Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

Pan-cancer analysis of whole genomes

(2020)   NATURE

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

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

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

Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands”

(2019) Zach Rolfs et al.   Science Immunology

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

(2019) Siranush Sarkizova et al.   NATURE BIOTECHNOLOGY

Accurate annotation of human protein-coding small open reading frames

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

The Cancer Genome Atlas: Creating Lasting Value beyond Its Data

(2018) Carolyn Hutter et al.   CELL

SnapShot: TCGA-Analyzed Tumors

(2018) Amy Blum et al.   CELL

Improved Ribo-seq enables identification of cryptic translation events

(2018) Florian Erhard et al.   NATURE METHODS

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

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

Actively personalized vaccination trial for newly diagnosed glioblastoma

(2018) Norbert Hilf et al.   NATURE

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

(2018) Derin B. Keskin et al.   NATURE

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish 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

Widespread Translational Remodeling during Human Neuronal Differentiation

(2017) John D. Blair et al.   Cell Reports

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

(2016) Juliane Liepe 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

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

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

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

(2016) Anil Raj et al.   eLife

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

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

Non-coding recurrent mutations in chronic lymphocytic leukaemia

(2015) Xose S. Puente et al.   NATURE

Mutations driving CLL and their evolution in progression and relapse

(2015) Dan A. Landau et al.   NATURE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

(2015) Zhe Ji et al.   eLife

Expression of Cancer/Testis Antigens is Correlated with Improved Survival in Glioblastoma

(2015) Marcelo R.P. Freitas et al.   Oncotarget

Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

(2014) M. Rajasagi et al.   BLOOD

Ribosome Profiling Reveals a Cell-Type-Specific Translational Landscape in Brain Tumors

(2014) C. Gonzalez et al.   JOURNAL OF NEUROSCIENCE

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

(2013) P. G. Ferreira et al.   GENOME RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Molecular Characterization of Chronic Lymphocytic Leukemia Patients with a High Number of Losses in 13q14

(2012) Ana Eugenia Rodríguez et al.   PLoS One

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2009) N. T. Ingolia et al.   SCIENCE