Upstream open reading frames regulate translation of cancer-associated transcripts and encode HLA-presented immunogenic tumor antigens

Noncanonical open reading frames encode functional proteins essential for cancer cell survival

(2021) John R. Prensner et al.   NATURE BIOTECHNOLOGY

HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

(2021) Ana Marcu et al.   Journal for ImmunoTherapy of Cancer

Somatic Functional Deletions of Upstream Open Reading Frame-Associated Initiation and Termination Codons in Human Cancer

(2021) Lara Jürgens et al.   Biomedicines

Unraveling the hidden role of a uORF-encoded peptide as a kinase inhibitor of PKCs

(2021) Divya Ram Jayaram et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

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

(2020) Chloe Chong et al.   Nature Communications

Characterising the loss-of-function impact of 5’ untranslated region variants in 15,708 individuals

(2020) Nicola Whiffin et al.   Nature Communications

Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection

(2020) Jessica Sook Yuin Ho et al.   CELL

Identification of the Cryptic HLA-I Immunopeptidome

(2020) Florian Erhard et al.   Cancer Immunology Research

Magnesium-sensitive upstream ORF controls PRL phosphatase expression to mediate energy metabolism

(2019) Serge Hardy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

uORF-mediated translational control: recently elucidated mechanisms and implications in cancer

(2019) Hung-Hsi Chen et al.   RNA Biology

Alternative ORFs and small ORFs: shedding light on the dark proteome

(2019) Mona Wu Orr et al.   NUCLEIC ACIDS RESEARCH

Upstream ORF-Encoded ASDURF Is a Novel Prefoldin-like Subunit of the PAQosome

(2019) Philippe Cloutier et al.   JOURNAL OF PROTEOME RESEARCH

The natural HLA ligandome of glioblastoma stem-like cells: antigen discovery for T cell-based immunotherapy

(2018) Marian Christoph Neidert et al.   ACTA NEUROPATHOLOGICA

iwCLL guidelines for diagnosis, indications for treatment, response assessment, and supportive management of CLL

(2018) Michael Hallek et al.   BLOOD

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Oncogenic Signaling Pathways in The Cancer Genome Atlas

(2018) Francisco Sanchez-Vega et al.   CELL

A comprehensive catalog of predicted functional upstream open reading frames in humans

(2018) Patrick McGillivray et al.   NUCLEIC ACIDS RESEARCH

HLA ligandome analysis of primary chronic lymphocytic leukemia (CLL) cells under lenalidomide treatment confirms the suitability of lenalidomide for combination with T-cell-based immunotherapy

(2018) Annika Nelde et al.   OncoImmunology

Loss-of-function uORF mutations in human malignancies

(2018) Julia Schulz et al.   Scientific Reports

The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy

(2018) Tatjana Bilich et al.   BLOOD

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

Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data

(2017) Pieter Spealman et al.   GENOME RESEARCH

Mass spectrometry-based identification of a naturally presented receptor tyrosine kinase-like orphan receptor 1-derived epitope recognized by CD8 + cytotoxic T cells

(2017) Falk Heidenreich et al.   HAEMATOLOGICA

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

The immunopeptidomic landscape of ovarian carcinomas

(2017) Heiko Schuster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved split fluorescent proteins for endogenous protein labeling

(2017) Siyu Feng et al.   Nature Communications

Mass spectrometry-based identification of a naturally presented receptor tyrosine kinase-like orphan receptor 1-derived epitope recognized by CD8 + cytotoxic T cells

(2017) Falk Heidenreich et al.   HAEMATOLOGICA

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

(2016) Thomas E. Dever et al.   GENETICS

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

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

Immunogenicity of HLA Class I and II Double Restricted Influenza A-Derived Peptides

(2016) Sara Ram Pedersen et al.   PLoS One

Versatile protein tagging in cells with split fluorescent protein

(2016) Daichi Kamiyama 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

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

(2016) Thomas E. Dever et al.   GENETICS

Nonsense-Mediated mRNA Decay: Degradation of Defective Transcripts Is Only Part of the Story

(2015) Feng He et al.   Annual Review of Genetics

The antigenic landscape of multiple myeloma: mass spectrometry (re)defines targets for T-cell-based immunotherapy

(2015) S. Walz et al.   BLOOD

Comprehensive translational control of tyrosine kinase expression by upstream open reading frames

(2015) K Wethmar et al.   ONCOGENE

HLA ligandomics identifies histone deacetylase 1 as target for ovarian cancer immunotherapy

(2015) Janet Kerstin Peper et al.   OncoImmunology

Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy

(2014) C Berlin et al.   LEUKEMIA

Emerging evidence for functional peptides encoded by short open reading frames

(2014) Shea J. Andrews et al.   NATURE REVIEWS GENETICS

Identification of a Mg2+-sensitive ORF in the 5′-leader of TRPM7 magnesium channel mRNA

(2014) Inna A. Nikonorova et al.   NUCLEIC ACIDS RESEARCH

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL)

(2014) Daniel J. Kowalewski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The regulatory potential of upstream open reading frames in eukaryotic gene expression

(2014) Klaus Wethmar   Wiley Interdisciplinary Reviews-RNA

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

(2013) Jeroen Crappé et al.   BMC GENOMICS

Identification of HLA ligands and T-cell epitopes for immunotherapy of lung cancer

(2013) Anneke Neumann et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

A perspective on mammalian upstream open reading frame function

(2013) Joanna Somers et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

uORFdb—a comprehensive literature database on eukaryotic uORF biology

(2013) Klaus Wethmar et al.   NUCLEIC ACIDS RESEARCH

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Mouse urinary peptides provide a molecular basis for genotype discrimination by nasal sensory neurons

(2013) Theo Sturm et al.   Nature Communications

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

A Novel Mutation in the Upstream Open Reading Frame of the CDKN1B Gene Causes a MEN4 Phenotype

(2013) Gianluca Occhi et al.   PLoS Genetics

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

(2012) C. Fritsch et al.   GENOME RESEARCH

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

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

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

(2011) Nicholas T. Ingolia et al.   CELL

Promiscuous survivin peptide induces robust CD4+ T-cell responses in the majority of vaccinated cancer patients

(2011) Melanie Widenmeyer et al.   INTERNATIONAL JOURNAL OF CANCER

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) N. T. Ingolia et al.   SCIENCE

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

(2008) Tim Hulsen et al.   BMC GENOMICS

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS