List of works - John Sidney

A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach

scientific article

NetMHCpan, a method for MHC class I binding prediction beyond humans

scientific article published on 12 November 2008

HLA class I supertypes: a revised and updated classification

scientific article

A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus

scientific article

Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells

scientific article published on 11 April 2013

Reversion of CTL escape–variant immunodeficiency viruses in vivo

article

The immune epitope database and analysis resource: from vision to blueprint

scientific article

Identification of poxvirus CD8+ T cell determinants to enable rational design and characterization of smallpox vaccines

scientific article published on 28 December 2004

Peptide binding predictions for HLA DR, DP and DQ molecules

scientific article

A Protective Role for Dengue Virus-Specific CD8+ T Cells

scientific article (publication date: 15 April 2009)

Cellular immune selection with hepatitis C virus persistence in humans

scientific article

Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data

scientific article

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries

scientific article

A community resource benchmarking predictions of peptide binding to MHC-I molecules

scientific article published on 9 June 2006

Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

scientific article

Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire

scientific article

Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes

scientific article published on 9 February 2011

Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity

scientific article

Human Ebola virus infection results in substantial immune activation

scientific article

Naive precursor frequencies and MHC binding rather than the degree of epitope diversity shape CD8+ T cell immunodominance

scientific article published in August 2008

Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications

scientific article published on 3 May 2005

Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes

scholarly article

Immunomic analysis of the repertoire of T-cell specificities for influenza A virus in humans

scientific article published on 08 October 2008

Dengue virus infection elicits highly polarized CX3CR1+ cytotoxic CD4+ T cells associated with protective immunity

scientific article published on 20 July 2015

T cells from patients with Parkinson's disease recognize α-synuclein peptides

scientific article

Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset

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

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

scientific article

Predicting population coverage of T-cell epitope-based diagnostics and vaccines

scientific article published on 17 March 2006

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

scientific article published on February 2017

Comprehensive analysis of human immunodeficiency virus type 1-specific CD4 responses reveals marked immunodominance of gag and nef and the presence of broadly recognized peptides

scientific article published on May 2004

A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infection

scientific article

Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses

scientific article published in April 2006

Molecular determinants of T cell epitope recognition to the common Timothy grass allergen

scientific article published on 16 June 2010

HLA class I-restricted responses to vaccinia recognize a broad array of proteins mainly involved in virulence and viral gene regulation

scientific article

HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity

scientific article

A large fraction of HLA class I ligands are proteasome-generated spliced peptides.

scientific article published on 20 October 2016

High-functional-avidity cytotoxic T lymphocyte responses to HLA-B-restricted Gag-derived epitopes associated with relative HIV control

scientific article published on 13 July 2011

Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines

scientific article

Rationally engineered therapeutic proteins with reduced immunogenicity

scientific article published in March 2005

Immunodominant tuberculosis CD8 antigens preferentially restricted by HLA-B

scientific article

High-programmed death-1 levels on hepatitis C virus-specific T cells during acute infection are associated with viral persistence and require preservation of cognate antigen during chronic infection

scientific article

The human CD8+ T cell responses induced by a live attenuated tetravalent dengue vaccine are directed against highly conserved epitopes

scientific article

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

scientific article published on 16 March 2020

Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design

scientific article

Two MHC class I molecules associated with elite control of immunodeficiency virus replication, Mamu-B08 and HLA-B2705, bind peptides with sequence similarity

scientific article

Poxvirus CD8+ T-cell determinants and cross-reactivity in BALB/c mice

scientific article

Extensive HLA class I allele promiscuity among viral CTL epitopes

scientific article published on September 2007

Identification of seventeen new simian immunodeficiency virus-derived CD8+ T cell epitopes restricted by the high frequency molecule, Mamu-A*02, and potential escape from CTL recognition

scientific article published in October 2004

Relapse or eradication of cancer is predicted by peptide-major histocompatibility complex affinity

scientific article

List of works by John Sidney

A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach

NetMHCpan, a method for MHC class I binding prediction beyond humans

HLA class I supertypes: a revised and updated classification

A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus

Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells

Reversion of CTL escape–variant immunodeficiency viruses in vivo

The immune epitope database and analysis resource: from vision to blueprint

Identification of poxvirus CD8+ T cell determinants to enable rational design and characterization of smallpox vaccines

Peptide binding predictions for HLA DR, DP and DQ molecules

A Protective Role for Dengue Virus-Specific CD8+ T Cells

Cellular immune selection with hepatitis C virus persistence in humans

Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries

A community resource benchmarking predictions of peptide binding to MHC-I molecules

Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire

Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes

Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity

Human Ebola virus infection results in substantial immune activation

Naive precursor frequencies and MHC binding rather than the degree of epitope diversity shape CD8+ T cell immunodominance

Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications

Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes

Immunomic analysis of the repertoire of T-cell specificities for influenza A virus in humans

Dengue virus infection elicits highly polarized CX3CR1+ cytotoxic CD4+ T cells associated with protective immunity

T cells from patients with Parkinson's disease recognize α-synuclein peptides

Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset

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

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

Predicting population coverage of T-cell epitope-based diagnostics and vaccines

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

Comprehensive analysis of human immunodeficiency virus type 1-specific CD4 responses reveals marked immunodominance of gag and nef and the presence of broadly recognized peptides

A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infection

Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses

Molecular determinants of T cell epitope recognition to the common Timothy grass allergen

HLA class I-restricted responses to vaccinia recognize a broad array of proteins mainly involved in virulence and viral gene regulation

HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity

A large fraction of HLA class I ligands are proteasome-generated spliced peptides.

High-functional-avidity cytotoxic T lymphocyte responses to HLA-B-restricted Gag-derived epitopes associated with relative HIV control

Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines

Rationally engineered therapeutic proteins with reduced immunogenicity

Immunodominant tuberculosis CD8 antigens preferentially restricted by HLA-B

High-programmed death-1 levels on hepatitis C virus-specific T cells during acute infection are associated with viral persistence and require preservation of cognate antigen during chronic infection

The human CD8+ T cell responses induced by a live attenuated tetravalent dengue vaccine are directed against highly conserved epitopes

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design

Two MHC class I molecules associated with elite control of immunodeficiency virus replication, Mamu-B*08 and HLA-B*2705, bind peptides with sequence similarity

Poxvirus CD8+ T-cell determinants and cross-reactivity in BALB/c mice

Extensive HLA class I allele promiscuity among viral CTL epitopes

Identification of seventeen new simian immunodeficiency virus-derived CD8+ T cell epitopes restricted by the high frequency molecule, Mamu-A*02, and potential escape from CTL recognition

Relapse or eradication of cancer is predicted by peptide-major histocompatibility complex affinity

Two MHC class I molecules associated with elite control of immunodeficiency virus replication, Mamu-B08 and HLA-B2705, bind peptides with sequence similarity