Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Todd Allen, Ph.D.

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Institution
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Address
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Overview
overview
My laboratory has 4 major areas of interest designed to aid in the development of effective vaccines and therapeutics against HIV and HCV: 1) Applying next-generation 454 sequencing approaches to investigate how these viruses evade critical immune responses in order to identify critical targets for vaccine design. 2) Investigating the role of viral replication capacity on disease progression in HIV and HCV infections to identify critical regions of the virus susceptible to host selection pressures, and testing of novel vaccine approaches in the humanized mouse model. 3) Identifying genetic, immunological and virological correlates of control of HIV in the Thai population which exhibits unique host and viral genetics. 4) Investigating evolution of HIV and HCV to intrinsic anti-viral host factors to identify novel host proteins related to the control of these viral infections.

I am also a member of the Ragon Institute (http://www.ragoninstitute.org/research_allen.html) and the Harvard Virology Department http://www.hms.harvard.edu/dms/virology/fac/allen.html) where additional information is provided.

Research
research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
Most Recent  |  List All
  1. U24DA044801 (ALLEN, TODD M) Aug 15, 2017 - Jul 31, 2022
    NIH/NIDA
    Next-Generation Sequencing Center for GHOSTing Hepatitis C Virus: Transforming Community Based Molecular Surveillance and Outbreak Investigation
    Role: Principal Investigator
  2. U19HL129903 (SCADDEN, DAVID T) Apr 1, 2015 - Mar 31, 2020
    NIH/NHLBI
    A defend and destroy approach to curing HIV
    Role: Co-Principal Investigator
  3. P01AI104715 (ALLEN, TODD M) Feb 7, 2013 - Jan 31, 2018
    NIH/NIAID
    Optimizing Human B and T Cell Vaccines Against HIV Using Humanized BLT Mice
    Role: Principal Investigator
  4. P01AI074415 (ALLEN, TODD M) Aug 2, 2010 - Aug 31, 2014
    NIH/NIAID
    Acute HIV Infection: Implications for vaccine design
    Role: Principal Investigator
  5. R01AI090698 (ALLEN, TODD M) Jun 1, 2010 - May 31, 2014
    NIH/NIAID
    Protective Role of Subdominant Responses to HIV Restricted by Common HLA Alleles
    Role: Principal Investigator

Bibliographic
selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Joshi VR, Newman RM, Pack ML, Power KA, Munro JB, Okawa K, Madani N, Sodroski JG, Schmidt AG, Allen TM. Gp41-targeted antibodies restore infectivity of a fusion-deficient HIV-1 envelope glycoprotein. PLoS Pathog. 2020 May; 16(5):e1008577. PMID: 32392227.
    Citations:    
  2. Claiborne DT, Dudek TE, Maldini CR, Power KA, Ghebremichael M, Seung E, Mellors EF, Vrbanac VD, Krupp K, Bisesi A, Tager AM, Knipe DM, Boutwell CL, Allen TM. Immunization of BLT Humanized Mice Redirects T Cell Responses to Gag and Reduces Acute HIV-1 Viremia. J Virol. 2019 10 15; 93(20). PMID: 31375576.
    Citations:    
  3. Allen TM, Brehm MA, Bridges S, Ferguson S, Kumar P, Mirochnitchenko O, Palucka K, Pelanda R, Sanders-Beer B, Shultz LD, Su L, PrabhuDas M. Humanized immune system mouse models: progress, challenges and opportunities. Nat Immunol. 2019 07; 20(7):770-774. PMID: 31160798.
    Citations:    
  4. Gaiha GD, Rossin EJ, Urbach J, Landeros C, Collins DR, Nwonu C, Muzhingi I, Anahtar MN, Waring OM, Piechocka-Trocha A, Waring M, Worrall DP, Ghebremichael MS, Newman RM, Power KA, Allen TM, Chodosh J, Walker BD. Structural topology defines protective CD8+ T cell epitopes in the HIV proteome. Science. 2019 05 03; 364(6439):480-484. PMID: 31048489.
    Citations:    
  5. Hahn JA, Tully DC, Evans JL, Morris MD, Briceno A, Bean DJ, Allen TM, Page K. Role of HCV Viremia in Corroborated HCV Transmission Events Within Young Adult Injecting Partnerships. Open Forum Infect Dis. 2019 Apr; 6(4):ofz125. PMID: 31041340.
    Citations:    
  6. Euler Z, VAN DEN Kerkhof TL, Kouyos RD, Tully DC, Allen TM, Trkola A, Sanders RW, Schuitemaker H, VAN Gils MJ. Lower Broadly Neutralizing Antibody Responses in Female Versus Male HIV-1 Infected Injecting Drug Users. Viruses. 2019 04 25; 11(4). PMID: 31027215.
    Citations:    
  7. Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A, Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, Matranga CB. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat Biotechnol. 2019 02; 37(2):160-168. PMID: 30718881.
    Citations:    
  8. Usmani SM, Murooka TT, Deruaz M, Koh WH, Sharaf RR, Di Pilato M, Power KA, Lopez P, Hnatiuk R, Vrbanac VD, Tager AM, Allen TM, Luster AD, Mempel TR. HIV-1 Balances the Fitness Costs and Benefits of Disrupting the Host Cell Actin Cytoskeleton Early after Mucosal Transmission. Cell Host Microbe. 2019 01 09; 25(1):73-86.e5. PMID: 30629922.
    Citations:    Fields:    
  9. Piantadosi A, Freije CA, Gosmann C, Ye S, Park D, Schaffner SF, Tully DC, Allen TM, Dong KL, Sabeti PC, Kwon DS. Metagenomic Sequencing of HIV-1 in the Blood and Female Genital Tract Reveals Little Quasispecies Diversity during Acute Infection. J Virol. 2019 01 15; 93(2). PMID: 30381486.
    Citations:    Fields:    
  10. Martins MA, Tully DC, Pedreño-Lopez N, von Bredow B, Pauthner MG, Shin YC, Yuan M, Lima NS, Bean DJ, Gonzalez-Nieto L, Domingues A, Gutman MJ, Maxwell HS, Magnani DM, Ricciardi MJ, Bailey VK, Altman JD, Burton DR, Ejima K, Allison DB, Evans DT, Rakasz EG, Parks CL, Bonaldo MC, Capuano S, Lifson JD, Desrosiers RC, Allen TM, Watkins DI. Mamu-B*17+ Rhesus Macaques Vaccinated with env, vif, and nef Manifest Early Control of SIVmac239 Replication. J Virol. 2018 08 15; 92(16). PMID: 29875239.
    Citations:    Fields:    Translation:AnimalsCells
  11. Brener J, Gall A, Hurst J, Batorsky R, Lavandier N, Chen F, Edwards A, Bolton C, Dsouza R, Allen T, Pybus OG, Kellam P, Matthews PC, Goulder PJR. Rapid HIV disease progression following superinfection in an HLA-B*27:05/B*57:01-positive transmission recipient. Retrovirology. 2018 01 16; 15(1):7. PMID: 29338738.
    Citations: 2     Fields:    Translation:HumansCells
  12. Wolski D, Foote PK, Chen DY, Lewis-Ximenez LL, Fauvelle C, Aneja J, Walker A, Tonnerre P, Torres-Cornejo A, Kvistad D, Imam S, Waring MT, Tully DC, Allen TM, Chung RT, Timm J, Haining WN, Kim AY, Baumert TF, Lauer GM. Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8+ T Cells in Chronic versus Acute Infection. Immunity. 2017 10 17; 47(4):648-663.e8. PMID: 29045899.
    Citations:    Fields:    Translation:HumansCells
  13. Julg B, Sok D, Schmidt SD, Abbink P, Newman RM, Broge T, Linde C, Nkolola J, Le K, Su D, Torabi J, Pack M, Pegu A, Allen TM, Mascola JR, Burton DR, Barouch DH. Protective Efficacy of Broadly Neutralizing Antibodies with Incomplete Neutralization Activity against Simian-Human Immunodeficiency Virus in Rhesus Monkeys. J Virol. 2017 10 15; 91(20). PMID: 28768869.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  14. Magnani DM, Ricciardi MJ, Bailey VK, Gutman MJ, Pedreño-Lopez N, Silveira CGT, Maxwell HS, Domingues A, Gonzalez-Nieto L, Su Q, Newman RM, Pack M, Martins MA, Martinez-Navio JM, Fuchs SP, Rakasz EG, Allen TM, Whitehead SS, Burton DR, Gao G, Desrosiers RC, Kallas EG, Watkins DI. Dengue Virus Evades AAV-Mediated Neutralizing Antibody Prophylaxis in Rhesus Monkeys. Mol Ther. 2017 10 04; 25(10):2323-2331. PMID: 28750738.
    Citations: 2     Fields:    Translation:AnimalsCells
  15. Martins MA, Tully DC, Shin YC, Gonzalez-Nieto L, Weisgrau KL, Bean DJ, Gadgil R, Gutman MJ, Domingues A, Maxwell HS, Magnani DM, Ricciardi M, Pedreño-Lopez N, Bailey V, Cruz MA, Lima NS, Bonaldo MC, Altman JD, Rakasz E, Capuano S, Reimann KA, Piatak M, Lifson JD, Desrosiers RC, Allen TM, Watkins DI. Rare Control of SIVmac239 Infection in a Vaccinated Rhesus Macaque. AIDS Res Hum Retroviruses. 2017 08; 33(8):843-858. PMID: 28503929.
    Citations:    Fields:    Translation:AnimalsCells
  16. Tully DC, Claiborne DT, Allen TM. Interferon-I: The Pièce de Résistance of HIV-1 Transmission? Trends Microbiol. 2017 05; 25(5):332-334. PMID: 28285909.
    Citations:    Fields:    Translation:HumansCells
  17. Corleis B, Lisanti AC, Körner C, Schiff AE, Rosenberg ES, Allen TM, Altfeld M, Kwon DS. Early type I Interferon response induces upregulation of human ß-defensin 1 during acute HIV-1 infection. PLoS One. 2017; 12(3):e0173161. PMID: 28253319.
    Citations: 2     Fields:    Translation:HumansCells
  18. Jones RB, Mueller S, Kumari S, Vrbanac V, Genel S, Tager AM, Allen TM, Walker BD, Irvine DJ. Antigen recognition-triggered drug delivery mediated by nanocapsule-functionalized cytotoxic T-cells. Biomaterials. 2017 02; 117:44-53. PMID: 27936416.
    Citations: 6     Fields:    Translation:AnimalsCells
  19. Sen DR, Kaminski J, Barnitz RA, Kurachi M, Gerdemann U, Yates KB, Tsao HW, Godec J, LaFleur MW, Brown FD, Tonnerre P, Chung RT, Tully DC, Allen TM, Frahm N, Lauer GM, Wherry EJ, Yosef N, Haining WN. The epigenetic landscape of T cell exhaustion. Science. 2016 12 02; 354(6316):1165-1169. PMID: 27789799.
    Citations: 55     Fields:    Translation:HumansAnimalsCells
  20. Ranasinghe S, Lamothe PA, Soghoian DZ, Kazer SW, Cole MB, Shalek AK, Yosef N, Jones RB, Donaghey F, Nwonu C, Jani P, Clayton GM, Crawford F, White J, Montoya A, Power K, Allen TM, Streeck H, Kaufmann DE, Picker LJ, Kappler JW, Walker BD. Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion. Immunity. 2016 10 18; 45(4):917-930. PMID: 27760342.
    Citations: 9     Fields:    Translation:HumansCells
  21. Hedegaard DL, Tully DC, Rowe IA, Reynolds GM, Bean DJ, Hu K, Davis C, Wilhelm A, Ogilvie CB, Power KA, Tarr AW, Kelly D, Allen TM, Balfe P, McKeating JA. High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease. J Hepatol. 2017 01; 66(1):28-38. PMID: 27531641.
    Citations: 1     Fields:    Translation:HumansCells
  22. Deruaz M, Moldt B, Le KM, Power KA, Vrbanac VD, Tanno S, Ghebremichael MS, Allen TM, Tager AM, Burton DR, Luster AD. Protection of Humanized Mice From Repeated Intravaginal HIV Challenge by Passive Immunization: A Model for Studying the Efficacy of Neutralizing Antibodies In Vivo. J Infect Dis. 2016 08 15; 214(4):612-6. PMID: 27357340.
    Citations: 6     Fields:    Translation:Animals
  23. Carlson JM, Du VY, Pfeifer N, Bansal A, Tan VY, Power K, Brumme CJ, Kreimer A, DeZiel CE, Fusi N, Schaefer M, Brockman MA, Gilmour J, Price MA, Kilembe W, Haubrich R, John M, Mallal S, Shapiro R, Frater J, Harrigan PR, Ndung'u T, Allen S, Heckerman D, Sidney J, Allen TM, Goulder PJ, Brumme ZL, Hunter E, Goepfert PA. Impact of pre-adapted HIV transmission. Nat Med. 2016 06; 22(6):606-13. PMID: 27183217.
    Citations: 23     Fields:    Translation:HumansCells
  24. 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. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus. PLoS Pathog. 2016 05; 12(5):e1005619. PMID: 27163788.
    Citations: 13     Fields:    Translation:HumansCells
  25. Tully DC, Hjerrild S, Leutscher PD, Renvillard SG, Ogilvie CB, Bean DJ, Videbech P, Allen TM, McKeating JA, Fletcher NF. Deep sequencing of hepatitis C virus reveals genetic compartmentalization in cerebrospinal fluid from cognitively impaired patients. Liver Int. 2016 10; 36(10):1418-24. PMID: 27045383.
    Citations: 6     Fields:    Translation:HumansCells
  26. Scully EP, Lockhart A, Garcia-Beltran W, Palmer CD, Musante C, Rosenberg E, Allen TM, Chang JJ, Bosch RJ, Altfeld M. Innate immune reconstitution with suppression of HIV-1. JCI Insight. 2016 Mar 17; 1(3):e85433. PMID: 27158667.
    Citations: 2     Fields:    
  27. Rowe IA, Tully DC, Armstrong MJ, Parker R, Guo K, Barton D, Morse GD, Venuto CS, Ogilvie CB, Hedegaard DL, McKelvy JF, Wong-Staal F, Allen TM, Balfe P, McKeating JA, Mutimer DJ. Effect of scavenger receptor class B type I antagonist ITX5061 in patients with hepatitis C virus infection undergoing liver transplantation. Liver Transpl. 2016 Mar; 22(3):287-97. PMID: 26437376.
    Citations: 5     Fields:    Translation:HumansCellsCTClinical Trials
  28. Salazar-Gonzalez JF, Salazar MG, Tully DC, Ogilvie CB, Learn GH, Allen TM, Heath SL, Goepfert P, Bar KJ. Use of Dried Blood Spots to Elucidate Full-Length Transmitted/Founder HIV-1 Genomes. Pathog Immun. 2016; 1(1):129-153. PMID: 27819061.
    Citations: 2     
  29. Palmer CD, Romero-Tejeda M, Sirignano M, Sharma S, Allen TM, Altfeld M, Jost S. Naturally Occurring Subclinical Endotoxemia in Humans Alters Adaptive and Innate Immune Functions through Reduced MAPK and Increased STAT1 Phosphorylation. J Immunol. 2016 Jan 15; 196(2):668-77. PMID: 26643479.
    Citations: 2     Fields:    Translation:HumansCells
  30. Walker A, Skibbe K, Steinmann E, Pfaender S, Kuntzen T, Megger DA, Groten S, Sitek B, Lauer GM, Kim AY, Pietschmann T, Allen TM, Timm J. Distinct Escape Pathway by Hepatitis C Virus Genotype 1a from a Dominant CD8+ T Cell Response by Selection of Altered Epitope Processing. J Virol. 2016 01 01; 90(1):33-42. PMID: 26446603.
    Citations: 1     Fields:    Translation:HumansCells
  31. Martins MA, Tully DC, Cruz MA, Power KA, Veloso de Santana MG, Bean DJ, Ogilvie CB, Gadgil R, Lima NS, Magnani DM, Ejima K, Allison DB, Piatak M, Altman JD, Parks CL, Rakasz EG, Capuano S, Galler R, Bonaldo MC, Lifson JD, Allen TM, Watkins DI. Vaccine-Induced Simian Immunodeficiency Virus-Specific CD8+ T-Cell Responses Focused on a Single Nef Epitope Select for Escape Variants Shortly after Infection. J Virol. 2015 Nov; 89(21):10802-20. PMID: 26292326.
    Citations: 9     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  32. Brener J, Gall A, Batorsky R, Riddell L, Buus S, Leitman E, Kellam P, Allen T, Goulder P, Matthews PC. Disease progression despite protective HLA expression in an HIV-infected transmission pair. Retrovirology. 2015 Jun 30; 12:55. PMID: 26123575.
    Citations: 2     Fields:    Translation:HumansCells
  33. Karpel ME, Boutwell CL, Allen TM. BLT humanized mice as a small animal model of HIV infection. Curr Opin Virol. 2015 Aug; 13:75-80. PMID: 26083316.
    Citations: 20     Fields:    Translation:HumansAnimalsCells
  34. Sacks-Davis R, Grebely J, Dore GJ, Osburn W, Cox AL, Rice TM, Spelman T, Bruneau J, Prins M, Kim AY, McGovern BH, Shoukry NH, Schinkel J, Allen TM, Morris M, Hajarizadeh B, Maher L, Lloyd AR, Page K, Hellard M. Hepatitis C Virus Reinfection and Spontaneous Clearance of Reinfection--the InC3 Study. J Infect Dis. 2015 Nov 01; 212(9):1407-19. PMID: 25883387.
    Citations: 12     Fields:    Translation:HumansCells
  35. Mandal PK, Ferreira LM, Collins R, Meissner TB, Boutwell CL, Friesen M, Vrbanac V, Garrison BS, Stortchevoi A, Bryder D, Musunuru K, Brand H, Tager AM, Allen TM, Talkowski ME, Rossi DJ, Cowan CA. Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. Cell Stem Cell. 2014 Nov 06; 15(5):643-52. PMID: 25517468.
    Citations: 104     Fields:    Translation:HumansAnimalsCells
  36. Tully DC, Ogilvie CB, Batorsky R, Power KA, Bedard H, Seese A, Amero M, Bazner S, Tinsley J, Lennon NJ, Henn MR, Rosenberg E, Mayer KH, Jessen H, Altfeld M, Allen TM. Genetic Footprints within the HIV-1 Envelope Glycoprotein Associated with Transmission in Men Who Have Sex with Men. AIDS Res Hum Retroviruses. 2014 Oct; 30 Suppl 1:A57. PMID: 25357888.
    Citations:    
  37. Corleis B, Lisanti A, Korner C, Amero MA, Rosenberg ES, Allen TM, Altfeld M, Kwon DS. Protective Role of TLR3 Induced Human Beta Defensins during Acute HIV-1 Infection. AIDS Res Hum Retroviruses. 2014 Oct; 30 Suppl 1:A124-5. PMID: 25357346.
    Citations:    
  38. Brener J, Gall A, Batorsky R, Kellam P, Allen T, Matthews P, Goulder P. HIV Minor Variants Detected by Next Generation Sequencing: Impact on Immune Control of HIV in the Context of HLA-B*27:05 and HLA-B*57:01. AIDS Res Hum Retroviruses. 2014 Oct; 30 Suppl 1:A180-1. PMID: 25357507.
    Citations:    
  39. Palmer CD, Tomassilli J, Sirignano M, Romero-Tejeda M, Arnold KB, Che D, Lauffenburger DA, Jost S, Allen T, Mayer KH, Altfeld M. Enhanced immune activation linked to endotoxemia in HIV-1 seronegative MSM. AIDS. 2014 Sep 10; 28(14):2162-6. PMID: 25003719.
    Citations: 7     Fields:    Translation:HumansCells
  40. Martin E, Carlson JM, Le AQ, Chopera DR, McGovern R, Rahman MA, Ng C, Jessen H, Kelleher AD, Markowitz M, Allen TM, Milloy MJ, Carrington M, Wainberg MA, Brumme ZL. Early immune adaptation in HIV-1 revealed by population-level approaches. Retrovirology. 2014 Aug 29; 11:64. PMID: 25212686.
    Citations: 6     Fields:    Translation:HumansCells
  41. Körner C, Granoff ME, Amero MA, Sirignano MN, Vaidya SA, Jost S, Allen TM, Rosenberg ES, Altfeld M. Increased frequency and function of KIR2DL1-3? NK cells in primary HIV-1 infection are determined by HLA-C group haplotypes. Eur J Immunol. 2014 Oct; 44(10):2938-48. PMID: 25043727.
    Citations: 12     Fields:    Translation:HumansCells
  42. Carlson JM, Schaefer M, Monaco DC, Batorsky R, Claiborne DT, Prince J, Deymier MJ, Ende ZS, Klatt NR, DeZiel CE, Lin TH, Peng J, Seese AM, Shapiro R, Frater J, Ndung'u T, Tang J, Goepfert P, Gilmour J, Price MA, Kilembe W, Heckerman D, Goulder PJ, Allen TM, Allen S, Hunter E. HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck. Science. 2014 Jul 11; 345(6193):1254031. PMID: 25013080.
    Citations: 72     Fields:    Translation:HumansCells
  43. Veerapu NS, Park SH, Tully DC, Allen TM, Rehermann B. Trace amounts of sporadically reappearing HCV RNA can cause infection. J Clin Invest. 2014 Aug; 124(8):3469-78. PMID: 25003189.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  44. Vaidya SA, Korner C, Sirignano MN, Amero M, Bazner S, Rychert J, Allen TM, Rosenberg ES, Bosch RJ, Altfeld M. Tumor necrosis factor a is associated with viral control and early disease progression in patients with HIV type 1 infection. J Infect Dis. 2014 Oct 01; 210(7):1042-6. PMID: 24688071.
    Citations: 10     Fields:    Translation:HumansCells
  45. Jessen H, Allen TM, Streeck H. How a single patient influenced HIV research--15-year follow-up. N Engl J Med. 2014 Feb 13; 370(7):682-3. PMID: 24521131.
    Citations: 11     Fields:    Translation:HumansCells
  46. Wan C, Allen TM, Cullis PR. Lipid nanoparticle delivery systems for siRNA-based therapeutics. Drug Deliv Transl Res. 2014 Feb; 4(1):74-83. PMID: 25786618.
    Citations: 17     Fields:    
  47. Vaidya SA, Streeck H, Beckwith N, Ghebremichael M, Pereyra F, Kwon DS, Addo MM, Rychert J, Routy JP, Jessen H, Kelleher AD, Hecht F, Sekaly RP, Carrington M, Walker BD, Allen TM, Rosenberg ES, Altfeld M. Temporal effect of HLA-B*57 on viral control during primary HIV-1 infection. Retrovirology. 2013 Nov 18; 10:139. PMID: 24245727.
    Citations: 4     Fields:    Translation:HumansCells
  48. Tager AM, Pensiero M, Allen TM. Recent advances in humanized mice: accelerating the development of an HIV vaccine. J Infect Dis. 2013 Nov; 208 Suppl 2:S121-4. PMID: 24151317.
    Citations: 6     Fields:    Translation:HumansAnimals
  49. Dudek TE, Allen TM. HIV-specific CD8? T-cell immunity in humanized bone marrow-liver-thymus mice. J Infect Dis. 2013 Nov; 208 Suppl 2:S150-4. PMID: 24151322.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  50. Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, John M, Haas DW, Martinez-Picado J, Dalmau J, López-Galíndez C, Casado C, Rauch A, Günthard HF, Bernasconi E, Vernazza P, Klimkait T, Yerly S, O'Brien SJ, Listgarten J, Pfeifer N, Lippert C, Fusi N, Kutalik Z, Allen TM, Müller V, Harrigan PR, Heckerman D, Telenti A, Fellay J. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. Elife. 2013 Oct 29; 2:e01123. PMID: 24171102.
    Citations: 26     Fields:    Translation:HumansCells
  51. Seung E, Dudek TE, Allen TM, Freeman GJ, Luster AD, Tager AM. PD-1 blockade in chronically HIV-1-infected humanized mice suppresses viral loads. PLoS One. 2013; 8(10):e77780. PMID: 24204962.
    Citations: 28     Fields:    Translation:HumansAnimalsCells
  52. Lavender KJ, Pang WW, Messer RJ, Duley AK, Race B, Phillips K, Scott D, Peterson KE, Chan CK, Dittmer U, Dudek T, Allen TM, Weissman IL, Hasenkrug KJ. BLT-humanized C57BL/6 Rag2-/-?c-/-CD47-/- mice are resistant to GVHD and develop B- and T-cell immunity to HIV infection. Blood. 2013 Dec 12; 122(25):4013-20. PMID: 24021673.
    Citations: 26     Fields:    Translation:HumansAnimalsCells
  53. Nitschke K, Barriga A, Schmidt J, Timm J, Viazov S, Kuntzen T, Kim AY, Lauer GM, Allen TM, Gaudieri S, Rauch A, Lange CM, Sarrazin C, Eiermann T, Sidney J, Sette A, Thimme R, López D, Neumann-Haefelin C. HLA-B*27 subtype specificity determines targeting and viral evolution of a hepatitis C virus-specific CD8+ T cell epitope. J Hepatol. 2014 Jan; 60(1):22-9. PMID: 23978718.
    Citations: 9     Fields:    Translation:HumansCells
  54. Youngblood B, Noto A, Porichis F, Akondy RS, Ndhlovu ZM, Austin JW, Bordi R, Procopio FA, Miura T, Allen TM, Sidney J, Sette A, Walker BD, Ahmed R, Boss JM, Sékaly RP, Kaufmann DE. Cutting edge: Prolonged exposure to HIV reinforces a poised epigenetic program for PD-1 expression in virus-specific CD8 T cells. J Immunol. 2013 Jul 15; 191(2):540-4. PMID: 23772031.
    Citations: 44     Fields:    Translation:HumansCells
  55. Boutwell CL, Carlson JM, Lin TH, Seese A, Power KA, Peng J, Tang Y, Brumme ZL, Heckerman D, Schneidewind A, Allen TM. Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins. J Virol. 2013 Apr; 87(7):3952-65. PMID: 23365420.
    Citations: 29     Fields:    Translation:HumansCells
  56. Ansari IU, Allen T, Berical A, Stock PG, Barin B, Striker R. Phenotypic analysis of NS5A variant from liver transplant patient with increased cyclosporine susceptibility. Virology. 2013 Feb 20; 436(2):268-73. PMID: 23290631.
    Citations: 6     Fields:    Translation:HumansCells
  57. Newman RM, Kuntzen T, Weiner B, Berical A, Charlebois P, Kuiken C, Murphy DG, Simmonds P, Bennett P, Lennon NJ, Birren BW, Zody MC, Allen TM, Henn MR. Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants. J Infect Dis. 2013 Jul; 208(1):17-31. PMID: 23136221.
    Citations: 13     Fields:    Translation:HumansCells
  58. Mudd PA, Martins MA, Ericsen AJ, Tully DC, Power KA, Bean AT, Piaskowski SM, Duan L, Seese A, Gladden AD, Weisgrau KL, Furlott JR, Kim YI, Veloso de Santana MG, Rakasz E, Capuano S, Wilson NA, Bonaldo MC, Galler R, Allison DB, Piatak M, Haase AT, Lifson JD, Allen TM, Watkins DI. Vaccine-induced CD8+ T cells control AIDS virus replication. Nature. 2012 Nov 01; 491(7422):129-33. PMID: 23023123.
    Citations: 86     Fields:    Translation:HumansAnimalsCells
  59. Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM, Casali M, Pesko KN, Boutwell CL, DeVincenzo JP, Ebel GD, Allen TM, Zody MC, Henn MR, Levin JZ. Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic Acids Res. 2013 Jan 07; 41(1):e13. PMID: 22962364.
    Citations: 36     Fields:    Translation:HumansCells
  60. 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. Rapid evolution of HIV-1 to functional CD8? T cell responses in humanized BLT mice. Sci Transl Med. 2012 Jul 18; 4(143):143ra98. PMID: 22814851.
    Citations: 40     Fields:    Translation:HumansAnimalsCells
  61. Chen H, Ndhlovu ZM, Liu D, Porter LC, Fang JW, Darko S, Brockman MA, Miura T, Brumme ZL, Schneidewind A, Piechocka-Trocha A, Cesa KT, Sela J, Cung TD, Toth I, Pereyra F, Yu XG, Douek DC, Kaufmann DE, Allen TM, Walker BD. TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection. Nat Immunol. 2012 Jun 10; 13(7):691-700. PMID: 22683743.
    Citations: 93     Fields:    Translation:HumansCells
  62. Thobakgale CF, Fadda L, Lane K, Toth I, Pereyra F, Bazner S, Ndung'u T, Walker BD, Rosenberg ES, Alter G, Carrington M, Allen TM, Altfeld M. Frequent and strong antibody-mediated natural killer cell activation in response to HIV-1 Env in individuals with chronic HIV-1 infection. J Virol. 2012 Jun; 86(12):6986-93. PMID: 22496218.
    Citations: 9     Fields:    Translation:HumansCells
  63. Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, Malboeuf CM, Ryan EM, Boutwell CL, Power KA, Brackney DE, Pesko KN, Levin JZ, Ebel GD, Allen TM, Birren BW, Henn MR. Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Comput Biol. 2012; 8(3):e1002417. PMID: 22438797.
    Citations: 48     Fields:    Translation:Cells
  64. Chang JJ, Lacas A, Lindsay RJ, Doyle EH, Axten KL, Pereyra F, Rosenberg ES, Walker BD, Allen TM, Altfeld M. Differential regulation of toll-like receptor pathways in acute and chronic HIV-1 infection. AIDS. 2012 Mar 13; 26(5):533-41. PMID: 22210629.
    Citations: 32     Fields:    Translation:HumansCells
  65. 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. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog. 2012; 8(3):e1002529. PMID: 22412369.
    Citations: 144     Fields:    Translation:HumansCells
  66. Schulze Zur Wiesch J, Ciuffreda D, Lewis-Ximenez L, Kasprowicz V, Nolan BE, Streeck H, Aneja J, Reyor LL, Allen TM, Lohse AW, McGovern B, Chung RT, Kwok WW, Kim AY, Lauer GM. Broadly directed virus-specific CD4+ T cell responses are primed during acute hepatitis C infection, but rapidly disappear from human blood with viral persistence. J Exp Med. 2012 Jan 16; 209(1):61-75. PMID: 22213804.
    Citations: 57     Fields:    Translation:HumansCells
  67. Mothe B, Llano A, Ibarrondo J, Daniels M, Miranda C, Zamarreño J, Bach V, Zuniga R, Pérez-Álvarez S, Berger CT, Puertas MC, Martinez-Picado J, Rolland M, Farfan M, Szinger JJ, Hildebrand WH, Yang OO, Sanchez-Merino V, Brumme CJ, Brumme ZL, Heckerman D, Allen TM, Mullins JI, Gómez G, Goulder PJ, Walker BD, Gatell JM, Clotet B, Korber BT, Sanchez J, Brander C. Definition of the viral targets of protective HIV-1-specific T cell responses. J Transl Med. 2011 Dec 07; 9:208. PMID: 22152067.
    Citations: 67     Fields:    Translation:HumansCells
  68. Ruhl M, Chhatwal P, Strathmann H, Kuntzen T, Bankwitz D, Skibbe K, Walker A, Heinemann FM, Horn PA, Allen TM, Hoffmann D, Pietschmann T, Timm J. Escape from a dominant HLA-B*15-restricted CD8+ T cell response against hepatitis C virus requires compensatory mutations outside the epitope. J Virol. 2012 Jan; 86(2):991-1000. PMID: 22072759.
    Citations: 6     Fields:    Translation:HumansCells
  69. Neumann-Haefelin C, Oniangue-Ndza C, Kuntzen T, Schmidt J, Nitschke K, Sidney J, Caillet-Saguy C, Binder M, Kersting N, Kemper MW, Power KA, Ingber S, Reyor LL, Hills-Evans K, Kim AY, Lauer GM, Lohmann V, Sette A, Henn MR, Bressanelli S, Thimme R, Allen TM. Human leukocyte antigen B27 selects for rare escape mutations that significantly impair hepatitis C virus replication and require compensatory mutations. Hepatology. 2011 Oct; 54(4):1157-66. PMID: 22006856.
    Citations: 16     Fields:    Translation:HumansCells
  70. 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. Compensatory mutations restore the replication defects caused by cytotoxic T lymphocyte escape mutations in hepatitis C virus polymerase. J Virol. 2011 Nov; 85(22):11883-90. PMID: 21880756.
    Citations: 9     Fields:    Translation:HumansCells
  71. Buranapraditkun S, Hempel U, Pitakpolrat P, Allgaier RL, Thantivorasit P, Lorenzen SI, Sirivichayakul S, Hildebrand WH, Altfeld M, Brander C, Walker BD, Phanuphak P, Hansasuta P, Rowland-Jones SL, Allen TM, Ruxrungtham K. A novel immunodominant CD8+ T cell response restricted by a common HLA-C allele targets a conserved region of Gag HIV-1 clade CRF01_AE infected Thais. PLoS One. 2011; 6(8):e23603. PMID: 21887282.
    Citations: 8     Fields:    Translation:HumansCells
  72. Peng LF, Schaefer EA, Maloof N, Skaff A, Berical A, Belon CA, Heck JA, Lin W, Frick DN, Allen TM, Miziorko HM, Schreiber SL, Chung RT. Ceestatin, a novel small molecule inhibitor of hepatitis C virus replication, inhibits 3-hydroxy-3-methylglutaryl-coenzyme A synthase. J Infect Dis. 2011 Aug 15; 204(4):609-16. PMID: 21791663.
    Citations: 4     Fields:    Translation:HumansCells
  73. Alter G, Heckerman D, Schneidewind A, Fadda L, Kadie CM, Carlson JM, Oniangue-Ndza C, Martin M, Li B, Khakoo SI, Carrington M, Allen TM, Altfeld M. HIV-1 adaptation to NK-cell-mediated immune pressure. Nature. 2011 Aug 03; 476(7358):96-100. PMID: 21814282.
    Citations: 147     Fields:    Translation:HumansCells
  74. Dahirel V, Shekhar K, Pereyra F, Miura T, Artyomov M, Talsania S, Allen TM, Altfeld M, Carrington M, Irvine DJ, Walker BD, Chakraborty AK. Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proc Natl Acad Sci U S A. 2011 Jul 12; 108(28):11530-5. PMID: 21690407.
    Citations: 72     Fields:    Translation:HumansCells
  75. Wheeler LA, Trifonova R, Vrbanac V, Basar E, McKernan S, Xu Z, Seung E, Deruaz M, Dudek T, Einarsson JI, Yang L, Allen TM, Luster AD, Tager AM, Dykxhoorn DM, Lieberman J. Inhibition of HIV transmission in human cervicovaginal explants and humanized mice using CD4 aptamer-siRNA chimeras. J Clin Invest. 2011 Jun; 121(6):2401-12. PMID: 21576818.
    Citations: 86     Fields:    Translation:HumansAnimalsCells
  76. Rolland M, Frahm N, Nickle DC, Jojic N, Deng W, Allen TM, Brander C, Heckerman DE, Mullins JI. Increased breadth and depth of cytotoxic T lymphocytes responses against HIV-1-B Nef by inclusion of epitope variant sequences. PLoS One. 2011 Mar 28; 6(3):e17969. PMID: 21464919.
    Citations: 13     Fields:    Translation:HumansCells
  77. Brumme ZL, Li C, Miura T, Sela J, Rosato PC, Brumme CJ, Markle TJ, Martin E, Block BL, Trocha A, Kadie CM, Allen TM, Pereyra F, Heckerman D, Walker BD, Brockman MA. Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers. J Acquir Immune Defic Syndr. 2011 Feb 01; 56(2):100-8. PMID: 21124229.
    Citations: 37     Fields:    Translation:HumansCells
  78. McMahan RH, Golden-Mason L, Nishimura MI, McMahon BJ, Kemper M, Allen TM, Gretch DR, Rosen HR. Tim-3 expression on PD-1+ HCV-specific human CTLs is associated with viral persistence, and its blockade restores hepatocyte-directed in vitro cytotoxicity. J Clin Invest. 2010 Dec; 120(12):4546-57. PMID: 21084749.
    Citations: 124     Fields:    Translation:HumansCells
  79. Yu Q, Ryan EM, Allen TM, Birren BW, Henn MR, Lennon NJ. PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes. Bioinformatics. 2011 Jan 15; 27(2):266-7. PMID: 21068001.
    Citations: 5     Fields:    Translation:HumansCells
  80. 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 G, 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 JC, 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 HL, 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 WF, 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 JM, 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. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science. 2010 Dec 10; 330(6010):1551-7. PMID: 21051598.
    Citations: 466     Fields:    Translation:HumansCells
  81. Boutwell CL, Rolland MM, Herbeck JT, Mullins JI, Allen TM. Viral evolution and escape during acute HIV-1 infection. J Infect Dis. 2010 Oct 15; 202 Suppl 2:S309-14. PMID: 20846038.
    Citations: 36     Fields:    Translation:HumansCells
  82. Kim AY, Kuntzen T, Timm J, Nolan BE, Baca MA, Reyor LL, Berical AC, Feller AJ, Johnson KL, Schulze zur Wiesch J, Robbins GK, Chung RT, Walker BD, Carrington M, Allen TM, Lauer GM. Spontaneous control of HCV is associated with expression of HLA-B 57 and preservation of targeted epitopes. Gastroenterology. 2011 Feb; 140(2):686-696.e1. PMID: 20875418.
    Citations: 51     Fields:    Translation:HumansCells
  83. Brockman MA, Brumme ZL, Brumme CJ, Miura T, Sela J, Rosato PC, Kadie CM, Carlson JM, Markle TJ, Streeck H, Kelleher AD, Markowitz M, Jessen H, Rosenberg E, Altfeld M, Harrigan PR, Heckerman D, Walker BD, Allen TM. Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection. J Virol. 2010 Nov; 84(22):11937-49. PMID: 20810731.
    Citations: 68     Fields:    Translation:HumansCells
  84. Kosmrlj A, Read EL, Qi Y, Allen TM, Altfeld M, Deeks SG, Pereyra F, Carrington M, Walker BD, Chakraborty AK. Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature. 2010 May 20; 465(7296):350-4. PMID: 20445539.
    Citations: 106     Fields:    Translation:HumansCells
  85. Neumann-Haefelin C, Timm J, Schmidt J, Kersting N, Fitzmaurice K, Oniangue-Ndza C, Kemper MN, Humphreys I, McKiernan S, Kelleher D, Lohmann V, Bowness P, Huzly D, Rosen HR, Kim AY, Lauer GM, Allen TM, Barnes E, Roggendorf M, Blum HE, Thimme R. Protective effect of human leukocyte antigen B27 in hepatitis C virus infection requires the presence of a genotype-specific immunodominant CD8+ T-cell epitope. Hepatology. 2010 Jan; 51(1):54-62. PMID: 20034048.
    Citations: 23     Fields:    Translation:HumansCells
  86. Kasprowicz V, Kang YH, Lucas M, Schulze zur Wiesch J, Kuntzen T, Fleming V, Nolan BE, Longworth S, Berical A, Bengsch B, Thimme R, Lewis-Ximenez L, Allen TM, Kim AY, Klenerman P, Lauer GM. Hepatitis C virus (HCV) sequence variation induces an HCV-specific T-cell phenotype analogous to spontaneous resolution. J Virol. 2010 Feb; 84(3):1656-63. PMID: 19906915.
    Citations: 33     Fields:    Translation:HumansCells
  87. Hoot NR, Epstein SK, Allen TL, Jones SS, Baumlin KM, Chawla N, Lee AT, Pines JM, Klair AK, Gordon BD, Flottemesch TJ, LeBlanc LJ, Jones I, Levin SR, Zhou C, Gadd CS, Aronsky D. Forecasting emergency department crowding: an external, multicenter evaluation. Ann Emerg Med. 2009 Oct; 54(4):514-522.e19. PMID: 19716629.
    Citations: 4     Fields:    Translation:Humans
  88. Schneidewind A, Tang Y, Brockman MA, Ryland EG, Dunkley-Thompson J, Steel-Duncan JC, St John MA, Conrad JA, Kalams SA, Noel F, Allen TM, Christie CD, Feeney ME. Maternal transmission of human immunodeficiency virus escape mutations subverts HLA-B57 immunodominance but facilitates viral control in the haploidentical infant. J Virol. 2009 Sep; 83(17):8616-27. PMID: 19515764.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  89. Kim AY, Timm J, Nolan BE, Reyor LL, Kane K, Berical AC, Zachary KC, Lauer GM, Kuntzen T, Allen TM. Temporal dynamics of a predominant protease inhibitor-resistance mutation in a treatment-naive, hepatitis C virus-infected individual. J Infect Dis. 2009 Mar 01; 199(5):737-41. PMID: 19199553.
    Citations: 6     Fields:    Translation:HumansCells
  90. Kawashima Y, Pfafferott K, Frater J, Matthews P, Payne R, Addo M, Gatanaga H, Fujiwara M, Hachiya A, Koizumi H, Kuse N, Oka S, Duda A, Prendergast A, Crawford H, Leslie A, Brumme Z, Brumme C, Allen T, Brander C, Kaslow R, Tang J, Hunter E, Allen S, Mulenga J, Branch S, Roach T, John M, Mallal S, Ogwu A, Shapiro R, Prado JG, Fidler S, Weber J, Pybus OG, Klenerman P, Ndung'u T, Phillips R, Heckerman D, Harrigan PR, Walker BD, Takiguchi M, Goulder P. Adaptation of HIV-1 to human leukocyte antigen class I. Nature. 2009 Apr 02; 458(7238):641-5. PMID: 19242411.
    Citations: 198     Fields:    Translation:HumansCells
  91. Matthews PC, Leslie AJ, Katzourakis A, Crawford H, Payne R, Prendergast A, Power K, Kelleher AD, Klenerman P, Carlson J, Heckerman D, Ndung'u T, Walker BD, Allen TM, Pybus OG, Goulder PJ. HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering. J Virol. 2009 May; 83(9):4605-15. PMID: 19244334.
    Citations: 23     Fields:    Translation:Cells
  92. Chen H, Piechocka-Trocha A, Miura T, Brockman MA, Julg BD, Baker BM, Rothchild AC, Block BL, Schneidewind A, Koibuchi T, Pereyra F, Allen TM, Walker BD. Differential neutralization of human immunodeficiency virus (HIV) replication in autologous CD4 T cells by HIV-specific cytotoxic T lymphocytes. J Virol. 2009 Apr; 83(7):3138-49. PMID: 19158248.
    Citations: 53     Fields:    Translation:HumansCells
  93. Dalmau J, Puertas MC, Azuara M, Mariño A, Frahm N, Mothe B, Izquierdo-Useros N, Buzón MJ, Paredes R, Matas L, Allen TM, Brander C, Rodrigo C, Clotet B, Martinez-Picado J. Contribution of immunological and virological factors to extremely severe primary HIV type 1 infection. Clin Infect Dis. 2009 Jan 15; 48(2):229-38. PMID: 19093810.
    Citations: 12     Fields:    Translation:HumansCells
  94. Streeck H, Jessen H, Kuecherer C, Li B, Jessen AB, Dupke S, Baumgarten A, Stahmer I, van Lunzen J, Altfeld M, Walker BD, Allen TM. Epidemiologically linked transmission of HIV-1 illustrates the impact of host genetics on virological outcome. AIDS. 2009 Jan 14; 23(2):259-62. PMID: 19098497.
    Citations: 1     Fields:    Translation:HumansCells
  95. Miura T, Brockman MA, Schneidewind A, Lobritz M, Pereyra F, Rathod A, Block BL, Brumme ZL, Brumme CJ, Baker B, Rothchild AC, Li B, Trocha A, Cutrell E, Frahm N, Brander C, Toth I, Arts EJ, Allen TM, Walker BD. HLA-B57/B*5801 human immunodeficiency virus type 1 elite controllers select for rare gag variants associated with reduced viral replication capacity and strong cytotoxic T-lymphocyte [corrected] recognition. J Virol. 2009 Mar; 83(6):2743-55. PMID: 19116253.
    Citations: 153     Fields:    Translation:HumansCells
  96. 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. Transmission and long-term stability of compensated CD8 escape mutations. J Virol. 2009 Apr; 83(8):3993-7. PMID: 19091871.
    Citations: 37     Fields:    Translation:HumansAnimalsCells
  97. Kuntzen T, Timm J, Berical A, Lennon N, Berlin AM, Young SK, Lee B, Heckerman D, Carlson J, Reyor LL, Kleyman M, McMahon CM, Birch C, Schulze Zur Wiesch J, Ledlie T, Koehrsen M, Kodira C, Roberts AD, Lauer GM, Rosen HR, Bihl F, Cerny A, Spengler U, Liu Z, Kim AY, Xing Y, Schneidewind A, Madey MA, Fleckenstein JF, Park VM, Galagan JE, Nusbaum C, Walker BD, Lake-Bakaar GV, Daar ES, Jacobson IM, Gomperts ED, Edlin BR, Donfield SM, Chung RT, Talal AH, Marion T, Birren BW, Henn MR, Allen TM. Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients. Hepatology. 2008 Dec; 48(6):1769-78. PMID: 19026009.
    Citations: 117     Fields:    Translation:HumansCells
  98. 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. 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. J Virol. 2009 Feb; 83(4):1845-55. PMID: 19036810.
    Citations: 70     Fields:    Translation:HumansCells
  99. Yerly D, Heckerman D, Allen T, Suscovich TJ, Jojic N, Kadie C, Pichler WJ, Cerny A, Brander C. Design, expression, and processing of epitomized hepatitis C virus-encoded CTL epitopes. J Immunol. 2008 Nov 01; 181(9):6361-70. PMID: 18941227.
    Citations: 7     Fields:    Translation:HumansCells
  100. Wölfl M, Rutebemberwa A, Mosbruger T, Mao Q, Li HM, Netski D, Ray SC, Pardoll D, Sidney J, Sette A, Allen T, Kuntzen T, Kavanagh DG, Kuball J, Greenberg PD, Cox AL. Hepatitis C virus immune escape via exploitation of a hole in the T cell repertoire. J Immunol. 2008 Nov 01; 181(9):6435-46. PMID: 18941234.
    Citations: 28     Fields:    Translation:HumansCells
  101. Miura T, Brockman MA, Brumme ZL, Brumme CJ, Pereyra F, Trocha A, Block BL, Schneidewind A, Allen TM, Heckerman D, Walker BD. HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1. J Virol. 2009 Jan; 83(1):140-9. PMID: 18971283.
    Citations: 70     Fields:    Translation:HumansCells
  102. Kuntzen T, Berical A, Ndjomou J, Bennett P, Schneidewind A, Lennon N, Birren BW, Kuiken C, Henn MR, Simmonds P, Allen TM. A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame. J Med Virol. 2008 Aug; 80(8):1370-8. PMID: 18551618.
    Citations: 4     Fields:    Translation:HumansCells
  103. 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. Immune-driven recombination and loss of control after HIV superinfection. J Exp Med. 2008 Aug 04; 205(8):1789-96. PMID: 18625749.
    Citations: 50     Fields:    Translation:HumansCells
  104. Brumme ZL, Brumme CJ, Carlson J, Streeck H, John M, Eichbaum Q, Block BL, Baker B, Kadie C, Markowitz M, Jessen H, Kelleher AD, Rosenberg E, Kaldor J, Yuki Y, Carrington M, Allen TM, Mallal S, Altfeld M, Heckerman D, Walker BD. Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. J Virol. 2008 Sep; 82(18):9216-27. PMID: 18614631.
    Citations: 107     Fields:    Translation:HumansCells
  105. Miura T, Brockman MA, Brumme CJ, Brumme ZL, Carlson JM, Pereyra F, Trocha A, Addo MM, Block BL, Rothchild AC, Baker BM, Flynn T, Schneidewind A, Li B, Wang YE, Heckerman D, Allen TM, Walker BD. Genetic characterization of human immunodeficiency virus type 1 in elite controllers: lack of gross genetic defects or common amino acid changes. J Virol. 2008 Sep; 82(17):8422-30. PMID: 18562530.
    Citations: 68     Fields:    Translation:HumansCells
  106. Streeck S, Li B, Poon AFY, Schneidewind A, Gladden AD, Power KA, Daskalakis D, Bazner S, Zuniga R, Brander C, Rosenberg E, Frost SDW, Altfeld M, Allen TM. Immune Driven Recombination and Loss of Control Following HIV Superinfection. of Experimental Medicine. 2008; In Press.
  107. Neumann-Haefelin C, Timm J, Spangenberg HC, Wischniowski N, Nazarova N, Kersting N, Roggendorf M, Allen TM, Blum HE, Thimme R. Virological and immunological determinants of intrahepatic virus-specific CD8+ T-cell failure in chronic hepatitis C virus infection. Hepatology. 2008 Jun; 47(6):1824-36. PMID: 18454507.
    Citations: 27     Fields:    Translation:HumansCells
  108. Streeck H, Brumme ZL, Anastario M, Cohen KW, Jolin JS, Meier A, Brumme CJ, Rosenberg ES, Alter G, Allen TM, Walker BD, Altfeld M. Antigen load and viral sequence diversification determine the functional profile of HIV-1-specific CD8+ T cells. PLoS Med. 2008 May 06; 5(5):e100. PMID: 18462013.
    Citations: 114     Fields:    Translation:HumansCells
  109. Allen TM, Altfeld M. Crippling HIV one mutation at a time. J Exp Med. 2008 May 12; 205(5):1003-7. PMID: 18458116.
    Citations: 20     Fields:    Translation:HumansCells
  110. Schneidewind A, Brockman MA, Sidney J, Wang YE, Chen H, Suscovich TJ, Li B, Adam RI, Allgaier RL, Mothé BR, Kuntzen T, Oniangue-Ndza C, Trocha A, Yu XG, Brander C, Sette A, Walker BD, Allen TM. Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLA-B27-restricted epitope in human immunodeficiency virus type 1 capsid. J Virol. 2008 Jun; 82(11):5594-605. PMID: 18385228.
    Citations: 88     Fields:    Translation:HumansCells
  111. Frahm N, Nickle DC, Linde CH, Cohen DE, Zuñiga R, Lucchetti A, Roach T, Walker BD, Allen TM, Korber BT, Mullins JI, Brander C. Increased detection of HIV-specific T cell responses by combination of central sequences with comparable immunogenicity. AIDS. 2008 Feb 19; 22(4):447-56. PMID: 18301057.
    Citations: 19     Fields:    Translation:HumansCells
  112. Yerly D, Heckerman D, Allen TM, Chisholm JV, Faircloth K, Linde CH, Frahm N, Timm J, Pichler WJ, Cerny A, Brander C. Increased cytotoxic T-lymphocyte epitope variant cross-recognition and functional avidity are associated with hepatitis C virus clearance. J Virol. 2008 Mar; 82(6):3147-53. PMID: 18184704.
    Citations: 23     Fields:    Translation:HumansCells
  113. Mullins JI, Rolland M, Allen TM. Viral evolution and escape during primary human immunodeficiency virus-1 infection: implications for vaccine design. Curr Opin HIV AIDS. 2008 Jan; 3(1):60-6. PMID: 19372945.
    Citations: 1     Fields:    
  114. Kasprowicz V, Schulze Zur Wiesch J, Kuntzen T, Nolan BE, Longworth S, Berical A, Blum J, McMahon C, Reyor LL, Elias N, Kwok WW, McGovern BG, Freeman G, Chung RT, Klenerman P, Lewis-Ximenez L, Walker BD, Allen TM, Kim AY, Lauer GM. High level of PD-1 expression on hepatitis C virus (HCV)-specific CD8+ and CD4+ T cells during acute HCV infection, irrespective of clinical outcome. J Virol. 2008 Mar; 82(6):3154-60. PMID: 18160439.
    Citations: 73     Fields:    Translation:HumansCells
  115. Alter G, Martin MP, Teigen N, Carr WH, Suscovich TJ, Schneidewind A, Streeck H, Waring M, Meier A, Brander C, Lifson JD, Allen TM, Carrington M, Altfeld M. Differential natural killer cell-mediated inhibition of HIV-1 replication based on distinct KIR/HLA subtypes. J Exp Med. 2007 Nov 26; 204(12):3027-36. PMID: 18025129.
    Citations: 207     Fields:    Translation:HumansCells
  116. Lichterfeld M, Kavanagh DG, Williams KL, Moza B, Mui SK, Miura T, Sivamurthy R, Allgaier R, Pereyra F, Trocha A, Feeney M, Gandhi RT, Rosenberg ES, Altfeld M, Allen TM, Allen R, Walker BD, Sundberg EJ, Yu XG. A viral CTL escape mutation leading to immunoglobulin-like transcript 4-mediated functional inhibition of myelomonocytic cells. J Exp Med. 2007 Nov 26; 204(12):2813-24. PMID: 18025130.
    Citations: 48     Fields:    Translation:HumansCells
  117. Frahm N, Kaufmann DE, Yusim K, Muldoon M, Kesmir C, Linde CH, Fischer W, Allen TM, Li B, McMahon BH, Faircloth KL, Hewitt HS, Mackey EW, Miura T, Khatri A, Wolinsky S, McMichael A, Funkhouser RK, Walker BD, Brander C, Korber BT. Increased sequence diversity coverage improves detection of HIV-specific T cell responses. J Immunol. 2007 Nov 15; 179(10):6638-50. PMID: 17982054.
    Citations: 21     Fields:    Translation:HumansCells
  118. Schneidewind A, Brockman MA, Yang R, Adam RI, Li B, Le Gall S, Rinaldo CR, Craggs SL, Allgaier RL, Power KA, Kuntzen T, Tung CS, LaBute MX, Mueller SM, Harrer T, McMichael AJ, Goulder PJ, Aiken C, Brander C, Kelleher AD, Allen TM. Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication. J Virol. 2007 Nov; 81(22):12382-93. PMID: 17804494.
    Citations: 187     Fields:    Translation:HumansCells
  119. Brockman MA, Schneidewind A, Lahaie M, Schmidt A, Miura T, Desouza I, Ryvkin F, Derdeyn CA, Allen S, Hunter E, Mulenga J, Goepfert PA, Walker BD, Allen TM. Escape and compensation from early HLA-B57-mediated cytotoxic T-lymphocyte pressure on human immunodeficiency virus type 1 Gag alter capsid interactions with cyclophilin A. J Virol. 2007 Nov; 81(22):12608-18. PMID: 17728232.
    Citations: 164     Fields:    Translation:HumansCells
  120. Kuntzen T, Timm J, Berical A, Lewis-Ximenez LL, Jones A, Nolan B, Schulze zur Wiesch J, Li B, Schneidewind A, Kim AY, Chung RT, Lauer GM, Allen TM. Viral sequence evolution in acute hepatitis C virus infection. J Virol. 2007 Nov; 81(21):11658-68. PMID: 17699568.
    Citations: 50     Fields:    Translation:HumansCells
  121. Timm J, Li B, Daniels MG, Bhattacharya T, Reyor LL, Allgaier R, Kuntzen T, Fischer W, Nolan BE, Duncan J, Schulze zur Wiesch J, Kim AY, Frahm N, Brander C, Chung RT, Lauer GM, Korber BT, Allen TM. Human leukocyte antigen-associated sequence polymorphisms in hepatitis C virus reveal reproducible immune responses and constraints on viral evolution. Hepatology. 2007 Aug; 46(2):339-49. PMID: 17559151.
    Citations: 41     Fields:    Translation:HumansCells
  122. Schulze Zur Wiesch J, Lauer GM, Timm J, Kuntzen T, Neukamm M, Berical A, Jones AM, Nolan BE, Longworth SA, Kasprowicz V, McMahon C, Wurcel A, Lohse AW, Lewis-Ximenez LL, Chung RT, Kim AY, Allen TM, Walker BD. Immunologic evidence for lack of heterologous protection following resolution of HCV in patients with non-genotype 1 infection. Blood. 2007 Sep 01; 110(5):1559-69. PMID: 17475911.
    Citations: 17     Fields:    Translation:HumansCellsCTClinical Trials
  123. Timm J, Neukamm M, Kuntzen T, Kim AY, Chung RT, Brander C, Lauer GM, Walker BD, Allen TM. Characterization of full-length hepatitis C virus genotype 4 sequences. J Viral Hepat. 2007 May; 14(5):330-7. PMID: 17439522.
    Citations: 8     Fields:    Translation:HumansCells
  124. Timm, J., Neukamm, M., Kuntzen, T., Kim, A.Y., Chung, R.T., Brander, C., Lauer, G.M., Walker, B.D., Allen, T.M. Characterization of Full Length HCV Genotype 4 Sequences. J Viral Hepat. 2007; 14(5):330-7.
  125. Streeck H, Schweighardt B, Jessen H, Allgaier RL, Wrin T, Stawiski EW, Jessen AB, Allen TM, Walker BD, Altfeld M. Loss of HIV-1-specific T-cell responses associated with very rapid HIV-1 disease progression. AIDS. 2007 Apr 23; 21(7):889-91. PMID: 17415054.
    Citations: 7     Fields:    Translation:HumansCells
  126. Fuller DH, Shipley T, Allen TM, Fuller JT, Wu MS, Horton H, Wilson N, Widera G, Watkins DI. Immunogenicity of hybrid DNA vaccines expressing hepatitis B core particles carrying human and simian immunodeficiency virus epitopes in mice and rhesus macaques. Virology. 2007 Aug 01; 364(2):245-55. PMID: 17428516.
    Citations:    
  127. Lichterfeld M, Yu XG, Mui SK, Williams KL, Trocha A, Brockman MA, Allgaier RL, Waring MT, Koibuchi T, Johnston MN, Cohen D, Allen TM, Rosenberg ES, Walker BD, Altfeld M. Selective depletion of high-avidity human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T cells after early HIV-1 infection. J Virol. 2007 Apr; 81(8):4199-214. PMID: 17287271.
    Citations: 45     Fields:    Translation:HumansCells
  128. Kim AY, Schulze zur Wiesch J, Kuntzen T, Timm J, Kaufmann DE, Duncan JE, Jones AM, Wurcel AG, Davis BT, Gandhi RT, Robbins GK, Allen TM, Chung RT, Lauer GM, Walker BD. Impaired hepatitis C virus-specific T cell responses and recurrent hepatitis C virus in HIV coinfection. PLoS Med. 2006 Dec; 3(12):e492. PMID: 17194190.
    Citations: 33     Fields:    Translation:HumansCells
  129. Yu XG, Lichterfeld M, Chetty S, Williams KL, Mui SK, Miura T, Frahm N, Feeney ME, Tang Y, Pereyra F, Labute MX, Pfafferott K, Leslie A, Crawford H, Allgaier R, Hildebrand W, Kaslow R, Brander C, Allen TM, Rosenberg ES, Kiepiela P, Vajpayee M, Goepfert PA, Altfeld M, Goulder PJ, Walker BD. Mutually exclusive T-cell receptor induction and differential susceptibility to human immunodeficiency virus type 1 mutational escape associated with a two-amino-acid difference between HLA class I subtypes. J Virol. 2007 Feb; 81(4):1619-31. PMID: 17121793.
    Citations: 44     Fields:    Translation:HumansCells
  130. Li B, Gladden AD, Altfeld M, Kaldor JM, Cooper DA, Kelleher AD, Allen TM. Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution. J Virol. 2007 Jan; 81(1):193-201. PMID: 17065207.
    Citations: 83     Fields:    Translation:HumansCells
  131. Altfeld M, Kalife ET, Qi Y, Streeck H, Lichterfeld M, Johnston MN, Burgett N, Swartz ME, Yang A, Alter G, Yu XG, Meier A, Rockstroh JK, Allen TM, Jessen H, Rosenberg ES, Carrington M, Walker BD. HLA Alleles Associated with Delayed Progression to AIDS Contribute Strongly to the Initial CD8(+) T Cell Response against HIV-1. PLoS Med. 2006 Oct; 3(10):e403. PMID: 17076553.
    Citations: 151     Fields:    Translation:HumansCells
  132. Altfeld M, Allen TM. Hitting HIV where it hurts: an alternative approach to HIV vaccine design. Trends Immunol. 2006 Nov; 27(11):504-10. PMID: 16997629.
    Citations: 48     Fields:    Translation:HumansAnimalsCells
  133. Streeck, H., Jessen, H., Alter, G., Teigen, N., Waring, M.T., Jessen, A., Stahmer, I., Lunzen, J., Lichterfeld, M., Gao, X., Allen, T.M., Carrington, M., Walker, B.D., Rockstroh, J.K., Altfeld, M. Virological Impact of Highly Active Antiretroviral Therapy Initiated during Acute HIV-1 Infection. . 2006 Sep 15;194(6):734-9. . J Infect Dis. 2006; 194(6):734-9.
  134. Streeck H, Jessen H, Alter G, Teigen N, Waring MT, Jessen A, Stahmer I, van Lunzen J, Lichterfeld M, Gao X, Allen TM, Carrington M, Walker BD, Rockstroh JK, Altfeld M. Immunological and virological impact of highly active antiretroviral therapy initiated during acute HIV-1 infection. J Infect Dis. 2006 Sep 15; 194(6):734-9. PMID: 16941338.
    Citations: 29     Fields:    Translation:HumansCells
  135. Draenert R, Allen TM, Liu Y, Wrin T, Chappey C, Verrill CL, Sirera G, Eldridge RL, Lahaie MP, Ruiz L, Clotet B, Petropoulos CJ, Walker BD, Martinez-Picado J. Constraints on HIV-1 evolution and immunodominance revealed in monozygotic adult twins infected with the same virus. J Exp Med. 2006 Mar 20; 203(3):529-39. PMID: 16533886.
    Citations: 42     Fields:    Translation:HumansCells
  136. Zuñiga R, Lucchetti A, Galvan P, Sanchez S, Sanchez C, Hernandez A, Sanchez H, Frahm N, Linde CH, Hewitt HS, Hildebrand W, Altfeld M, Allen TM, Walker BD, Korber BT, Leitner T, Sanchez J, Brander C. Relative dominance of Gag p24-specific cytotoxic T lymphocytes is associated with human immunodeficiency virus control. J Virol. 2006 Mar; 80(6):3122-5. PMID: 16501126.
    Citations: 133     Fields:    Translation:HumansCells
  137. Fuller DH, Rajakumar PA, Wu MS, McMahon CW, Shipley T, Fuller JT, Bazmi A, Trichel AM, Allen TM, Mothe B, Haynes JR, Watkins DI, Murphey-Corb M. DNA immunization in combination with effective antiretroviral drug therapy controls viral rebound and prevents simian AIDS after treatment is discontinued. Virology. 2006 Apr 25; 348(1):200-15. PMID: 16439000.
    Citations: 12     Fields:    Translation:AnimalsCells
  138. Frahm N, Kiepiela P, Adams S, Linde CH, Hewitt HS, Sango K, Feeney ME, Addo MM, Lichterfeld M, Lahaie MP, Pae E, Wurcel AG, Roach T, St John MA, Altfeld M, Marincola FM, Moore C, Mallal S, Carrington M, Heckerman D, Allen TM, Mullins JI, Korber BT, Goulder PJ, Walker BD, Brander C. Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes. Nat Immunol. 2006 Feb; 7(2):173-8. PMID: 16369537.
    Citations: 108     Fields:    Translation:HumansCells
  139. Meyer-Olson D, Brady KW, Bartman MT, O'Sullivan KM, Simons BC, Conrad JA, Duncan CB, Lorey S, Siddique A, Draenert R, Addo M, Altfeld M, Rosenberg E, Allen TM, Walker BD, Kalams SA. Fluctuations of functionally distinct CD8+ T-cell clonotypes demonstrate flexibility of the HIV-specific TCR repertoire. Blood. 2006 Mar 15; 107(6):2373-83. PMID: 16322475.
    Citations: 27     Fields:    Translation:HumansCells
  140. Allen TM, Altfeld M, Geer SC, Kalife ET, Moore C, O'sullivan KM, Desouza I, Feeney ME, Eldridge RL, Maier EL, Kaufmann DE, Lahaie MP, Reyor L, Tanzi G, Johnston MN, Brander C, Draenert R, Rockstroh JK, Jessen H, Rosenberg ES, Mallal SA, Walker BD. Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution. J Virol. 2005 Nov; 79(21):13239-49. PMID: 16227247.
    Citations: 171     Fields:    Translation:HumansCells
  141. Lauer GM, Lucas M, Timm J, Ouchi K, Kim AY, Day CL, Schulze Zur Wiesch J, Paranhos-Baccala G, Sheridan I, Casson DR, Reiser M, Gandhi RT, Li B, Allen TM, Chung RT, Klenerman P, Walker BD. Full-breadth analysis of CD8+ T-cell responses in acute hepatitis C virus infection and early therapy. J Virol. 2005 Oct; 79(20):12979-88. PMID: 16189000.
    Citations: 36     Fields:    Translation:HumansCells
  142. Allen TM, Yu XG, Kalife ET, Reyor LL, Lichterfeld M, John M, Cheng M, Allgaier RL, Mui S, Frahm N, Alter G, Brown NV, Johnston MN, Rosenberg ES, Mallal SA, Brander C, Walker BD, Altfeld M. De novo generation of escape variant-specific CD8+ T-cell responses following cytotoxic T-lymphocyte escape in chronic human immunodeficiency virus type 1 infection. J Virol. 2005 Oct; 79(20):12952-60. PMID: 16188997.
    Citations: 61     Fields:    Translation:HumansCells
  143. Brockman MA, Tanzi GO, Walker BD, Allen TM. Use of a novel GFP reporter cell line to examine replication capacity of CXCR4- and CCR5-tropic HIV-1 by flow cytometry. J Virol Methods. 2006 Feb; 131(2):134-42. PMID: 16182382.
    Citations: 36     Fields:    Translation:HumansCells
  144. Schulze zur Wiesch J, Lauer GM, Day CL, Kim AY, Ouchi K, Duncan JE, Wurcel AG, Timm J, Jones AM, Mothe B, Allen TM, McGovern B, Lewis-Ximenez L, Sidney J, Sette A, Chung RT, Walker BD. Broad repertoire of the CD4+ Th cell response in spontaneously controlled hepatitis C virus infection includes dominant and highly promiscuous epitopes. J Immunol. 2005 Sep 15; 175(6):3603-13. PMID: 16148104.
    Citations: 52     Fields:    Translation:HumansCells
  145. Frahm N, Adams S, Kiepiela P, Linde CH, Hewitt HS, Lichterfeld M, Sango K, Brown NV, Pae E, Wurcel AG, Altfeld M, Feeney ME, Allen TM, Roach T, St John MA, Daar ES, Rosenberg E, Korber B, Marincola F, Walker BD, Goulder PJ, Brander C. HLA-B63 presents HLA-B57/B58-restricted cytotoxic T-lymphocyte epitopes and is associated with low human immunodeficiency virus load. J Virol. 2005 Aug; 79(16):10218-25. PMID: 16051815.
    Citations: 38     Fields:    Translation:HumansCells
  146. Koibuchi T, Allen TM, Lichterfeld M, Mui SK, O'Sullivan KM, Trocha A, Kalams SA, Johnson RP, Walker BD. Limited sequence evolution within persistently targeted CD8 epitopes in chronic human immunodeficiency virus type 1 infection. J Virol. 2005 Jul; 79(13):8171-81. PMID: 15956562.
    Citations: 20     Fields:    Translation:HumansCells
  147. Feeney ME, Tang Y, Pfafferott K, Roosevelt KA, Draenert R, Trocha A, Yu XG, Verrill C, Allen T, Moore C, Mallal S, Burchett S, McIntosh K, Pelton SI, St John MA, Hazra R, Klenerman P, Altfeld M, Walker BD, Goulder PJ. HIV-1 viral escape in infancy followed by emergence of a variant-specific CTL response. J Immunol. 2005 Jun 15; 174(12):7524-30. PMID: 15944251.
    Citations: 58     Fields:    Translation:HumansCells
  148. Altfeld M, Allen TM, Kalife ET, Frahm N, Addo MM, Mothe BR, Rathod A, Reyor LL, Harlow J, Yu XG, Perkins B, Robinson LK, Sidney J, Alter G, Lichterfeld M, Sette A, Rosenberg ES, Goulder PJ, Brander C, Walker BD. The majority of currently circulating human immunodeficiency virus type 1 clade B viruses fail to prime cytotoxic T-lymphocyte responses against an otherwise immunodominant HLA-A2-restricted epitope: implications for vaccine design. J Virol. 2005 Apr; 79(8):5000-5. PMID: 15795285.
    Citations: 19     Fields:    Translation:HumansCells
  149. Timm J, Lauer GM, Kavanagh DG, Sheridan I, Kim AY, Lucas M, Pillay T, Ouchi K, Reyor LL, Schulze zur Wiesch J, Gandhi RT, Chung RT, Bhardwaj N, Klenerman P, Walker BD, Allen TM. CD8 epitope escape and reversion in acute HCV infection. J Exp Med. 2004 Dec 20; 200(12):1593-604. PMID: 15611288.
    Citations: 105     Fields:    Translation:HumansAnimalsCells
  150. Kiepiela P, Leslie AJ, Honeyborne I, Ramduth D, Thobakgale C, Chetty S, Rathnavalu P, Moore C, Pfafferott KJ, Hilton L, Zimbwa P, Moore S, Allen T, Brander C, Addo MM, Altfeld M, James I, Mallal S, Bunce M, Barber LD, Szinger J, Day C, Klenerman P, Mullins J, Korber B, Coovadia HM, Walker BD, Goulder PJ. Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature. 2004 Dec 09; 432(7018):769-75. PMID: 15592417.
    Citations: 350     Fields:    Translation:HumansCells
  151. Lauer GM, Barnes E, Lucas M, Timm J, Ouchi K, Kim AY, Day CL, Robbins GK, Casson DR, Reiser M, Dusheiko G, Allen TM, Chung RT, Walker BD, Klenerman P. High resolution analysis of cellular immune responses in resolved and persistent hepatitis C virus infection. Gastroenterology. 2004 Sep; 127(3):924-36. PMID: 15362047.
    Citations: 97     Fields:    Translation:HumansCells
  152. Lichterfeld M, Yu XG, Cohen D, Addo MM, Malenfant J, Perkins B, Pae E, Johnston MN, Strick D, Allen TM, Rosenberg ES, Korber B, Walker BD, Altfeld M. HIV-1 Nef is preferentially recognized by CD8 T cells in primary HIV-1 infection despite a relatively high degree of genetic diversity. AIDS. 2004 Jul 02; 18(10):1383-92. PMID: 15199314.
    Citations: 51     Fields:    Translation:HumansCells
  153. Allen TM, Altfeld M, Yu XG, O'Sullivan KM, Lichterfeld M, Le Gall S, John M, Mothe BR, Lee PK, Kalife ET, Cohen DE, Freedberg KA, Strick DA, Johnston MN, Sette A, Rosenberg ES, Mallal SA, Goulder PJ, Brander C, Walker BD. Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection. J Virol. 2004 Jul; 78(13):7069-78. PMID: 15194783.
    Citations: 140     Fields:    Translation:HumansCells
  154. Yu XG, Addo MM, Perkins BA, Wej F, Rathod A, Geer SC, Parta M, Cohen D, Stone DR, Russell CJ, Tanzi G, Mei S, Wurcel AG, Frahm N, Lichterfeld M, Heath L, Mullins JI, Marincola F, Goulder PJ, Brander C, Allen T, Cao Y, Walker BD, Altfeld M. Differences in the expressed HLA class I alleles effect the differential clustering of HIV type 1-specific T cell responses in infected Chinese and caucasians. AIDS Res Hum Retroviruses. 2004 May; 20(5):557-64. PMID: 15186531.
    Citations: 7     Fields:    Translation:HumansCells
  155. Lichterfeld M, Yu XG, Waring MT, Mui SK, Johnston MN, Cohen D, Addo MM, Zaunders J, Alter G, Pae E, Strick D, Allen TM, Rosenberg ES, Walker BD, Altfeld M. HIV-1-specific cytotoxicity is preferentially mediated by a subset of CD8(+) T cells producing both interferon-gamma and tumor necrosis factor-alpha. Blood. 2004 Jul 15; 104(2):487-94. PMID: 15059848.
    Citations: 47     Fields:    Translation:HumansCells
  156. Hess C, Altfeld M, Thomas SY, Addo MM, Rosenberg ES, Allen TM, Draenert R, Eldrige RL, van Lunzen J, Stellbrink HJ, Walker BD, Luster AD. HIV-1 specific CD8+ T cells with an effector phenotype and control of viral replication. Lancet. 2004 Mar 13; 363(9412):863-6. PMID: 15031033.
    Citations: 41     Fields:    Translation:HumansCells
  157. Norris PJ, Moffett HF, Brander C, Allen TM, O'Sullivan KM, Cosimi LA, Kaufmann DE, Walker BD, Rosenberg ES. Fine specificity and cross-clade reactivity of HIV type 1 Gag-specific CD4+ T cells. AIDS Res Hum Retroviruses. 2004 Mar; 20(3):315-25. PMID: 15117455.
    Citations: 17     Fields:    Translation:HumansCells
  158. Leslie AJ, Pfafferott KJ, Chetty P, Draenert R, Addo MM, Feeney M, Tang Y, Holmes EC, Allen T, Prado JG, Altfeld M, Brander C, Dixon C, Ramduth D, Jeena P, Thomas SA, St John A, Roach TA, Kupfer B, Luzzi G, Edwards A, Taylor G, Lyall H, Tudor-Williams G, Novelli V, Martinez-Picado J, Kiepiela P, Walker BD, Goulder PJ. HIV evolution: CTL escape mutation and reversion after transmission. Nat Med. 2004 Mar; 10(3):282-9. PMID: 14770175.
    Citations: 394     Fields:    Translation:HumansCells
  159. Draenert R, Verrill CL, Tang Y, Allen TM, Wurcel AG, Boczanowski M, Lechner A, Kim AY, Suscovich T, Brown NV, Addo MM, Walker BD. Persistent recognition of autologous virus by high-avidity CD8 T cells in chronic, progressive human immunodeficiency virus type 1 infection. J Virol. 2004 Jan; 78(2):630-41. PMID: 14694094.
    Citations: 68     Fields:    Translation:HumansCells
  160. Altfeld M, Addo MM, Rosenberg ES, Hecht FM, Lee PK, Vogel M, Yu XG, Draenert R, Johnston MN, Strick D, Allen TM, Feeney ME, Kahn JO, Sekaly RP, Levy JA, Rockstroh JK, Goulder PJ, Walker BD. Influence of HLA-B57 on clinical presentation and viral control during acute HIV-1 infection. AIDS. 2003 Dec 05; 17(18):2581-91. PMID: 14685052.
    Citations: 157     Fields:    Translation:HumansCells
  161. Allen TM, Altfeld M. HIV-1 superinfection. J Allergy Clin Immunol. 2003 Nov; 112(5):829-35; quiz 836. PMID: 14610465.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  162. 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. 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. 2003 Aug; 77(16):9029-40. PMID: 12885919.
    Citations: 95     Fields:    Translation:AnimalsCells
  163. Altfeld M, Addo MM, Shankarappa R, Lee PK, Allen TM, Yu XG, Rathod A, Harlow J, O'Sullivan K, Johnston MN, Goulder PJ, Mullins JI, Rosenberg ES, Brander C, Korber B, Walker BD. Enhanced detection of human immunodeficiency virus type 1-specific T-cell responses to highly variable regions by using peptides based on autologous virus sequences. 2003; 77(13):7330-40.