标题
Most non-canonical proteins uniquely populate the proteome or immunopeptidome
作者
关键词
computational biology, defective ribosomal products, major histocompatibility complex, mass spectrometry, non-canonical translation, peptides, protein isoforms, proteomic methods, ribosome profiling
出版物
Cell Reports
Volume 34, Issue 10, Pages 108815
出版商
Elsevier BV
发表日期
2021-03-10
DOI
10.1016/j.celrep.2021.108815
参考文献
相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。- 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
Create your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create NowAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started