Uncovering the Tumor Antigen Landscape: What to Know about the Discovery Process

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

(2020) Chloe Chong et al.   Nature Communications

Endogenous TAP-independent MHC-I antigen presentation: not just the ER lumen

(2020) Margarita Del Val et al.   CURRENT OPINION IN IMMUNOLOGY

Turning the corner on therapeutic cancer vaccines

(2019) Robert E. Hollingsworth et al.   npj Vaccines

APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations

(2019) Jayvee Abella et al.   MOLECULES

ACME: Pan-specific peptide-MHC class I binding prediction through attention-based deep neural networks

(2019) Yan Hu et al.   BIOINFORMATICS

Efficacy and Safety Analysis of Nelipepimut-S Vaccine to Prevent Breast Cancer Recurrence: A Randomized, Multicenter, Phase III Clinical Trial

(2019) Elizabeth A. Mittendorf et al.   CLINICAL CANCER RESEARCH

Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics

(2019) Anthony W. Purcell et al.   Nature Protocols

DeepLigand: accurate prediction of MHC class I ligands using peptide embedding

(2019) Haoyang Zeng et al.   BIOINFORMATICS

Combination of CTLA-4 and PD-1 blockers for treatment of cancer

(2019) Anand Rotte   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space

(2019) Masato Ogishi et al.   Frontiers in Immunology

Quantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design

(2019) Haoyang Zeng et al.   Cell Systems

Cancer Testis Antigens and Immunotherapy: Where Do We Stand in the Targeting of PRAME?

(2019) Ghaneya Al-Khadairi et al.   Cancers

TCR-like antibodies in cancer immunotherapy

(2019) Qinghua He et al.   Journal of Hematology & Oncology

Proteogenomic discovery of cancer antigens: Neoantigens and beyond

(2019) Takayuki Kanaseki et al.   PATHOLOGY INTERNATIONAL

The Human Immunopeptidome Project: a roadmap to predict and treat immune diseases

(2019) Juan Antonio Vizcaíno et al.   MOLECULAR & CELLULAR PROTEOMICS

NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions

(2019) Bruno Alvarez et al.   MOLECULAR & CELLULAR PROTEOMICS

IPD-IMGT/HLA Database

(2019) James Robinson et al.   NUCLEIC ACIDS RESEARCH

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium

(2019) Dmitry V Bagaev et al.   NUCLEIC ACIDS RESEARCH

TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes

(2019) Kamilla Kjærgaard Jensen et al.   Scientific Reports

Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires

(2019) Sofie Gielis et al.   Frontiers in Immunology

DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity

(2019) Jingcheng Wu et al.   Frontiers in Immunology

Peptide-Major Histocompatibility Complex Class I Binding Prediction Based on Deep Learning With Novel Feature

(2019) Tianyi Zhao et al.   Frontiers in Genetics

Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation

(2018) Markus W. Löffler et al.   CANCER RESEARCH

The Role of Mass Spectrometry and Proteogenomics in the Advancement of HLA Epitope Prediction

(2018) Amanda L. Creech et al.   PROTEOMICS

General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept

(2018) Dinler A. Antunes et al.   Scientific Reports

HERVs New Role in Cancer: From Accused Perpetrators to Cheerful Protectors

(2018) Norbert Bannert et al.   Frontiers in Microbiology

NY-ESO-1 Based Immunotherapy of Cancer: Current Perspectives

(2018) Remy Thomas et al.   Frontiers in Immunology

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

(2018) Timothy J. O'Donnell et al.   Cell Systems

Human endogenous retroviruses and their implication for immunotherapeutics of cancer

(2018) A S Attermann et al.   ANNALS OF ONCOLOGY

Cytosolic Processing Governs TAP-Independent Presentation of a Critical Melanoma Antigen

(2018) Nathalie Vigneron et al.   JOURNAL OF IMMUNOLOGY

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome

(2018) Roman Mylonas et al.   MOLECULAR & CELLULAR PROTEOMICS

Epigenetic regulation of MAGE family in human cancer progression-DNA methylation, histone modification, and non-coding RNAs

(2018) Yishui Lian et al.   Clinical Epigenetics

Predicting Antigen Presentation—What Could We Learn From a Million Peptides?

(2018) David Gfeller et al.   Frontiers in Immunology

Cancer Neoantigens

(2018) Ton N. Schumacher et al.   Annual Review of Immunology

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments

(2018) Massimo Andreatta et al.   PROTEOMICS

A Case for a Human Immuno-Peptidome Project Consortium

(2017) Etienne Caron et al.   IMMUNITY

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome

(2017) Chloe Chong et al.   MOLECULAR & CELLULAR PROTEOMICS

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens

(2017) Michael S. Khodadoust et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

STCRDab: the structural T-cell receptor database

(2017) Jinwoo Leem et al.   NUCLEIC ACIDS RESEARCH

GibbsCluster: unsupervised clustering and alignment of peptide sequences

(2017) Massimo Andreatta et al.   NUCLEIC ACIDS RESEARCH

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

(2017) Mikhail Shugay et al.   NUCLEIC ACIDS RESEARCH

ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes

(2017) Tyler Borrman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Soluble HLA-associated peptide from PSF1 has a cancer vaccine potency

(2017) Mari Yoshida et al.   Scientific Reports

Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia

(2017) Stacy A. Malaker et al.   Cancer Immunology Research

PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity

(2017) Geng Liu et al.   GigaScience

Detection of an Immunogenic HERV-E Envelope with Selective Expression in Clear Cell Kidney Cancer

(2016) Elena Cherkasova et al.   CANCER RESEARCH

Immunotherapy against cancer-related viruses

(2016) Haruko Tashiro et al.   CELL RESEARCH

Mass spectrometry-based antigen discovery for cancer immunotherapy

(2016) Michal Bassani-Sternberg et al.   CURRENT OPINION IN IMMUNOLOGY

The development and use of the E75 (HER2 369–377) peptide vaccine

(2016) Guy T Clifton et al.   Future Oncology

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide–HLA Interactions

(2016) Michal Bassani-Sternberg et al.   JOURNAL OF IMMUNOLOGY

Pan-Specific Prediction of Peptide–MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity

(2016) Michael Rasmussen et al.   JOURNAL OF IMMUNOLOGY

The Length Distribution of Class I–Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele–Specific Binding Preference

(2016) Thomas Trolle et al.   JOURNAL OF IMMUNOLOGY

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

(2016) Michal Bassani-Sternberg et al.   Nature Communications

Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens

(2016) Shelly Kalaora et al.   Oncotarget

Global burden of cancers attributable to infections in 2012: a synthetic analysis

(2016) Martyn Plummer et al.   Lancet Global Health

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

(2015) Massimo Andreatta et al.   BIOINFORMATICS

CD19-targeted chimeric antigen receptor T-cell therapy for acute lymphoblastic leukemia

(2015) S. L. Maude et al.   BLOOD

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Immune Checkpoint Targeting in Cancer Therapy: Toward Combination Strategies with Curative Potential

(2015) Padmanee Sharma et al.   CELL

The MAGE protein family and cancer

(2015) Jenny L Weon et al.   CURRENT OPINION IN CELL BIOLOGY

An overview of bioinformatics tools for epitope prediction: Implications on vaccine development

(2015) Ruth E. Soria-Guerra et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Tumor neoantigens: building a framework for personalized cancer immunotherapy

(2015) Matthew M. Gubin et al.   JOURNAL OF CLINICAL INVESTIGATION

Landscape of Tumor Antigens in T Cell Immunotherapy

(2015) S. Ilyas et al.   JOURNAL OF IMMUNOLOGY

LYRA, a webserver for lymphocyte receptor structural modeling

(2015) Michael Schantz Klausen et al.   NUCLEIC ACIDS RESEARCH

Adoptive cell transfer as personalized immunotherapy for human cancer

(2015) S. A. Rosenberg et al.   SCIENCE

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

The future of immune checkpoint therapy

(2015) P. Sharma et al.   SCIENCE

DockTope: a Web-based tool for automated pMHC-I modelling

(2015) Maurício Menegatti Rigo et al.   Scientific Reports

Immunoinformatics and epitope prediction in the age of genomic medicine

(2015) Linus Backert et al.   Genome Medicine

Human Tumor Antigens and Cancer Immunotherapy

(2015) Nathalie Vigneron   Biomed Research International

Accurate Prediction of Immunogenic T-Cell Epitopes from Epitope Sequences Using the Genetic Algorithm-Based Ensemble Learning

(2015) Wen Zhang et al.   PLoS One

A Recombinant Modified Vaccinia Ankara Vaccine Encoding Epstein-Barr Virus (EBV) Target Antigens: A Phase I Trial in UK Patients with EBV-Positive Cancer

(2014) G. S. Taylor et al.   CLINICAL CANCER RESEARCH

NetTepi: an integrated method for the prediction of T cell epitopes

(2014) Thomas Trolle et al.   IMMUNOGENETICS

Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs

(2014) Jorg J. A. Calis et al.   IMMUNOGENETICS

Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes

(2014) Chopie Hassan et al.   Journal of Proteomics

Direct Interrogation of Viral Peptides Presented by the Class I HLA of HIV-Infected T Cells

(2014) J. C. Yaciuk et al.   JOURNAL OF VIROLOGY

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL)

(2014) Daniel J. Kowalewski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immunotherapeutic Agents in Non-small-cell Lung Cancer Finally Coming to the Front Lines

(2014) Rossana Ruiz et al.   Current Oncology Reports

NetMHCstab- predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery

(2013) Kasper W. Jørgensen et al.   IMMUNOLOGY

Discovering naturally processed antigenic determinants that confer protective T cell immunity

(2013) Pavlo Gilchuk et al.   JOURNAL OF CLINICAL INVESTIGATION

Comparison of Vaccine-Induced Effector CD8 T Cell Responses Directed against Self- and Non-Self-Tumor Antigens: Implications for Cancer Immunotherapy

(2013) S. R. Pedersen et al.   JOURNAL OF IMMUNOLOGY

Cancer Regression and Neurological Toxicity Following Anti-MAGE-A3 TCR Gene Therapy

(2013) Richard A. Morgan et al.   JOURNAL OF IMMUNOTHERAPY

Treatment of Metastatic Renal Cell Carcinoma With CAIX CAR-engineered T cells: Clinical Evaluation and Management of On-target Toxicity

(2013) Cor HJ Lamers et al.   MOLECULAR THERAPY

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

(2013) Jorg J. A. Calis et al.   PLoS Computational Biology

Abacavir induces loading of novel self-peptides into HLA-B*57

(2012) Michael A. Norcross et al.   AIDS

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

(2012) Massimo Andreatta et al.   BIOINFORMATICS

PAAQD: Predicting immunogenicity of MHC class I binding peptides using amino acid pairwise contact potentials and quantum topological molecular similarity descriptors

(2012) Thammakorn Saethang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Human Papillomavirus Type 16 E6/E7-specific Cytotoxic T Lymphocytes for Adoptive Immunotherapy of HPV-associated Malignancies

(2012) Carlos A. Ramos et al.   JOURNAL OF IMMUNOTHERAPY

Secreted HLA recapitulates the immunopeptidome and allows in-depth coverage of HLA A*02:01 ligands

(2012) Katherine E. Scull et al.   MOLECULAR IMMUNOLOGY

High-avidity cytotoxic T lymphocytes specific for a new PRAME-derived peptide can target leukemic and leukemic-precursor cells

(2011) C. Quintarelli et al.   BLOOD

B-cell depletion and remissions of malignancy along with cytokine-associated toxicity in a clinical trial of anti-CD19 chimeric-antigen-receptor-transduced T cells

(2011) J. N. Kochenderfer et al.   BLOOD

POPISK: T-cell reactivity prediction using support vector machines and string kernels

(2011) Chun-Wei Tung et al.   BMC BIOINFORMATICS

Insights into the processing of MHC class I ligands gained from the study of human tumor epitopes

(2011) Nathalie Vigneron et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions

(2011) Edita Karosiene et al.   IMMUNOGENETICS

The biology of cancer testis antigens: Putative function, regulation and therapeutic potential

(2011) Elisabetta Fratta et al.   Molecular Oncology

Eradication of B-lineage cells and regression of lymphoma in a patient treated with autologous T cells genetically engineered to recognize CD19

(2010) J. N. Kochenderfer et al.   BLOOD

HLA-A2-restricted T-cell epitopes specific for prostatic acid phosphatase

(2010) Brian M. Olson et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

The SSX Family of Cancer-Testis Antigens as Target Proteins for Tumor Therapy

(2010) Heath A. Smith et al.   Clinical & Developmental Immunology

NetCTLpan: pan-specific MHC class I pathway epitope predictions

(2010) Thomas Stranzl et al.   IMMUNOGENETICS

T Cells Targeting Carcinoembryonic Antigen Can Mediate Regression of Metastatic Colorectal Cancer but Induce Severe Transient Colitis

(2010) Maria R Parkhurst et al.   MOLECULAR THERAPY

Soluble plasma HLA peptidome as a potential source for cancer biomarkers

(2010) M. Bassani-Sternberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Impact of HER2/neu Expression Level on Response to the E75 Vaccine: From U.S. Military Cancer Institute Clinical Trials Group Study I-01 and I-02

(2009) L. C. Benavides et al.   CLINICAL CANCER RESEARCH

MAGRIT: The Largest-Ever Phase III Lung Cancer Trial Aims to Establish a Novel Tumor-Specific Approach to Therapy

(2009) Preeta Tyagi et al.   Clinical Lung Cancer

HLA class I molecules consistently present internal influenza epitopes

(2009) A. Wahl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HLA class I supertypes: a revised and updated classification

(2008) John Sidney et al.   BMC IMMUNOLOGY

The History of Tumor Virology

(2008) R. T. Javier et al.   CANCER RESEARCH

Epitope Landscape in Breast and Colorectal Cancer

(2008) N. H. Segal et al.   CANCER RESEARCH

Characterization of Genetically Modified T-Cell Receptors that Recognize the CEA:691-699 Peptide in the Context of HLA-A2.1 on Human Colorectal Cancer Cells

(2008) M. R. Parkhurst et al.   CLINICAL CANCER RESEARCH

Features of TAP-independent MHC class I ligands revealed by quantitative mass spectrometry

(2008) Andreas O. Weinzierl et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Regression of human kidney cancer following allogeneic stem cell transplantation is associated with recognition of an HERV-E antigen by T cells

(2008) Yoshiyuki Takahashi et al.   JOURNAL OF CLINICAL INVESTIGATION

CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens

(2008) L. G. Almeida et al.   NUCLEIC ACIDS RESEARCH

EBV-Associated Lymphoproliferative Disorders: Classification and Treatment

(2008) A. Carbone et al.   ONCOLOGIST