, Friedrich TC, Allison DB, Patki A, Picker LJ, Burton DR, Lin J, Huang L, Patel D, Heindecker G, Fan J, Citron M, Horton M, Wang F, Liang X, Shiver JW, Casimiro DR, Watkins DI. 2006. Vaccine-induced cellular immune responses reduce plasma viral concentrations after repeated low-dose challenge with pathogenic simian immunodeficiency virus SIVmac239. J Virol 80:5875. PMC1472612.

Yant LJ, Friedrich TC, Johnson RC, May GE, Maness NJ, Enz AM, Lifson JD, O’Connor DH, Carrington M, Watkins DI. 2006. The high-frequency major histocompatibility complex class I allele Mamu-B*17 is associated with control of simian immunodeficiency virus SIVmac239 replication. J Virol 80:5074. PMC1472056.

Pratt BF, O’Connor DH, Lafont BA, Mankowski JL, Fernandez CS, Triastuti R, Brooks AG, Kent SJ, Smith MZ. 2006. MHC class I allele frequencies in pigtail macaques of diverse origin. Immunogenetics 58:995.

O’Connor DH, Burton DR. 2006. Immune responses and HIV: a little order from the chaos. J Exp Med 203:501. PMC2118239.

Hughes AL, Piontkivska H, Krebs KC, O’Connor DH, Watkins DI. 2005. Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus. Bioinformatics 21 Suppl 3:iii39.

Krebs KC, Jin Z, Rudersdorf R, Hughes AL, O’Connor DH. 2005. Unusually high frequency MHC class I alleles in Mauritian origin cynomolgus macaques. J Immunol 175:5230.

Smith MZ, Fernandez CS, Chung A, Dale CJ, De Rose R, Lin J, Brooks AG, Krebs KC, Watkins DI, O’Connor DH, Davenport MP, Kent SJ. 2005. The pigtail macaque MHC class I allele Mane-A*10 presents an immundominant SIV Gag epitope: identification, tetramer development and implications of immune escape and reversion. J Med Primatol 34:282.

Loffredo JT, Sidney J, Piaskowski S, Szymanski A, Furlott J, Rudersdorf R, Reed J, Peters B, Hickman-Miller HD, Bardet W, Rehrauer WM, O’Connor DH, Wilson NA, Hildebrand WH, Sette A, Watkins DI. 2005. The high frequency Indian rhesus macaque MHC class I molecule, Mamu-B*01, does not appear to be involved in CD8+ T lymphocyte responses to SIVmac239. J Immunol 175:5986.

Fernandez CS, Stratov I, De Rose R, Walsh K, Dale CJ, Smith MZ, Agy MB, Hu SL, Krebs K, Watkins DI, O’connor DH, Davenport MP, Kent SJ. 2005. Rapid viral escape at an immunodominant simian-human immunodeficiency virus cytotoxic T-lymphocyte epitope exacts a dramatic fitness cost. J Virol 79:5721. PMC1082732.

McDermott AB, O’Connor DH, Fuenger S, Piaskowski S, Martin S, Loffredo J, Reynolds M, Reed J, Furlott J, Jacoby T, Riek C, Dodds E, Krebs K, Davies ME, Schleif WA, Casimiro DR, Shiver JW, Watkins DI. 2005. Cytotoxic T-lymphocyte escape does not always explain the transient control of simian immunodeficiency virus SIVmac239 viremia in adenovirus-boosted and DNA-primed Mamu-A*01-positive rhesus macaques. J Virol 79:15556. PMC1315992.

Casimiro DR, Wang F, Schleif WA, Liang X, Zhang ZQ, Tobery TW, Davies ME, McDermott AB, O’Connor DH, Fridman A, Bagchi A, Tussey LG, Bett AJ, Finnefrock AC, Fu TM, Tang A, Wilson KA, Chen M, Perry HC, Heidecker GJ, Freed DC, Carella A, Punt KS, Sykes KJ, Huang L, Ausensi VI, Bachinsky M, Sadasivan-Nair U, Watkins DI, Emini EA, Shiver JW. 2005. Attenuation of simian immunodeficiency virus SIVmac239 infection by prophylactic immunization with dna and recombinant adenoviral vaccine vectors expressing Gag. J Virol 79:15547. PMC1315991.

Smith MZ, Dale CJ, De Rose R, Stratov I, Fernandez CS, Brooks AG, Weinfurter J, Krebs K, Riek C, Watkins DI, O’connor DH, Kent SJ. 2005. Analysis of pigtail macaque major histocompatibility complex class I molecules presenting immunodominant simian immunodeficiency virus epitopes. J Virol 79:684. PMC538543.

Friedrich TC, Dodds EJ, Yant LJ, Vojnov L, Rudersdorf R, Cullen C, Evans DT, Desrosiers RC, Mothe BR, Sidney J, Sette A, Kunstman K, Wolinsky S, Piatak M, Lifson J, Hughes AL, Wilson N, O’Connor DH, Watkins DI. 2004. Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nat Med 10:275.

Loffredo JT, Sidney J, Wojewoda C, Dodds E, Reynolds MR, Napoe G, Mothe BR, O’Connor DH, Wilson NA, Watkins DI, Sette A. 2004. Identification of seventeen new simian immunodeficiency virus-derived CD8+ T cell epitopes restricted by the high frequency molecule, Mamu-A*02, and potential escape from CTL recognition. J Immunol 173:5064.

Friedrich TC, Frye CA, Yant LJ, O’Connor DH, Kriewaldt NA, Benson M, Vojnov L, Dodds EJ, Cullen C, Rudersdorf R, Hughes AL, Wilson N, Watkins DI. 2004. Extraepitopic compensatory substitutions partially restore fitness to simian immunodeficiency virus variants that escape from an immunodominant cytotoxic-T-lymphocyte response. J Virol 78:2581. PMC369222.

Matano T, Kobayashi M, Igarashi H, Takeda A, Nakamura H, Kano M, Sugimoto C, Mori K, Iida A, Hirata T, Hasegawa M, Yuasa T, Miyazawa M, Takahashi Y, Yasunami M, Kimura A, O’Connor DH, Watkins DI, Nagai Y. 2004. Cytotoxic T lymphocyte-based control of simian immunodeficiency virus replication in a preclinical AIDS vaccine trial. J Exp Med 199:1709. PMC2212812.

Friedrich TC, McDermott AB, Reynolds MR, Piaskowski S, Fuenger S, De Souza IP, Rudersdorf R, Cullen C, Yant LJ, Vojnov L, Stephany J, Martin S, O’Connor DH, Wilson N, Watkins DI. 2004. Consequences of cytotoxic T-lymphocyte escape: common escape mutations in simian immunodeficiency virus are poorly recognized in naive hosts. J Virol 78:10064. PMC515024.

O’Connor DH, McDermott AB, Krebs KC, Dodds EJ, Miller JE, Gonzalez EJ, Jacoby TJ, Yant L, Piontkivska H, Pantophlet R, Burton DR, Rehrauer WM, Wilson N, Hughes AL, Watkins DI. 2004. A dominant role for CD8+-T-lymphocyte selection in simian immunodeficiency virus sequence variation. J Virol 78:14012. PMC533930.

O’Connor DH, Mothe BR, Weinfurter JT, Fuenger S, Rehrauer WM, Jing P, Rudersdorf RR, Liebl ME, Krebs K, Vasquez J, Dodds E, Loffredo J, Martin S, McDermott AB, Allen TM, Wang C, Doxiadis GG, Montefiori DC, Hughes A, Burton DR, Allison DB, Wolinsky SM, Bontrop R, Picker LJ, Watkins DI. 2003. Major histocompatibility complex class I alleles associated with slow simian immunodeficiency virus disease progression bind epitopes recognized by dominant acute-phase cytotoxic-T-lymphocyte responses. J Virol 77:9029. PMC167227.

Allen TM, Mortara L, Mothe BR, Liebl M, Jing P, Calore B, Piekarczyk M, Ruddersdorf R, O’Connor DH, Wang X, Wang C, Allison DB, Altman JD, Sette A, Desrosiers RC, Sutter G, Watkins DI. 2002. Tat-vaccinated macaques do not control simian immunodeficiency virus SIVmac239 replication. J Virol 76:4108. PMC136098.

Altfeld M, Allen TM, Yu XG, Johnston MN, Agrawal D, Korber BT, Montefiori DC, O’Connor DH, Davis BT, Lee PK, Maier EL, Harlow J, Goulder PJ, Brander C, Rosenberg ES, Walker BD. 2002. HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature 420:434.

Vogel TU, Friedrich TC, O’Connor DH, Rehrauer W, Dodds EJ, Hickman H, Hildebrand W, Sidney J, Sette A, Hughes A, Horton H, Vielhuber K, Rudersdorf R, De Souza IP, Reynolds MR, Allen TM, Wilson N, Watkins DI. 2002. Escape in one of two cytotoxic T-lymphocyte epitopes bound by a high-frequency major histocompatibility complex class I molecule, Mamu-A*02: a paradigm for virus evolution and persistence. J Virol 76:11623. PMC136802.

Allen TM, Jing P, Calore B, Horton H, O’Connor DH, Hanke T, Piekarczyk M, Ruddersdorf R, Mothe BR, Emerson C, Wilson N, Lifson JD, Belyakov IM, Berzofsky JA, Wang C, Allison DB, Montefiori DC, Desrosiers RC, Wolinsky S, Kunstman KJ, Altman JD, Sette A, McMichael AJ, Watkins DI. 2002. Effects of cytotoxic T lymphocytes (CTL) directed against a single simian immunodeficiency virus (SIV) Gag CTL epitope on the course of SIVmac239 infection. J Virol 76:10507. PMC136573.

Vogel TU, Horton H, Fuller DH, Carter DK, Vielhuber K, O’Connor DH, Shipley T, Fuller J, Sutter G, Erfle V, Wilson N, Picker LJ, Watkins DI. 2002. Differences between T cell epitopes recognized after immunization and after infection. J Immunol 169:4511.

O’Connor DH, Allen TM, Watkins DI. 2002. Cytotoxic T-lymphocyte escape monitoring in simian immunodeficiency virus vaccine challenge studies. DNA Cell Biol 21:659.

Horton H, Vogel T, O’Connor D, Picker L, Watkins DI. 2002. Analysis of the immune response and viral evolution during the acute phase of SIV infection. Vaccine 20:1927.

O’Connor DH, Allen TM, Vogel TU, Jing P, DeSouza IP, Dodds E, Dunphy EJ, Melsaether C, Mothe B, Yamamoto H, Horton H, Wilson N, Hughes AL, Watkins DI. 2002. Acute phase cytotoxic T lymphocyte escape is a hallmark of simian immunodeficiency virus infection. Nat Med 8:493.

O’Connor D, Allen T, Watkins DI. 2001. Vaccination with CTL epitopes that escape: an alternative approach to HIV vaccine development. Immunol Lett 79:77.

O’Connor D, Friedrich T, Hughes A, Allen TM, Watkins D. 2001. Understanding cytotoxic T-lymphocyte escape during simian immunodeficiency virus infection. Immunol Rev 183:115.

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