Harvard Catalyst Profiles

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

Todd Allen, Ph.D.

Title
Institution
Department
Address
Phone
Fax

Overview
overview
My laboratory has 3 major areas of interest: 1) Determining the host and viral factors impacting the transmission of HIV; 2) Translating gene-editing and CAR-T immunotherapies in vivo using humanized mouse models to explore novel approaches to cure HIV; 3) Determining the role of HIV envelope evolution in the development of broadly neutralizing antibodies. 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. U19AI149680 (RILEY, JAMES L) May 15, 2020 - Apr 30, 2025
    NIH
    Engineering T cells to Provide Durable Control of HIV-1 Replication
    Role: Co-Investigator
  2. U19HL156247 (CANNON, PAULA M) May 15, 2020 - Apr 30, 2025
    NIH
    Novel hematopoietic stem cell engineering and transplantation approaches for HIV cure
    Role: Co-Investigator
  3. U24DA044801 (ALLEN, TODD M) Aug 15, 2017 - Jul 31, 2022
    NIH
    Next-Generation Sequencing Center for GHOSTing Hepatitis C Virus: Transforming Community Based Molecular Surveillance and Outbreak Investigation
    Role: Principal Investigator
  4. U19HL129903 (SCADDEN, DAVID T) Apr 1, 2015 - Mar 31, 2021
    NIH
    A defend and destroy approach to curing HIV
    Role: Co-Principal Investigator
  5. P01AI104715 (ALLEN, TODD M) Feb 7, 2013 - Jan 31, 2020
    NIH
    Optimizing Human B and T Cell Vaccines Against HIV Using Humanized BLT Mice
    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.
Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
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. Collins DR, Urbach JM, Racenet ZJ, Arshad U, Power KA, Newman RM, Mylvaganam GH, Ly NL, Lian X, Rull A, Rassadkina Y, Yanez AG, Peluso MJ, Deeks SG, Vidal F, Lichterfeld M, Yu XG, Gaiha GD, Allen TM, Walker BD. Functional impairment of HIV-specific CD8+ T cells precedes aborted spontaneous control of viremia. Immunity. 2021 10 12; 54(10):2372-2384.e7. PMID: 34496223.
    Citations:    Fields:    
  2. Tully DC, Hahn JA, Bean DJ, Evans JL, Morris MD, Page K, Allen TM. Identification of Genetically Related HCV Infections Among Self-Described Injecting Partnerships. Clin Infect Dis. 2021 Aug 27. PMID: 34448809.
    Citations:    Fields:    
  3. Yates KB, Tonnerre P, Martin GE, Gerdemann U, Al Abosy R, Comstock DE, Weiss SA, Wolski D, Tully DC, Chung RT, Allen TM, Kim AY, Fidler S, Fox J, Frater J, Lauer GM, Haining WN, Sen DR. Epigenetic scars of CD8+ T cell exhaustion persist after cure of chronic infection in humans. Nat Immunol. 2021 08; 22(8):1020-1029. PMID: 34312547.
    Citations: 2     Fields:    Translation:HumansCellsCTClinical Trials
  4. Tonnerre P, Wolski D, Subudhi S, Aljabban J, Hoogeveen RC, Damasio M, Drescher HK, Bartsch LM, Tully DC, Sen DR, Bean DJ, Brown J, Torres-Cornejo A, Robidoux M, Kvistad D, Alatrakchi N, Cui A, Lieb D, Cheney JA, Gustafson J, Lewis-Ximenez LL, Massenet-Regad L, Eisenhaure T, Aneja J, Haining WN, Chung RT, Hacohen N, Allen TM, Kim AY, Lauer GM. Differentiation of exhausted CD8+ T cells after termination of chronic antigen stimulation stops short of achieving functional T cell memory. Nat Immunol. 2021 08; 22(8):1030-1041. PMID: 34312544.
    Citations: 2     Fields:    Translation:HumansCells
  5. Garcia-Beltran WF, Claiborne DT, Maldini CR, Phelps M, Vrbanac V, Karpel ME, Krupp KL, Power KA, Boutwell CL, Balazs AB, Tager AM, Altfeld M, Allen TM. Innate Immune Reconstitution in Humanized Bone Marrow-Liver-Thymus (HuBLT) Mice Governs Adaptive Cellular Immune Function and Responses to HIV-1 Infection. Front Immunol. 2021; 12:667393. PMID: 34122425.
    Citations: 1     Fields:    
  6. Hochstatter KR, Tully DC, Power KA, Koepke R, Akhtar WZ, Prieve AF, Whyte T, Bean DJ, Seal DW, Allen TM, Westergaard RP. Hepatitis C Virus Transmission Clusters in Public Health and Correctional Settings, Wisconsin, USA, 2016-20171. Emerg Infect Dis. 2021 02; 27(2):480-489. PMID: 33496239.
    Citations:    Fields:    Translation:HumansCellsPHPublic Health
  7. Offersen R, Yu WH, Scully EP, Julg B, Euler Z, Sadanand S, Garcia-Dominguez D, Zheng L, Rasmussen TA, Jennewein MF, Linde C, Sassic J, Lofano G, Vigano S, Stephenson KE, Fischinger S, Suscovich TJ, Lichterfeld M, Lauffenburger D, Rosenberg ES, Allen T, Altfeld M, Charles RC, Østergaard L, Tolstrup M, Barouch DH, Søgaard OS, Alter G. HIV Antibody Fc N-Linked Glycosylation Is Associated with Viral Rebound. Cell Rep. 2020 12 15; 33(11):108502. PMID: 33326789.
    Citations: 2     Fields:    
  8. Maldini CR, Claiborne DT, Okawa K, Chen T, Dopkin DL, Shan X, Power KA, Trifonova RT, Krupp K, Phelps M, Vrbanac VD, Tanno S, Bateson T, Leslie GJ, Hoxie JA, Boutwell CL, Riley JL, Allen TM. Dual CD4-based CAR T cells with distinct costimulatory domains mitigate HIV pathogenesis in vivo. Nat Med. 2020 11; 26(11):1776-1787. PMID: 32868878.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  9. 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 05; 16(5):e1008577. PMID: 32392227.
    Citations:    Fields:    Translation:HumansCells
  10. 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: 6     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  11. 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: 43     Fields:    Translation:HumansAnimals
  12. 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: 40     Fields:    Translation:HumansCells
  13. 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: 2     
  14. 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: 1     Fields:    Translation:HumansCells
  15. 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: 35     Fields:    Translation:HumansAnimalsPHPublic Health
  16. 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. . 2019 01 09; 25(1):73-86.e5. PMID: 30629922.
    Citations: 4     Translation:HumansAnimalsCells
  17. 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: 2     Fields:    Translation:HumansCells
  18. 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: 7     Fields:    Translation:AnimalsCells
  19. 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: 5     Fields:    Translation:HumansCells
  20. 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: 24     Fields:    Translation:HumansCells
  21. 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: 19     Fields:    Translation:HumansAnimalsCells
  22. 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: 3     Fields:    Translation:AnimalsCells
  23. 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: 9     Fields:    Translation:AnimalsCells
  24. 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
  25. 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: 5     Fields:    Translation:HumansCells
  26. 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: 17     Fields:    Translation:AnimalsCells
  27. 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: 257     Fields:    Translation:HumansAnimalsCells
  28. 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: 22     Fields:    Translation:HumansCells
  29. 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: 9     Fields:    Translation:HumansCells
  30. 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: 15     Fields:    Translation:Animals
  31. 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: 49     Fields:    Translation:HumansCells
  32. 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: 42     Fields:    Translation:HumansCells
  33. 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: 9     Fields:    Translation:HumansCells
  34. 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: 4     Fields:    
  35. 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: 8     Fields:    Translation:HumansCellsCTClinical Trials
  36. 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: 3     
  37. 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: 9     Fields:    Translation:HumansCells
  38. 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: 5     Fields:    Translation:HumansCells
  39. 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: 19     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  40. 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: 5     Fields:    Translation:HumansCells
  41. 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: 45     Fields:    Translation:HumansAnimalsCells
  42. 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: 30     Fields:    Translation:HumansCells
  43. 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: 167     Fields:    Translation:HumansAnimalsCells
  44. 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:    
  45. 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:    
  46. 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:    
  47. 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: 15     Fields:    Translation:HumansCells
  48. 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: 10     Fields:    Translation:HumansCells
  49. 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: 15     Fields:    Translation:HumansCells
  50. 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: 132     Fields:    Translation:HumansCells
  51. 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: 9     Fields:    Translation:HumansAnimalsCells
  52. 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: 22     Fields:    Translation:HumansCells
  53. 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: 13     Fields:    Translation:HumansCells
  54. 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: 32     Fields:    
  55. 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: 6     Fields:    Translation:HumansCells
  56. 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: 9     Fields:    Translation:HumansAnimals
  57. 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: 8     Fields:    Translation:HumansAnimalsCells
  58. 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: 52     Fields:    Translation:HumansCells
  59. 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: 46     Fields:    Translation:HumansAnimalsCells
  60. 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: 50     Fields:    Translation:HumansAnimalsCells
  61. 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: 12     Fields:    Translation:HumansCells
  62. 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: 75     Fields:    Translation:HumansCells
  63. 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: 33     Fields:    Translation:HumansCells
  64. 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
  65. 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: 15     Fields:    Translation:HumansCells
  66. 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: 109     Fields:    Translation:HumansAnimalsCells
  67. 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: 48     Fields:    Translation:HumansCells
  68. 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: 57     Fields:    Translation:HumansAnimalsCells
  69. 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: 123     Fields:    Translation:HumansCells
  70. 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: 12     Fields:    Translation:HumansCells
  71. 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: 64     Fields:    Translation:Cells
  72. 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: 38     Fields:    Translation:HumansCells
  73. 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: 186     Fields:    Translation:HumansCells
  74. 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: 96     Fields:    Translation:HumansCells
  75. 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: 96     Fields:    Translation:HumansCells
  76. 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: 9     Fields:    Translation:HumansCells
  77. 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: 22     Fields:    Translation:HumansCells
  78. 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: 14     Fields:    Translation:HumansCells
  79. 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
  80. 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: 6     Fields:    Translation:HumansCells
  81. 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: 172     Fields:    Translation:HumansCells
  82. 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: 96     Fields:    Translation:HumansCells
  83. 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: 101     Fields:    Translation:HumansAnimalsCells
  84. 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: 14     Fields:    Translation:HumansCells
  85. 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: 40     Fields:    Translation:HumansCells
  86. 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: 153     Fields:    Translation:HumansCells
  87. 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: 6     Fields:    Translation:HumansCells
  88. 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, et al. 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: 597     Fields:    Translation:HumansCells
  89. 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: 45     Fields:    Translation:HumansCells
  90. 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: 62     Fields:    Translation:HumansCells
  91. 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: 78     Fields:    Translation:HumansCells
  92. 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: 144     Fields:    Translation:HumansCells
  93. 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: 26     Fields:    Translation:HumansCells
  94. 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: 42     Fields:    Translation:HumansCells
  95. 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
  96. 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: 27     Fields:    Translation:HumansAnimalsCells
  97. 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: 7     Fields:    Translation:HumansCells
  98. 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: 239     Fields:    Translation:HumansCells
  99. 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: 26     Fields:    Translation:Cells
  100. 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: 58     Fields:    Translation:HumansCells
  101. 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: 14     Fields:    Translation:HumansCells
  102. 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: 2     Fields:    Translation:HumansCells
  103. 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: 173     Fields:    Translation:HumansCells
  104. 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: 39     Fields:    Translation:HumansAnimalsCells
  105. 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: 125     Fields:    Translation:HumansCells
  106. 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: 76     Fields:    Translation:HumansCells
  107. 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: 8     Fields:    Translation:HumansCells
  108. 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: 40     Fields:    Translation:HumansCells
  109. 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: 78     Fields:    Translation:HumansCells
  110. 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: 6     Fields:    Translation:HumansCells
  111. 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: 63     Fields:    Translation:HumansCells
  112. 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: 122     Fields:    Translation:HumansCells
  113. 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: 72     Fields:    Translation:HumansCells
  114. 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.