Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

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

Identification of essential genes for cancer immunotherapy

(2017) Shashank J. Patel et al.   NATURE

In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target

(2017) Robert T. Manguso et al.   NATURE

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma

(2016) Jesse M. Zaretsky et al.   NEW ENGLAND JOURNAL OF MEDICINE

2016 update of the PRIDE database and its related tools

(2016) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Immunoproteasome deficiency is a feature of non-small cell lung cancer with a mesenchymal phenotype and is associated with a poor outcome

(2016) Satyendra C. Tripathi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Proteomic analysis uncovers common effects of IFN-γ and IL-27 on the HLA class I antigen presentation machinery in human cancer cells

(2016) Andrea Petretto et al.   Oncotarget

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

(2016) Shelly Kalaora et al.   Oncotarget

Mismatch in epitope specificities between IFNγ inflamed and uninflamed conditions leads to escape from T lymphocyte killing in melanoma

(2016) Katherine Woods et al.   Journal for ImmunoTherapy of Cancer

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

(2015) Michael S. Rooney et al.   CELL

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Effect of Proteasome Inhibition on the Generation of the Human Leukocyte Antigen (HLA) Peptidome

(2013) Elena Milner et al.   MOLECULAR & CELLULAR PROTEOMICS

A peptide's perspective on antigen presentation to the immune system

(2013) Jacques Neefjes et al.   Nature Chemical Biology

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

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

(2012) Massimo Andreatta et al.   BIOINFORMATICS

Dissection of T-cell Antigen Specificity in Human Melanoma

(2012) R. S. Andersen et al.   CANCER RESEARCH

Analysis of the Processing of Seven Human Tumor Antigens by Intermediate Proteasomes

(2012) B. Guillaume et al.   JOURNAL OF IMMUNOLOGY

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

(2012) Martin Christen Frølund Thomsen et al.   NUCLEIC ACIDS RESEARCH

A MAGE-C2 antigenic peptide processed by the immunoproteasome is recognized by cytolytic T cells isolated from a melanoma patient after successful immunotherapy

(2011) Wenbin Ma et al.   INTERNATIONAL JOURNAL OF CANCER

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

(2011) Xiaomu Wei et al.   NATURE GENETICS

Dissecting Interferon-Induced Transcriptional Programs in Human Peripheral Blood Cells

(2010) Simon J. Waddell et al.   PLoS One

Two abundant proteasome subtypes that uniquely process some antigens presented by HLA class I molecules

(2010) B. Guillaume et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) Ilka Hoof et al.   IMMUNOGENETICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

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

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