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

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

PsORF: a database of small ORFs in plants

(2020) Yanjun Chen et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2020) Nicola Whiffin et al.   Nature Communications

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

(2019) Hila Sberro et al.   CELL

The GenomeAsia 100K Project enables genetic discoveries across Asia

(2019)   NATURE

C9ORF72 GGGGCC repeat-associated non-AUG translation is upregulated by stress through eIF2α phosphorylation

(2018) Weiwei Cheng et al.   Nature Communications

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

piRBase: a comprehensive database of piRNA sequences

(2018) Jiajia Wang et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish 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

Peptides/Proteins Encoded by Non-coding RNA: A Novel Resource Bank for Drug Targets and Biomarkers

(2018) Song Zhu et al.   Frontiers in Pharmacology

Translation of noncoding RNAs: Focus on lncRNAs, pri-miRNAs, and circRNAs

(2017) Lian-Ju Li et al.   EXPERIMENTAL CELL RESEARCH

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

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

Classification and function of small open reading frames

(2017) Juan-Pablo Couso et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

(2017) Shashikant Pujar et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

The European Nucleotide Archive in 2017

(2017) Nicole Silvester et al.   NUCLEIC ACIDS RESEARCH

Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants

(2017) Polly Yingshan Hsu et al.   PROTEOMICS

Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome

(2017) Lorenzo Calviello et al.   TRENDS IN GENETICS

Genome-wide identification and differential analysis of translational initiation

(2017) Peng Zhang et al.   Nature Communications

Loss of Apela Peptide in Mice Causes Low Penetrance Embryonic Lethality and Defects in Early Mesodermal Derivatives

(2017) Laina Freyer et al.   Cell Reports

Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs

(2017) Brandon Razooky et al.   Genes

SPECtre: a spectral coherence-­based classifier of actively translated transcripts from ribosome profiling sequence data

(2016) Sang Y. Chun et al.   BMC BIOINFORMATICS

The neXtProt knowledgebase on human proteins: 2017 update

(2016) Pascale Gaudet et al.   NUCLEIC ACIDS RESEARCH

Proline-rich Antimicrobial Peptides Optimized for Binding to Escherichia coli Chaperone DnaK

(2016) Daniel Knappe et al.   PROTEIN AND PEPTIDE LETTERS

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

(2016) Anil Raj et al.   eLife

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

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

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

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

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

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

Fail-safe mechanism of GCN4 translational control—uORF2 promotes reinitiation by analogous mechanism to uORF1 and thus secures its key role in GCN4 expression

(2014) Stanislava Gunišová et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration

(2014) R. Ishimura et al.   SCIENCE

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

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

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

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Translation Goes Global

(2011) R. B. Weiss et al.   SCIENCE

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin

(2010) Tilman Schneider-Poetsch et al.   Nature Chemical Biology

Loss-of-function mutations of an inhibitory upstream ORF in the human hairless transcript cause Marie Unna hereditary hypotrichosis

(2009) Yaran Wen et al.   NATURE GENETICS

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