Immunopeptidogenomics: harnessing RNA-seq to illuminate the dark immunopeptidome

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

(2021) Grégory Ehx et al.   IMMUNITY

Proteogenomics Uncovers a Vast Repertoire of Shared Tumor-Specific Antigens in Ovarian Cancer

(2020) Qingchuan Zhao et al.   Cancer Immunology Research

ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection

(2020) Yuyu Li et al.   BMC Medical Genomics

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

(2020) Chloe Chong et al.   Nature Communications

Alternative splicing and cancer: insights, opportunities, and challenges from an expanding view of the transcriptome

(2020) Sara Cherry et al.   GENES & DEVELOPMENT

In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies

(2020) Kirti Pandey et al.   MOLECULAR IMMUNOLOGY

Identification of the Cryptic HLA-I Immunopeptidome

(2020) Florian Erhard et al.   Cancer Immunology Research

ncRNA-Encoded Peptides or Proteins and Cancer

(2019) Jizhong Wang et al.   MOLECULAR THERAPY

Accurate annotation of human protein-coding small open reading frames

(2019) Thomas F. Martinez et al.   Nature Chemical Biology

Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry

(2018) Lena Katharina Freudenmann et al.   IMMUNOLOGY

MHC class I presented antigens from malignancies: A perspective on analytical characterization & immunogenicity

(2018) Maike Schmidt et al.   Journal of Proteomics

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

(2018) Qingsong Gao et al.   Cell Reports

Discrimination Between Human Leukocyte Antigen Class I-Bound and Co-Purified HIV-Derived Peptides in Immunopeptidomics Workflows

(2018) Thomas Partridge et al.   Frontiers in Immunology

Primary transcripts: from the discovery of RNA processing to current concepts of gene expression - Review

(2018) Klaus Scherrer   EXPERIMENTAL CELL RESEARCH

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching

(2018) Paolo Cifani et al.   JOURNAL OF PROTEOME 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

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

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

RUNX1 cooperates with FLT3-ITD to induce leukemia

(2017) Kira Behrens et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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 Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

(2017) Malgorzata A. Komor et al.   MOLECULAR & CELLULAR PROTEOMICS

Translation from unconventional 5′ start sites drives tumour initiation

(2017) Ataman Sendoel et al.   NATURE

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq

(2016) Bo Wen et al.   BMC BIOINFORMATICS

Mass spectrometry-based antigen discovery for cancer immunotherapy

(2016) Michal Bassani-Sternberg 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

A large fraction of HLA class I ligands are proteasome-generated spliced peptides

(2016) Juliane Liepe et al.   SCIENCE

MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms

(2015) Franziska Zickmann et al.   BIOINFORMATICS

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

The nature of self for T cells—a systems-level perspective

(2015) Diana P Granados et al.   CURRENT OPINION IN IMMUNOLOGY

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer

(2015) Kelly V. Ruggles et al.   MOLECULAR & CELLULAR PROTEOMICS

Intron retention is a widespread mechanism of tumor-suppressor inactivation

(2015) Hyunchul Jung et al.   NATURE GENETICS

Neoantigens in cancer immunotherapy

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

Widespread intron retention diversifies most cancer transcriptomes

(2015) Heidi Dvinge et al.   Genome Medicine

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

(2014) Gloria M Sheynkman et al.   BMC GENOMICS

Onco-proteogenomics: cancer proteomics joins forces with genomics

(2014) Javier A Alfaro et al.   NATURE METHODS

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses

(2014) Heejin Park et al.   PROTEOMICS

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

(2013) Xiaojing Wang et al.   BIOINFORMATICS

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Using iRT, a normalized retention time for more targeted measurement of peptides

(2012) Claudia Escher et al.   PROTEOMICS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

A Cryptic Vascular Endothelial Growth Factor T-Cell Epitope: Identification and Characterization by Mass Spectrometry and T-Cell Assays

(2008) A. O. Weinzierl et al.   CANCER RESEARCH