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List of works by Todd M Allen

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

scientific article

A viral CTL escape mutation leading to immunoglobulin-like transcript 4-mediated functional inhibition of myelomonocytic cells

scientific article

Adaptation of HIV-1 to human leukocyte antigen class I

scientific article published on 25 February 2009

Analysis of Gag-specific Cytotoxic T Lymphocytes in Simian Immunodeficiency Virus–infected Rhesus Monkeys by Cell Staining with a Tetrameric Major Histocompatibility Complex Class I–Peptide Complex ⬇️

scientific article published on May 4, 1998

Antigen load and viral sequence diversification determine the functional profile of HIV-1-specific CD8+ T cells

scientific article (publication date: 6 May 2008)

Antigen recognition-triggered drug delivery mediated by nanocapsule-functionalized cytotoxic T-cells

scientific article published on 25 November 2016

Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion

scientific article published on October 2016

Broad repertoire of the CD4+ Th cell response in spontaneously controlled hepatitis C virus infection includes dominant and highly promiscuous epitopes

scientific article

Broadly directed virus-specific CD4+ T cell responses are primed during acute hepatitis C infection, but rapidly disappear from human blood with viral persistence ⬇️

scientific article published on January 2, 2012

CD8 Epitope Escape and Reversion in Acute HCV Infection

scientific article

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification ⬇️

scientific article published on September 8, 2012

Constraints on HIV-1 evolution and immunodominance revealed in monozygotic adult twins infected with the same virus

scientific article

Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes

scientific article published on 20 December 2005

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

scientific article

Cutting edge: Prolonged exposure to HIV reinforces a poised epigenetic program for PD-1 expression in virus-specific CD8 T cells

scientific article published on 14 June 2013

De novo generation of escape variant-specific CD8+ T-cell responses following cytotoxic T-lymphocyte escape in chronic human immunodeficiency virus type 1 infection

scientific article

Definition of the viral targets of protective HIV-1-specific T cell responses

scientific article published on 7 December 2011

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

scientific article

Differences in the expressed HLA class I alleles effect the differential clustering of HIV type 1-specific T cell responses in infected Chinese and caucasians

scientific article published in May 2004

Differential neutralization of human immunodeficiency virus (HIV) replication in autologous CD4 T cells by HIV-specific cytotoxic T lymphocytes

scientific article published on 21 January 2009

Differential regulation of toll-like receptor pathways in acute and chronic HIV-1 infection

scientific article published on March 2012

Differentiation of exhausted CD8<sup>+</sup> T cells after termination of chronic antigen stimulation stops short of achieving functional T cell memory

scientific article published on 26 July 2021

Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA.

scientific article published in December 2004

Dual CD4-based CAR T cells with distinct costimulatory domains mitigate HIV pathogenesis in vivo

scientific article published on 31 August 2020

Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection

scientific article

Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection

scientific article

Enhanced detection of human immunodeficiency virus type 1-specific T-cell responses to highly variable regions by using peptides based on autologous virus sequences

scientific article

Epidemiologically linked transmission of HIV-1 illustrates the impact of host genetics on virological outcome

scientific article published on January 2009

Epigenetic scars of CD8<sup>+</sup> T cell exhaustion persist after cure of chronic infection in humans

scientific article published on 26 July 2021

Erratum: addendum: HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus

scientific article published in Nature

Escape and compensation from early HLA-B57-mediated cytotoxic T-lymphocyte pressure on human immunodeficiency virus type 1 Gag alter capsid interactions with cyclophilin A.

scientific article

Fine specificity and cross-clade reactivity of HIV type 1 Gag-specific CD4+ T cells

scientific article published on March 2004

Fluctuations of functionally distinct CD8+ T-cell clonotypes demonstrate flexibility of the HIV-specific TCR repertoire

scientific article published on December 2005

Frequent and strong antibody-mediated natural killer cell activation in response to HIV-1 Env in individuals with chronic HIV-1 infection

scientific article

Full-breadth analysis of CD8+ T-cell responses in acute hepatitis C virus infection and early therapy

scientific article

Genetic characterization of human immunodeficiency virus type 1 in elite controllers: lack of gross genetic defects or common amino acid changes

scientific article published on 18 June 2008

Gp41-targeted antibodies restore infectivity of a fusion-deficient HIV-1 envelope glycoprotein

scientific article published on 11 May 2020

HIV-1 Nef is preferentially recognized by CD8 T cells in primary HIV-1 infection despite a relatively high degree of genetic diversity

scientific article

HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus

scientific article published in November 2002

HIV-1 viral escape in infancy followed by emergence of a variant-specific CTL response

scientific article published in June 2005

HIV-1-specific cytotoxicity is preferentially mediated by a subset of CD8(+) T cells producing both interferon-gamma and tumor necrosis factor-alpha

scientific article published in April 2004

HLA Alleles Associated with Delayed Progression to AIDS Contribute Strongly to the Initial CD8(+) T Cell Response against HIV-1.

scientific article

HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering

scientific article published on 25 February 2009

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

scientific article published on 30 December 2008

HLA-B63 presents HLA-B57/B58-restricted cytotoxic T-lymphocyte epitopes and is associated with low human immunodeficiency virus load

scientific article

HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1.

scientific article published on 29 October 2008

High Level of PD-1 Expression on Hepatitis C Virus (HCV)-Specific CD8+ and CD4+ T Cells during Acute HCV Infection, Irrespective of Clinical Outcome

scientific article

High resolution analysis of cellular immune responses in resolved and persistent hepatitis C virus infection

scientific article published on September 2004

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data ⬇️

scientific article published on March 15, 2012

Human leukocyte antigen-associated sequence polymorphisms in hepatitis C virus reveal reproducible immune responses and constraints on viral evolution

scientific article published in August 2007

Immunologic evidence for lack of heterologous protection following resolution of HCV in patients with non genotype 1 infection

scientific article (publication date: September 2007)

Immunological and virological impact of highly active antiretroviral therapy initiated during acute HIV-1 infection

scientific article published on 15 August 2006

Impaired Hepatitis C Virus-Specific T Cell Responses and Recurrent Hepatitis C Virus in HIV Coinfection

scientific article

Increased detection of HIV-specific T cell responses by combination of central sequences with comparable immunogenicity

article

Increased sequence diversity coverage improves detection of HIV-specific T cell responses

scientific article published in November 2007

Influence of HLA-B57 on clinical presentation and viral control during acute HIV-1 infection

scientific article published in December 2003

Inhibition of HIV transmission in human cervicovaginal explants and humanized mice using CD4 aptamer-siRNA chimeras ⬇️

scientific article published on May 16, 2011

Limited sequence evolution within persistently targeted CD8 epitopes in chronic human immunodeficiency virus type 1 infection

scientific article

Loss of HIV-1-specific T-cell responses associated with very rapid HIV-1 disease progression

scientific article published in April 2007

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

scientific article published on 9 July 2008

Mutually exclusive T-cell receptor induction and differential susceptibility to human immunodeficiency virus type 1 mutational escape associated with a two-amino-acid difference between HLA class I subtypes

scientific article published on 22 November 2006

Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients

scientific article (publication date: December 2008)

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes ⬇️

scientific article published on November 9, 2010

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.

scientific article

Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers

scientific article published on February 2011

Relative dominance of Gag p24-specific cytotoxic T lymphocytes is associated with human immunodeficiency virus control

scientific article

STI and beyond: the prospects of boosting anti-HIV immune responses

scientific article

Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection

scientific article

Selective depletion of high-avidity human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T cells after early HIV-1 infection

scientific article published on 7 February 2007

Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution

scientific article

Sensitive population profiling and genome assembly of HIV and Flaviviruses using ultra-deep sequencing technologies.

scientific article published on 11 October 2010

Spontaneous control of HCV is associated with expression of HLA-B 57 and preservation of targeted epitopes

scientific article

Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLA-B27-restricted epitope in human immunodeficiency virus type 1 capsid

scientific article published on 2 April 2008

TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection

scientific article published on 10 June 2012

Temporal effect of HLA-B*57 on viral control during primary HIV-1 infection

scientific article

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation

scientific article

The majority of currently circulating human immunodeficiency virus type 1 clade B viruses fail to prime cytotoxic T-lymphocyte responses against an otherwise immunodominant HLA-A2-restricted epitope: implications for vaccine design

scientific article

Transmission and long-term stability of compensated CD8 escape mutations

scientific article published on 17 December 2008

Understanding cytotoxic T‐lymphocyte escape during simian immunodeficiency virus infection ⬇️

scientific article published on October 1, 2001

Use of a novel GFP reporter cell line to examine replication capacity of CXCR4- and CCR5-tropic HIV-1 by flow cytometry

scientific article

Viral Evolution and Escape during Acute HIV‐1 Infection ⬇️

scientific article published on October 15, 2010

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection

scientific article published on 8 March 2012

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