Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

(2020) David P. Nusinow et al.   CELL

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

(2020) Esther Rheinbay et al.   NATURE

ensembldb: an R package to create and use Ensembl-based annotation resources

(2019) Johannes Rainer et al.   BIOINFORMATICS

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

ncRNA-Encoded Peptides or Proteins and Cancer

(2019) Jizhong Wang et al.   MOLECULAR THERAPY

New universe of miniproteins is upending cell biology and genetics

(2019) Mitch Leslie   SCIENCE

The Mitochondrial-Encoded Peptide MOTS-c Translocates to the Nucleus to Regulate Nuclear Gene Expression in Response to Metabolic Stress

(2018) Kyung Hwa Kim et al.   Cell Metabolism

The role of long noncoding RNAs in cancer: the dark matter matters

(2018) Xiaowen Hu et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

(2018) Yafeng Zhu et al.   Nature Communications

Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency

(2018) Colleen S. Stein et al.   Cell Reports

Micropeptides Encoded in Transcripts Previously Identified as Long Noncoding RNAs: A New Chapter in Transcriptomics and Proteomics

(2018) Fouzia Yeasmin et al.   Frontiers in Genetics

Translation of neutrally evolving peptides provides a basis for de novo gene evolution

(2018) Jorge Ruiz-Orera et al.   Nature Ecology & Evolution

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

RNAcentral: a hub of information for non-coding RNA sequences

(2018) et al.   NUCLEIC ACIDS RESEARCH

RNAcentral: a hub of information for non-coding RNA sequences

(2018) et al.   NUCLEIC ACIDS RESEARCH

RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling

(2018) Hongwei Wang et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes

(2018) Marie A Brunet et al.   NUCLEIC ACIDS RESEARCH

A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma

(2018) Maolei Zhang et al.   Nature Communications

The Landscape of Isoform Switches in Human Cancers

(2017) Kristoffer Vitting-Seerup et al.   MOLECULAR CANCER RESEARCH

A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth

(2017) Jin-Zhou Huang et al.   MOLECULAR CELL

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

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

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

Global analysis of protein folding using massively parallel design, synthesis, and testing

(2017) Gabriel J. Rocklin et al.   SCIENCE

Genome annotation for clinical genomic diagnostics: strengths and weaknesses

(2017) Charles A. Steward et al.   Genome Medicine

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide

(2016) Akinobu Matsumoto et al.   NATURE

Open questions in the study of de novo genes: what, how and why

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

(2016) B. R. Nelson et al.   SCIENCE

Hemotin, a Regulator of Phagocytosis Encoded by a Small ORF and Conserved across Metazoans

(2016) José I. Pueyo et al.   PLOS BIOLOGY

The Genomic Landscape of Position Effects on Protein Expression Level and Noise in Yeast

(2016) Xiaoshu Chen et al.   Cell Systems

Are Human Translated Pseudogenes Functional?

(2015) Jinrui Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The neXtProt knowledgebase on human proteins: current status

(2015) Pascale Gaudet et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Zhe Ji et al.   eLife

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Everything old is new again: (linc)RNAs make proteins!

(2014) S. M. Cohen   EMBO JOURNAL

A Human Short Open Reading Frame (sORF)-encoded Polypeptide That Stimulates DNA End Joining

(2014) Sarah A. Slavoff et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The structural and functional signatures of proteins that undergo multiple events of post-translational modification

(2014) Vikas Pejaver et al.   PROTEIN SCIENCE

Quantitative profiling of peptides from RNAs classified as noncoding

(2014) Sudhakaran Prabakaran et al.   Nature Communications

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae

(2014) Jenna E. Smith et al.   Cell Reports

Data-based filtering for replicated high-throughput transcriptome sequencing experiments

(2013) Andrea Rau et al.   BIOINFORMATICS

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

(2013) Benoît Vanderperre et al.   PLoS One

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

ANCHOR: web server for predicting protein binding regions in disordered proteins

(2009) Z. Dosztanyi et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS