A Novel Proteogenomic Integration Strategy Expands the Breadth of Neo-Epitope Sources

IntroSpect: Motif-Guided Immunopeptidome Database Building Tool to Improve the Sensitivity of HLA I Binding Peptide Identification by Mass Spectrometry

(2022) Le Zhang et al.   Biomolecules

Proteasome-Generated cis-Spliced Peptides and Their Potential Role in CD8+ T Cell Tolerance

(2021) Artem Mansurkhodzhaev et al.   Frontiers in Immunology

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

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

(2021) Grégory Ehx et al.   IMMUNITY

Exploiting Tumor Neoantigens to Target Cancer Evolution: Current Challenges and Promising Therapeutic Approaches

(2021) Ravi G. Gupta et al.   Cancer Discovery

NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes

(2021) Jonas P. Becker et al.   iScience

An Integrated Approach for Discovering Noncanonical MHC-I Peptides Encoded by Small Open Reading Frames

(2021) Lei Chen et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling

(2021) Yanyan Li et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Proteogenomic identification of an immunogenic HLA class I neoantigen in mismatch repair–deficient colorectal cancer tissue

(2021) Tomomi Hirama et al.   JCI Insight

Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs

(2021) Mark Yarmarkovich et al.   NATURE

Identification of tumor antigens with immunopeptidomics

(2021) Chloe Chong et al.   NATURE BIOTECHNOLOGY

Proteogenomic discovery of neoantigens facilitates personalized multi-antigen targeted T cell immunotherapy for brain tumors

(2021) Samuel Rivero-Hinojosa et al.   Nature Communications

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

(2020) Birkir Reynisson et al.   NUCLEIC ACIDS RESEARCH

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

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

(2020) Daniel K. Wells et al.   CELL

Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma

(2020) Pouya Faridi et al.   Cancer Immunology Research

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

(2019) Wei Yang et al.   NATURE MEDICINE

pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework

(2019) Hao Yang et al.   BIOINFORMATICS

Low mutational load in pediatric medulloblastoma still translates into neoantigens as targets for specific T-cell immunotherapy

(2019) FRANZISKA BLAESCHKE et al.   CYTOTHERAPY

Contribution of proteasome-catalyzed peptide cis-splicing to viral targeting by CD8+ T cells in HIV-1 infection

(2019) Wayne Paes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OUP accepted manuscript

(2018)   BIOINFORMATICS

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

(2018) Reyka G. Jayasinghe et al.   Cell Reports

PDV: an integrative proteomics data viewer

(2018) Kai Li et al.   BIOINFORMATICS

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

(2018) André Kahles et al.   CANCER CELL

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome

(2018) Roman Mylonas et al.   MOLECULAR & CELLULAR PROTEOMICS

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

(2018) Allison A. Regier et al.   Nature Communications

Actively personalized vaccination trial for newly diagnosed glioblastoma

(2018) Norbert Hilf et al.   NATURE

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

(2018) Hao Chi et al.   NATURE BIOTECHNOLOGY

Clinical potential of mass spectrometry-based proteogenomics

(2018) Bing Zhang et al.   Nature Reviews Clinical Oncology

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate 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

Mapping the MHC Class I–Spliced Immunopeptidome of Cancer Cells

(2018) Juliane Liepe et al.   Cancer Immunology Research

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

Post-Translational Peptide Splicing and T Cell Responses

(2017) Michele Mishto et al.   TRENDS IN IMMUNOLOGY

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

(2016) Juliane Liepe et al.   SCIENCE

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

(2016) Michal Bassani-Sternberg et al.   Nature Communications

The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers

(2015) Leng Han et al.   CANCER CELL

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

Adoptive cell transfer as personalized immunotherapy for human cancer

(2015) S. A. Rosenberg et al.   SCIENCE

Neoantigens in cancer immunotherapy

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

Cancer Immunotherapy Based on Mutation-Specific CD4+ T Cells in a Patient with Epithelial Cancer

(2014) E. Tran et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Exome sequencing generates high quality data in non-target regions

(2012) Yan Guo et al.   BMC GENOMICS

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

(2012) Martin Christen Frølund Thomsen et al.   NUCLEIC ACIDS RESEARCH

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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