Most non-canonical proteins uniquely populate the proteome or immunopeptidome

Mutation position is an important determinant for predicting cancer neoantigens

(2020) Aude-Hélène Capietto et al.   JOURNAL OF EXPERIMENTAL MEDICINE

MAPDP: a cloud-based computational platform for immunopeptidomics analyses

(2020) Mathieu Courcelles et al.   JOURNAL OF PROTEOME RESEARCH

Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical Therapies

(2020) Michael Ghosh et al.   MOLECULAR & CELLULAR PROTEOMICS

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

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

(2020) Qingchuan Zhao et al.   Cancer Immunology Research

Mass Spectrometry-Based Identification of MHC-Associated Peptides

(2020) Sachin Kote et al.   Cancers

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

(2020) Chloe Chong et al.   Nature Communications

Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis

(2020) Bo Wen et al.   Nature Communications

Ribosomal Proteins Regulate MHC Class I Peptide Generation for Immunosurveillance

(2019) Jiajie Wei et al.   MOLECULAR CELL

Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics

(2019) Anthony W. Purcell et al.   Nature Protocols

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Identification of Tumor Antigens Among the HLA Peptidomes of Glioblastoma Tumors and Plasma

(2019) Bracha Shraibman et al.   MOLECULAR & CELLULAR PROTEOMICS

A hidden human proteome encoded by ‘non-coding’ genes

(2019) Shaohua Lu et al.   NUCLEIC ACIDS RESEARCH

Next-generation computational tools for interrogating cancer immunity

(2019) Francesca Finotello et al.   NATURE REVIEWS GENETICS

The Human Immunopeptidome Project: a roadmap to predict and treat immune diseases

(2019) Juan Antonio Vizcaíno et al.   MOLECULAR & CELLULAR PROTEOMICS

Peptide Channeling: The Key to MHC Class I Immunosurveillance?

(2019) Jonathan W. Yewdell et al.   TRENDS IN CELL BIOLOGY

At the crossway of ER-stress and proinflammatory responses

(2018) Marisa Reverendo et al.   FEBS Journal

Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship

(2018) Marie A. Brunet et al.   GENOME RESEARCH

Improved Ribo-seq enables identification of cryptic translation events

(2018) Florian Erhard et al.   NATURE METHODS

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

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Comparison of the MHC I Immunopeptidome Repertoire of B-Cell Lymphoblasts Using Two Isolation Methods

(2018) Joël Lanoix et al.   PROTEOMICS

The Disordered Landscape of the 20S Proteasome Substrates Reveals Tight Association with Phase Separated Granules

(2018) Nadav Myers et al.   PROTEOMICS

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

(2018) Fabio Lauria et al.   PLoS Computational Biology

Nuclear processing of nascent transcripts determines synthesis of full-length proteins and antigenic peptides

(2018) Rodrigo Prado Martins 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

High-Throughput Stability Screening of Neoantigen/HLA Complexes Improves Immunogenicity Predictions

(2018) Dylan T. Blaha et al.   Cancer Immunology Research

Similar Ratios of Introns to Intergenic Sequence across Animal Genomes

(2017) Warren R. Francis et al.   Genome Biology and Evolution

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini

(2017) Chan Hyun Na et al.   GENOME RESEARCH

Varied Role of Ubiquitylation in Generating MHC Class I Peptide Ligands

(2017) Jiajie Wei et al.   JOURNAL OF IMMUNOLOGY

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

Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets

(2017) K Karube et al.   LEUKEMIA

Transcriptome-wide measurement of translation by ribosome profiling

(2017) Nicholas J. McGlincy et al.   METHODS

Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

(2017) Sondos Samandi et al.   eLife

Ribosome Footprint Profiling of Translation throughout the Genome

(2016) Nicholas T. Ingolia   CELL

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

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

Upstream Open Reading Frames Differentially Regulate Gene-specific Translation in the Integrated Stress Response

(2016) Sara K. Young et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Allele-Independent Turnover of Human Leukocyte Antigen (HLA) Class Ia Molecules

(2016) Claudia Prevosto et al.   PLoS One

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

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

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

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

A Deeper Look into Comet—Implementation and Features

(2015) Jimmy K. Eng et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

(2015) Michal Bassani-Sternberg et al.   MOLECULAR & CELLULAR PROTEOMICS

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

(2015) Alexander P. Fields et al.   MOLECULAR CELL

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis

(2014) Daniel V. Veres et al.   NUCLEIC ACIDS RESEARCH

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

(2014) G. P. M. Mommen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Translation of pre-spliced RNAs in the nuclear compartment generates peptides for the MHC class I pathway

(2013) S. Apcher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies

(2012) Paul Blakeley et al.   JOURNAL OF PROTEOME RESEARCH

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

GPS-ARM: Computational Analysis of the APC/C Recognition Motif by Predicting D-Boxes and KEN-Boxes

(2012) Zexian Liu et al.   PLoS One

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Leucine-tRNA Initiates at CUG Start Codons for Protein Synthesis and Presentation by MHC Class I

(2012) S. R. Starck et al.   SCIENCE

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation

(2011) E. Caron et al.   Molecular Systems Biology

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences

(2011) Ivaylo P. Ivanov et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1)

(2010) I. P. Ivanov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Identification, analysis, and prediction of protein ubiquitination sites

(2009) Predrag Radivojac et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE