Predicting T cell recognition of MHC class I restricted neoepitopes

Neoepitopes as cancer immunotherapy targets: key challenges and opportunities

(2017) Cory A Brennick et al.   Immunotherapy

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

Reconstructing promoter activity from Lux bioluminescent reporters

(2017) Mudassar Iqbal et al.   PLoS Computational Biology

The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design

(2017) Ward Fleri et al.   Frontiers in Immunology

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes

(2017) Anne-Mette Bjerregaard et al.   Frontiers in Immunology

Immune targets and neoantigens for cancer immunotherapy and precision medicine

(2016) Rong-Fu Wang et al.   CELL RESEARCH

Neoantigens encoded in the cancer genome

(2016) Ton N Schumacher et al.   CURRENT OPINION IN IMMUNOLOGY

Nowhere to hide: unconventional translation yields cryptic peptides for immune surveillance

(2016) Shelley R. Starck et al.   IMMUNOLOGICAL REVIEWS

T-cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome

(2016) Anne Bresciani et al.   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

Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients

(2016) Alena Gros et al.   NATURE MEDICINE

Computational genomics tools for dissecting tumour–immune cell interactions

(2016) Hubert Hackl et al.   NATURE REVIEWS GENETICS

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires

(2016) E. Stronen et al.   SCIENCE

Automated benchmarking of peptide-MHC class I binding predictions

(2015) Thomas Trolle et al.   BIOINFORMATICS

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

(2015) Michael S. Rooney et al.   CELL

Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes

(2015) Cyrille J. Cohen et al.   JOURNAL OF CLINICAL INVESTIGATION

Tumor neoantigens: building a framework for personalized cancer immunotherapy

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

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

Combination cancer immunotherapies tailored to the tumour microenvironment

(2015) Mark J. Smyth et al.   Nature Reviews Clinical Oncology

Neo approaches to cancer vaccines

(2015) L. Delamarre et al.   SCIENCE

Neoantigens in cancer immunotherapy

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

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

(2015) B. M. Carreno et al.   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Immunoinformatics and epitope prediction in the age of genomic medicine

(2015) Linus Backert et al.   Genome Medicine

Efficient Identification of Mutated Cancer Antigens Recognized by T Cells Associated with Durable Tumor Regressions

(2014) Y.-C. Lu et al.   CLINICAL CANCER RESEARCH

Restoring the balance: immunotherapeutic combinations for autoimmune disease

(2014) D. E. Smilek et al.   Disease Models & Mechanisms

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival

(2014) S. D. Brown et al.   GENOME RESEARCH

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

(2014) Fei Duan et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Relapse or Eradication of Cancer Is Predicted by Peptide-Major Histocompatibility Complex Affinity

(2013) Boris Engels et al.   CANCER CELL

Oncology Meets Immunology: The Cancer-Immunity Cycle

(2013) Daniel S. Chen et al.   IMMUNITY

Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive Melanoma

(2013) Nienke van Rooij et al.   JOURNAL OF CLINICAL ONCOLOGY

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

(2013) Paul F Robbins et al.   NATURE MEDICINE

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

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

Getting Personal with Neoantigen-Based Therapeutic Cancer Vaccines

(2013) N. Hacohen et al.   Cancer Immunology Research

Immune epitope database analysis resource

(2012) Y. Kim et al.   NUCLEIC ACIDS RESEARCH

Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation

(2011) Emily Seymour et al.   BMC BIOINFORMATICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Non-conventional sources of peptides presented by MHC class I

(2011) Shelley R. Starck et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens

(2010) Magdalini Moutaftsi et al.   Future Microbiology

Major histocompatibility complex class I binding predictions as a tool in epitope discovery

(2010) Claus Lundegaard et al.   IMMUNOLOGY

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

(2008) Ilka Hoof et al.   IMMUNOGENETICS