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Allen, Todd
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Todd Allen, Ph.D.
Title
Professor of Medicine
Institution
Massachusetts General Hospital
Department
Medicine
Address
Ragon Institute of MGH, MIT and Harvard
Rm 764
400 Technology Square
Cambridge MA 02139
Phone
857/268-7002
Fax
857/268-7141
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overview
|
research activities and funding
|
selected publications
|
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
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
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
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
U19HL129903
(SCADDEN, DAVID T)
Apr 1, 2015 - Mar 31, 2021
NIH
A defend and destroy approach to curing HIV
Role: Co-Principal Investigator
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
R01AI090698
(ALLEN, TODD M)
Jun 1, 2010 - May 31, 2015
NIH
Protective Role of Subdominant Responses to HIV Restricted by Common HLA Alleles
Role: Principal Investigator
U19AI082630
(CHUNG, RAYMOND T)
Jun 8, 2009 - May 31, 2024
NIH
Impact of Immunotherapy on Viral Immunity in Humans
Role: Co-Principal Investigator
P01AI074415
(ALLEN, TODD M)
Sep 26, 2008 - Jul 31, 2015
NIH
Acute HIV Infection: Implications for vaccine design
Role: Principal Investigator
R21AI076706
(ALTFELD, MARCUS)
Jan 15, 2008 - Dec 31, 2009
NIH
Impact of NK Cell Immune Pressures on HCV Evolution and Viral Fitness
Role: Principal Investigator
R01AI067926
(ALLEN, TODD M)
Aug 15, 2006 - Jan 31, 2011
NIH
CD8 T Cell Selective Pressure and HCV Sequence Evolution
Role: Principal Investigator
U19AI066345
(LAUER, GEORG MICHAEL)
Aug 17, 2005 - Jul 31, 2016
NIH
Immune Control and Evasion during Acute HCV Infection
Role: Co-Principal Investigator
R21AI067078
(ALLEN, TODD M)
Jul 1, 2005 - Jun 30, 2007
NIH
Impact of CD8 Escape Mutations on Capsid Structure/Host
Role: Principal Investigator
R56AI054178
(ALLEN, TODD M)
Jan 1, 2003 - Aug 31, 2011
NIH
Impact of CTL Escape Mutations on HIV-1 Replicative Fitness
Role: Principal Investigator
R01AI054178
(ALLEN, TODD M)
Jan 1, 2003 - Dec 31, 2008
NIH
Acute CTL Escape and Viral Variation in HIV
Role: Principal Investigator
R01AI051231
(HUNTER, ERIC)
Mar 15, 2002 - Mar 31, 2023
NIH
Virologic Correlates of Heterosexual Transmission
Role: Co-Principal Investigator
P51RR000167
(CADWALLADER, MARTIN)
Jun 1, 1976 - Apr 30, 2013
NIH/NCRR
Wisconsin National Primate Research Center Support
Role: Co-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.
Jenkins RA, Whitney BM, Nance RM,
Allen TM
, Cooper HLF, Feinberg J, Fredericksen R, Friedmann PD, Go VF, Jenkins WD, Korthuis PT, Miller WC, Pho MT, Rudolph AE, Seal DW, Smith GS, Stopka TJ, Westergaard RP, Young AM, Zule WA, Delaney JAC, Tsui JI, Crane HM. The Rural Opioid Initiative Consortium description: providing evidence to Understand the Fourth Wave of the Opioid Crisis. Addict Sci Clin Pract. 2022 07 26; 17(1):38.
PMID:
35883197
; PMCID:
PMC9321271
.
Citations:
Fields:
Sub
Substance-Related Disorders
Translation:
Humans
PH
Public Health
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. 2022 03 23; 74(6):993-1003.
PMID:
34448809
; PMCID:
PMC8946742
.
Citations:
Fields:
Com
Communicable Diseases
Translation:
Humans
Cells
Calvet-Mirabent M, Claiborne DT, Deruaz M, Tanno S, Serra C, Delgado-Arévalo C, Sánchez-Cerrillo I, de Los Santos I, Sanz J, García-Fraile L, Sánchez-Madrid F, Alfranca A, Muñoz-Fernández MÁ,
Allen TM
, Buzón MJ,
Balazs A
, Vrbanac V, Martín-Gayo E. Poly I:C and STING agonist-primed DC increase lymphoid tissue polyfunctional HIV-1-specific CD8+ T cells and limit CD4+ T-cell loss in BLT mice. Eur J Immunol. 2022 03; 52(3):447-461.
PMID:
34935145
.
Citations:
1
Fields:
All
Allergy and Immunology
Translation:
Animals
Cells
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
; PMCID:
PMC8516715
.
Citations:
3
Fields:
All
Allergy and Immunology
Translation:
Humans
Cells
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
; PMCID:
PMC8323980
.
Citations:
8
Fields:
All
Allergy and Immunology
Translation:
Humans
Cells
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
; PMCID:
PMC8600539
.
Citations:
21
Fields:
All
Allergy and Immunology
Translation:
Humans
Cells
CT
Clinical Trials
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:
3
Fields:
All
Allergy and Immunology
Translation:
Humans
Animals
Cells
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
; PMCID:
PMC7853590
.
Citations:
Fields:
Com
Communicable Diseases
Translation:
Humans
Cells
PH
Public Health
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:
5
Fields:
Cel
Cell Biology
Mol
Molecular Biology
Translation:
Humans
Cells
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
; PMCID:
PMC9422086
.
Citations:
17
Fields:
Med
Medicine (General)
Mol
Molecular Biology
Translation:
Humans
Animals
Cells
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
; PMCID:
PMC7241850
.
Citations:
Fields:
Mic
Microbiology
Translation:
Humans
Cells
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:
Vir
Virology
Translation:
Humans
Animals
Cells
PH
Public Health
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
; PMCID:
PMC7265413
.
Citations:
57
Fields:
All
Allergy and Immunology
Translation:
Humans
Animals
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
; PMCID:
PMC6855781
.
Citations:
47
Fields:
Sci
Science
Translation:
Humans
Cells
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
; PMCID:
PMC6521154
.
Citations:
2
Fields:
Vir
Virology
Translation:
Humans
Cells
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
; PMCID:
PMC6483127
.
Citations:
3
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:
44
Fields:
Bio
Biotechnology
Translation:
Humans
Animals
PH
Public Health
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
; PMCID:
PMC6456338
.
Citations:
6
Fields:
Mic
Microbiology
Translation:
Humans
Animals
Cells
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
; PMCID:
PMC6321908
.
Citations:
2
Fields:
Vir
Virology
Translation:
Humans
Cells
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
; PMCID:
PMC6069176
.
Citations:
7
Fields:
Vir
Virology
Translation:
Animals
Cells
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:
7
Fields:
Vir
Virology
Translation:
Humans
Cells
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
; PMCID:
PMC5708133
.
Citations:
28
Fields:
All
Allergy and Immunology
Translation:
Humans
Cells
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
; PMCID:
PMC5625479
.
Citations:
27
Fields:
Vir
Virology
Translation:
Humans
Animals
Cells
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
; PMCID:
PMC5628771
.
Citations:
6
Fields:
Mol
Molecular Biology
The
Therapeutics
Translation:
Animals
Cells
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
; PMCID:
PMC5564033
.
Citations:
10
Fields:
Acq
Acquired Immunodeficiency Synd
Translation:
Animals
Cells
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
; PMCID:
PMC5400691
.
Citations:
Fields:
Mic
Microbiology
Translation:
Humans
Cells
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:
9
Fields:
Med
Medicine (General)
Sci
Science
Translation:
Humans
Cells
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
; PMCID:
PMC5204257
.
Citations:
20
Fields:
Bio
Biomedical Engineering
Translation:
Animals
Cells
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
; PMCID:
PMC5497589
.
Citations:
345
Fields:
Sci
Science
Translation:
Humans
Animals
Cells
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:
27
Fields:
All
Allergy and Immunology
Translation:
Humans
Cells
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:
12
Fields:
Gas
Gastroenterology
Translation:
Humans
Cells
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
; PMCID:
PMC4957443
.
Citations:
21
Fields:
Com
Communicable Diseases
Translation:
Animals
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
; PMCID:
PMC4899163
.
Citations:
60
Fields:
Med
Medicine (General)
Mol
Molecular Biology
Translation:
Humans
Cells
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:
50
Fields:
Mic
Microbiology
Translation:
Humans
Cells
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
; PMCID:
PMC5553127
.
Citations:
10
Fields:
Gas
Gastroenterology
Translation:
Humans
Cells
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:
5
Fields:
Med
Medicine (General)
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
; PMCID:
PMC4901184
.
Citations:
12
Fields:
Gas
Gastroenterology
Tra
Transplantation
Translation:
Humans
Cells
CT
Clinical Trials
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
; PMCID:
PMC5096837
.
Citations:
4
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
; PMCID:
PMC4707069
.
Citations:
10
Fields:
All
Allergy and Immunology
Translation:
Humans
Cells
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
; PMCID:
PMC4702586
.
Citations:
7
Fields:
Vir
Virology
Translation:
Humans
Cells
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
; PMCID:
PMC4621113
.
Citations:
21
Fields:
Vir
Virology
Translation:
Humans
Animals
Cells
PH
Public Health
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
; PMCID:
PMC4487201
.
Citations:
5
Fields:
Vir
Virology
Translation:
Humans
Cells
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:
54
Fields:
Vir
Virology
Translation:
Humans
Animals
Cells
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
; PMCID:
PMC4601911
.
Citations:
38
Fields:
Com
Communicable Diseases
Translation:
Humans
Cells
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:
207
Fields:
Cel
Cell Biology
Translation:
Humans
Animals
Cells
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:
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:
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:
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
; PMCID:
PMC4460793
.
Citations:
18
Fields:
Acq
Acquired Immunodeficiency Synd
Translation:
Humans
Cells
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:
11
Fields:
Vir
Virology
Translation:
Humans
Cells
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:
21
Fields:
All
Allergy and Immunology
Translation:
Humans
Cells
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
; PMCID:
PMC4289910
.
Citations:
150
Fields:
Sci
Science
Translation:
Humans
Cells
PH
Public Health
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
; PMCID:
PMC4109550
.
Citations:
12
Fields:
Med
Medicine (General)
Translation:
Humans
Animals
Cells
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
; PMCID:
PMC4215080
.
Citations:
23
Fields:
Com
Communicable Diseases
Translation:
Humans
Cells
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
; PMCID:
PMC4264571
.
Citations:
17
Fields:
Med
Medicine (General)
Translation:
Humans
Cells
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:
42
Fields:
Pha
Pharmacology
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:
7
Fields:
Vir
Virology
Translation:
Humans
Cells
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
; PMCID:
PMC3807973
.
Citations:
9
Fields:
Com
Communicable Diseases
Translation:
Humans
Animals
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
; PMCID:
PMC3807972
.
Citations:
12
Fields:
Com
Communicable Diseases
Translation:
Humans
Animals
Cells
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:
64
Fields:
Bio
Biology
Translation:
Humans
Cells
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:
52
Fields:
Med
Medicine (General)
Sci
Science
Translation:
Humans
Animals
Cells
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
; PMCID:
PMC3862274
.
Citations:
59
Fields:
Hem
Hematology
Translation:
Humans
Animals
Cells
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:
14
Fields:
Gas
Gastroenterology
Translation:
Humans
Cells
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
; PMCID:
PMC3702641
.
Citations:
89
Fields:
All
Allergy and Immunology
Translation:
Humans
Cells
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:
35
Fields:
Vir
Virology
Translation:
Humans
Cells
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:
Vir
Virology
Translation:
Humans
Cells
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
; PMCID:
PMC3666132
.
Citations:
16
Fields:
Com
Communicable Diseases
Translation:
Humans
Cells
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:
111
Fields:
Sci
Science
Translation:
Humans
Animals
Cells
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:
50
Fields:
Bio
Biochemistry
Translation:
Humans
Cells
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:
62
Fields:
Med
Medicine (General)
Sci
Science
Translation:
Humans
Animals
Cells
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:
133
Fields:
All
Allergy and Immunology
Translation:
Humans
Cells
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:
13
Fields:
Vir
Virology
Translation:
Humans
Cells
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:
67
Fields:
Com
Computational Biology
Translation:
Cells
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
; PMCID:
PMC3738004
.
Citations:
39
Fields:
Acq
Acquired Immunodeficiency Synd
Translation:
Humans
Cells
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:
199
Fields:
Mic
Microbiology
Translation:
Humans
Cells
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:
110
Fields:
All
Allergy and Immunology
Med
Medicine (General)
Translation:
Humans
Cells
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:
101
Fields:
Med
Medicine (General)
Translation:
Humans
Cells
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:
10
Fields:
Vir
Virology
Translation:
Humans
Cells
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:
25
Fields:
Gas
Gastroenterology
Translation:
Humans
Cells
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:
16
Fields:
Vir
Virology
Translation:
Humans
Cells
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:
Med
Medicine (General)
Sci
Science
Translation:
Humans
Cells
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
; PMCID:
PMC3144167
.
Citations:
7
Fields:
Com
Communicable Diseases
Translation:
Humans
Cells
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:
199
Fields:
Sci
Science
Translation:
Humans
Cells
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:
104
Fields:
Sci
Science
Translation:
Humans
Cells
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
; PMCID:
PMC3104760
.
Citations:
109
Fields:
Med
Medicine (General)
Translation:
Humans
Animals
Cells
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:
Med
Medicine (General)
Sci
Science
Translation:
Humans
Cells
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
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PMID:
21124229
; PMCID:
PMC3078702
.
Citations:
40
Fields:
Acq
Acquired Immunodeficiency Synd
Translation:
Humans
Cells
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
; PMCID:
PMC2994339
.
Citations:
166
Fields:
Med
Medicine (General)
Translation:
Humans
Cells
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:
Com
Computational Biology
Translation:
Humans
Cells
Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI,
Walker BD
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Allen TM
, Altfeld M, Henn MR, Le Gall S, Streeck H, Haas DW,
Kuritzkes DR
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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
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PMID:
21051598
; PMCID:
PMC3235490
.
Citations:
654
Fields:
Sci
Science
Translation:
Humans
Cells
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
; PMCID:
PMC2945609
.
Citations:
48
Fields:
Com
Communicable Diseases
Translation:
Humans
Cells
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
; PMCID:
PMC3021586
.
Citations:
68
Fields:
Gas
Gastroenterology
Translation:
Humans
Cells
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
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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:
81
Fields:
Vir
Virology
Translation:
Humans
Cells
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
; PMCID:
PMC3098720
.
Citations:
147
Fields:
Sci
Science
Translation:
Humans
Cells
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
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Lauer GM
,
Allen TM
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PMID:
20034048
.
Citations:
30
Fields:
Gas
Gastroenterology
Translation:
Humans
Cells
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
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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:
47
Fields:
Vir
Virology
Translation:
Humans
Cells
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
; PMCID:
PMC2800127
.
Citations:
6
Fields:
Eme
Emergency Medicine
Translation:
Humans
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:
29
Fields:
Vir
Virology
Translation:
Humans
Animals
Cells
PH
Public Health
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
; PMCID:
PMC2653266
.
Citations:
7
Fields:
Com
Communicable Diseases
Translation:
Humans
Cells
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
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PMID:
19244334
.
Citations:
27
Fields:
Vir
Virology
Translation:
Cells
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:
246
Fields:
Sci
Science
Translation:
Humans
Cells