Anti-tumour immunity induces aberrant peptide presentation in melanoma

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(2020) Hong-Dong Li et al.   BMC GENOMICS

Role for ribosome-associated quality control in sampling proteins for MHC class I-mediated antigen presentation

(2020) Débora Broch Trentini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

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

(2020) Chloe Chong et al.   Nature Communications

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(2019) Johannes Rainer et al.   BIOINFORMATICS

Induction of neoantigen-reactive T cells from healthy donors

(2019) Muhammad Ali et al.   Nature Protocols

Augmenting Immunotherapy Impact by Lowering Tumor TNF Cytotoxicity Threshold

(2019) David W. Vredevoogd et al.   CELL

Limitations and Off-Target Effects of Tryptophan-Related IDO Inhibitors in Cancer Treatment

(2019) Juliane Günther et al.   Frontiers in Immunology

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

(2019) Siranush Sarkizova et al.   NATURE BIOTECHNOLOGY

Improved Ribo-seq enables identification of cryptic translation events

(2018) Florian Erhard et al.   NATURE METHODS

Proteome-wide identification of ubiquitin interactions using UbIA-MS

(2018) Xiaofei Zhang et al.   Nature Protocols

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

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Combined analysis of antigen presentation and T cell recognition reveals restricted immune responses in melanoma

(2018) Shelly Kalaora et al.   Cancer Discovery

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

(2018) Fabio Lauria et al.   PLoS Computational Biology

Reimagining IDO Pathway Inhibition in Cancer Immunotherapy via Downstream Focus on the Tryptophan–Kynurenine–Aryl Hydrocarbon Axis

(2018) Brian W. Labadie et al.   CLINICAL CANCER RESEARCH

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Noncoding regions are the main source of targetable tumor-specific antigens

(2018) Céline M. Laumont et al.   Science Translational Medicine

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

(2017) Jennifer G. Abelin et al.   IMMUNITY

IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade

(2017) Mark Ayers et al.   JOURNAL OF CLINICAL INVESTIGATION

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

Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA

(2017) Neva Caliskan et al.   MOLECULAR CELL

GibbsCluster: unsupervised clustering and alignment of peptide sequences

(2017) Massimo Andreatta et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Amino Acid Sensing via General Control Nonderepressible-2 Kinase and Immunological Programming

(2017) Srikanth Battu et al.   Frontiers in Immunology

Nutritional Stress Induced by Tryptophan-Degrading Enzymes Results in ATF4-Dependent Reprogramming of the Amino Acid Transporter Profile in Tumor Cells

(2016) Elina Timosenko et al.   CANCER RESEARCH

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

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

MHC class I–associated peptides derive from selective regions of the human genome

(2016) Hillary Pearson et al.   JOURNAL OF CLINICAL INVESTIGATION

Presentation of Cryptic Peptides by MHC Class I Is Enhanced by Inflammatory Stimuli

(2016) Sharanya Prasad et al.   JOURNAL OF IMMUNOLOGY

Tumour-specific proline vulnerability uncovered by differential ribosome codon reading

(2016) Fabricio Loayza-Puch et al.   NATURE

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

(2016) Stefka Tyanova et al.   NATURE METHODS

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

(2016) E. Stronen et al.   SCIENCE

Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

(2016) Céline M. Laumont et al.   Nature Communications

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

(2016) Shelly Kalaora et al.   Oncotarget

Molecular Pathways: Targeting IDO1 and Other Tryptophan Dioxygenases for Cancer Immunotherapy

(2015) L. Zhai et al.   CLINICAL CANCER RESEARCH

A novel Fanconi anaemia subtype associated with a dominant-negative mutation in RAD51

(2015) Najim Ameziane et al.   Nature Communications

The immunoproteasome and viral infection: a complex regulator of inflammation

(2015) Mary K. McCarthy et al.   Frontiers in Microbiology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

The nature and extent of contributions by defective ribosome products to the HLA peptidome

(2014) D. Bourdetsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

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CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation

(2011) Laurent Gatto et al.   BIOINFORMATICS

An immune-active tumor microenvironment favors clinical response to ipilimumab

(2011) Rui-Ru Ji et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

DRiPs solidify: progress in understanding endogenous MHC class I antigen processing

(2011) Jonathan W. Yewdell   TRENDS IN IMMUNOLOGY

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

How do tumours adapt to nutrient stress?

(2010) Ronald C Wek et al.   EMBO JOURNAL

The GCN2-ATF4 pathway is critical for tumour cell survival and proliferation in response to nutrient deprivation

(2010) Jiangbin Ye et al.   EMBO JOURNAL

Public TCR Use by Herpes Simplex Virus-2-Specific Human CD8 CTLs

(2010) L. Dong et al.   JOURNAL OF IMMUNOLOGY

α-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel

(2010) Shashi Bhushan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Hungry Codons Promote Frameshifting in Human Mitochondrial Ribosomes

(2010) R. Temperley et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Peptide Retention Standards and Hydrophobicity Indexes in Reversed-Phase High-Performance Liquid Chromatography of Peptides

(2009) Oleg V. Krokhin et al.   ANALYTICAL CHEMISTRY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Molecular Mechanisms of IFN-γ to Up-Regulate MHC Class I Antigen Processing and Presentation

(2009) Fang Zhou   INTERNATIONAL REVIEWS OF IMMUNOLOGY

Parallel detection of antigen-specific T-cell responses by multidimensional encoding of MHC multimers

(2009) Sine Reker Hadrup et al.   NATURE METHODS

Ribosome can resume the translation in both +1 or −1 frames after encountering an AGA cluster in Escherichia coli

(2008) Sébastien Lainé et al.   GENE

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