Noncanonical splicing junctions between exons and transposable elements represent a source of immunogenic recurrent neo-antigens in patients with lung cancer

Single-cell RNA-seq-based proteogenomics identifies glioblastoma-specific transposable elements encoding HLA-I-presented peptides

(2022) Pierre-Emmanuel Bonté et al.   Cell Reports

Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes

(2021) Grégory Ehx et al.   IMMUNITY

Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison

(2021) Tobias Schmidt et al.   JOURNAL OF PROTEOME RESEARCH

Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity

(2021) Gabriel K. Griffin et al.   NATURE

Splicing patterns in SF3B1 mutated uveal melanoma generate shared immunogenic tumor-specific neo-epitopes

(2021) Jeremy Bigot et al.   Cancer Discovery

Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma

(2021) Giacomo Oliveira et al.   NATURE

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

(2021) Robbin Bouwmeester et al.   NATURE METHODS

An atlas of transposable element-derived alternative splicing in cancer

(2020) Evan A. Clayton et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

Roles and mechanisms of alternative splicing in cancer — implications for care

(2020) Sophie C. Bonnal et al.   Nature Reviews Clinical Oncology

SETDB1-Mediated Silencing of Retroelements

(2020) Kei Fukuda et al.   Viruses-Basel

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

(2020) Chloe Chong et al.   Nature Communications

Transposon clusters as substrates for aberrant splice-site activation

(2020) Maria Elena Vilar Alvarez et al.   RNA Biology

LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly

(2019) Jan Attig et al.   GENOME RESEARCH

Transposable element expression in tumors is associated with immune infiltration and increased antigenicity

(2019) Yu Kong et al.   Nature Communications

A Jurkat 76 based triple parameter reporter system to evaluate TCR functions and adoptive T cell strategies

(2018) Sandra Rosskopf et al.   Oncotarget

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

(2018) André Kahles et al.   CANCER CELL

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

(2018) Brendan Bulik-Sullivan et al.   NATURE BIOTECHNOLOGY

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

(2018) Yasset Perez-Riverol 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

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

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

(2017) Ugur Sahin et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

GibbsCluster: unsupervised clustering and alignment of peptide sequences

(2017) Massimo Andreatta et al.   NUCLEIC ACIDS RESEARCH

Approach for Identifying Human Leukocyte Antigen (HLA)-DR Bound Peptides from Scarce Clinical Samples

(2016) Tina Heyder et al.   MOLECULAR & CELLULAR PROTEOMICS

Lessons from non-canonical splicing

(2016) Christopher R. Sibley et al.   NATURE REVIEWS GENETICS

Toward a Shared Vision for Cancer Genomic Data

(2016) Robert L. Grossman et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

(2015) Michael S. Rooney et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Widespread intron retention diversifies most cancer transcriptomes

(2015) Heidi Dvinge et al.   Genome Medicine

Large-Scale Characterization of Natural Ligands Explains the Unique Gluten-Binding Properties of HLA-DQ2

(2014) D. Stepniak et al.   JOURNAL OF IMMUNOLOGY

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

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

(2012) Rikke Sick Andersen et al.   Nature Protocols

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Loss of epigenetic silencing in tumors preferentially affects primate-specific retroelements

(2009) Sebastian Szpakowski et al.   GENE

Intronic Alus Influence Alternative Splicing

(2008) Galit Lev-Maor et al.   PLoS Genetics