Standardized annotation of translated open reading frames

A platform for curated products from novel open reading frames prompts reinterpretation of disease variants

(2021) Matthew D.C. Neville et al.   GENOME RESEARCH

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

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

Multiplexed functional genomic analysis of 5’ untranslated region mutations across the spectrum of prostate cancer

(2021) Yiting Lim et al.   Nature Communications

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

(2021) Tamara Ouspenskaia et al.   NATURE BIOTECHNOLOGY

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

A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation

(2020) Bjoern Gaertner et al.   eLife

A high-stringency blueprint of the human proteome

(2020) Subash Adhikari et al.   Nature Communications

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

How evolution builds genes from scratch

(2019) Adam Levy   NATURE

ClinVar: improvements to accessing data

(2019) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Accurate annotation of human protein-coding small open reading frames

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

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

(2018) Patrick McGillivray et al.   NUCLEIC ACIDS RESEARCH

Trips-Viz: a transcriptome browser for exploring Ribo-Seq data

(2018) Stephen J Kiniry 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

Translation of Small Open Reading Frames: Roles in Regulation and Evolutionary Innovation

(2018) Jorge Ruiz-Orera et al.   TRENDS IN GENETICS

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project

(2017) Gilbert S. Omenn et al.   JOURNAL OF PROTEOME RESEARCH

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

GWIPS-viz: 2018 update

(2017) Audrey M Michel et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Anil Raj et al.   eLife

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

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

(2015) Zhe Ji et al.   eLife

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

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

(2011) Nicholas T. Ingolia et al.   CELL

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

(2009) N. T. Ingolia et al.   SCIENCE