Related references
Note: Only part of the references are listed.A cytosine base editor toolkit with varying activity windows and target scopes for versatile gene manipulation in plants
Xiangyu Xiong et al.
NUCLEIC ACIDS RESEARCH (2022)
The dark proteome: translation from noncanonical open reading frames
Bradley W. Wright et al.
TRENDS IN CELL BIOLOGY (2022)
Upstream open reading frames control PLK4 translation and centriole duplication in primordial germ cells
Thao P. Phan et al.
GENES & DEVELOPMENT (2022)
Standardized annotation of translated open reading frames
Jonathan M. Mudge et al.
NATURE BIOTECHNOLOGY (2022)
Annotating high-impact 5′untranslated region variants with the UTRannotator
Xiaolei Zhang et al.
BIOINFORMATICS (2021)
m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome
Yujiao Tang et al.
NUCLEIC ACIDS RESEARCH (2021)
RASP: an atlas of transcriptome-wide RNA secondary structure probing data
Pan Li et al.
NUCLEIC ACIDS RESEARCH (2021)
Disrupting upstream translation in mRNAs is associated with human disease
David S. M. Lee et al.
NATURE COMMUNICATIONS (2021)
Global miRNA dosage control of embryonic germ layer specification
Yingzi Cui et al.
NATURE (2021)
Translation of GGC repeat expansions into a toxic polyglycine protein in NIID defines a novel class of human genetic disorders: The polyG diseases
Manon Boivin et al.
NEURON (2021)
Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data
Stephen J. Kiniry et al.
NUCLEIC ACIDS RESEARCH (2021)
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling
Yanyan Li et al.
GENOMICS PROTEOMICS & BIOINFORMATICS (2021)
RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data
Carine Legrand et al.
NUCLEIC ACIDS RESEARCH (2020)
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
Yunhai Luo et al.
NUCLEIC ACIDS RESEARCH (2020)
RiboFlow, RiboR and RiboPy: an ecosystem for analyzing ribosome profiling data at read length resolution
Hakan Ozadam et al.
BIOINFORMATICS (2020)
Pervasive functional translation of noncanonical human open reading frames
Jin Chen et al.
SCIENCE (2020)
PsORF: a database of small ORFs in plants
Yanjun Chen et al.
PLANT BIOTECHNOLOGY JOURNAL (2020)
RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution
Qi Liu et al.
NUCLEIC ACIDS RESEARCH (2020)
Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation
Thomas E. Dever et al.
ANNUAL REVIEW OF GENETICS, VOL 54, 2020 (2020)
REPIC: a database for exploring the N6-methyladenosine methylome
Shun Liu et al.
GENOME BIOLOGY (2020)
uORFlight: a vehicle toward uORF-mediated translational regulation mechanisms in eukaryotes
Ruixia Niu et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2020)
POSTAR2: deciphering the post-transcriptional regulatory logics
Yumin Zhu et al.
NUCLEIC ACIDS RESEARCH (2019)
Function and Evolution of Upstream ORFs in Eukaryotes
Hong Zhang et al.
TRENDS IN BIOCHEMICAL SCIENCES (2019)
Human 5′ UTR design and variant effect prediction from a massively parallel translation assay
Paul J. Sample et al.
NATURE BIOTECHNOLOGY (2019)
Impacts of uORF codon identity and position on translation regulation
Yizhu Lin et al.
NUCLEIC ACIDS RESEARCH (2019)
RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling
Hongwei Wang et al.
NUCLEIC ACIDS RESEARCH (2019)
GENCODE reference annotation for the human and mouse genomes
Adam Frankish et al.
NUCLEIC ACIDS RESEARCH (2019)
Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data
Pieter Spealman et al.
GENOME RESEARCH (2018)
Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini
Chan Hyun Na et al.
GENOME RESEARCH (2018)
An update on sORFs.org: a repository of small ORFs identified by ribosome profiling
Volodimir Olexiouk et al.
NUCLEIC ACIDS RESEARCH (2018)
PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types
Jing Gong et al.
NUCLEIC ACIDS RESEARCH (2018)
RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data
Jia-Jia Xuan et al.
NUCLEIC ACIDS RESEARCH (2018)
MeT-DB V2.0: elucidating context-specific functions of N-6-methyl-adenosine methyltranscriptome
Hui Liu et al.
NUCLEIC ACIDS RESEARCH (2018)
IRESfinder: Identifying RNA internal ribosome entry site in eukaryotic cell using framed k-mer features
Jian Zhao et al.
JOURNAL OF GENETICS AND GENOMICS (2018)
m6A and eIF2α-(sic) Team Up to Tackle ATF4 Translation during Stress
Emily Nicole Powers et al.
MOLECULAR CELL (2018)
The Definition of Open Reading Frame Revisited
Patricia Sieber et al.
TRENDS IN GENETICS (2018)
Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development
Hong Zhang et al.
PLOS BIOLOGY (2018)
TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response
Dmitry E. Andreev et al.
ELIFE (2018)
Genome editing of upstream open reading frames enables translational control in plants
Huawei Zhang et al.
NATURE BIOTECHNOLOGY (2018)
REDIportal: a comprehensive database of A-to-I RNA editing events in humans
Ernesto Picardi et al.
NUCLEIC ACIDS RESEARCH (2017)
COSMIC: somatic cancer genetics at high-resolution
Simon A. Forbes et al.
NUCLEIC ACIDS RESEARCH (2017)
Genome-wide identification and differential analysis of translational initiation
Peng Zhang et al.
NATURE COMMUNICATIONS (2017)
Data Descriptor: FANTOM5 CAGE profiles of human and mouse samples
Shuhei Noguchi et al.
SCIENTIFIC DATA (2017)
Detecting actively translated open reading frames in ribosome profiling data
Lorenzo Calviello et al.
NATURE METHODS (2016)
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes
Patricia P. Chan et al.
NUCLEIC ACIDS RESEARCH (2016)
ClinVar: public archive of interpretations of clinically relevant variants
Melissa J. Landrum et al.
NUCLEIC ACIDS RESEARCH (2016)
Comprehensive translational control of tyrosine kinase expression by upstream open reading frames
K. Wethmar et al.
ONCOGENE (2016)
Ribosome Footprint Profiling of Translation throughout the Genome
Nicholas T. Ingolia
CELL (2016)
Upstream ORFs are prevalent translational repressors in vertebrates
Timothy G. Johnstone et al.
EMBO JOURNAL (2016)
Re-evaluation of G-quadruplex propensity with G4Hunter
Amina Bedrat et al.
NUCLEIC ACIDS RESEARCH (2016)
Translation from the 5′ untranslated region shapes the integrated stress response
Shelley R. Starck et al.
SCIENCE (2016)
Translational control by 5′-untranslated regions of eukaryotic mRNAs
Alan G. Hinnebusch et al.
SCIENCE (2016)
JBrowse: a dynamic web platform for genome visualization and analysis
Robert Buels et al.
GENOME BIOLOGY (2016)
The Ensembl Variant Effect Predictor
William McLaren et al.
GENOME BIOLOGY (2016)
The Genotype-Tissue Expression (GTEx) Project
Latarsha J. Carithers et al.
BIOPRESERVATION AND BIOBANKING (2015)
Functional Anatomy of the Human Microprocessor
Tuan Anh Nguyen et al.
CELL (2015)
The Genotype-Tissue Expression (GTEx) Project
Latarsha J. Carithers et al.
BIOPRESERVATION AND BIOBANKING (2015)
Many lncRNAs, 5′UTRs, and pseudogenes are translated and some are likely to express functional proteins
Zhe Ji et al.
ELIFE (2015)
RNA regulons in Hox 5 ' UTRs confer ribosome specificity to gene regulation
Shifeng Xue et al.
NATURE (2015)
A draft map of the human proteome
Min-Sik Kim et al.
NATURE (2014)
uORFdb-a comprehensive literature database on eukaryotic uORF biology
Klaus Wethmar et al.
NUCLEIC ACIDS RESEARCH (2014)
TISdb: a database for alternative translation initiation in mammalian cells
Ji Wan et al.
NUCLEIC ACIDS RESEARCH (2014)
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
Danielle Welter et al.
NUCLEIC ACIDS RESEARCH (2014)
Polyamine-Responsive Ribosomal Arrest at the Stop Codon of an Upstream Open Reading Frame of the AdoMetDC1 Gene Triggers Nonsense-Mediated mRNA Decay in Arabidopsis thaliana
Naoko Uchiyama-Kadokura et al.
PLANT AND CELL PHYSIOLOGY (2014)
Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis
Piyada Juntawong et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin et al.
BIOINFORMATICS (2013)
Gene Expression Regulation by Upstream Open Reading Frames and Human Disease
Cristina Barbosa et al.
PLOS GENETICS (2013)
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Nicholas T. Ingolia et al.
NATURE PROTOCOLS (2012)
5′-UTR RNA G-quadruplexes: translation regulation and targeting
Anthony Bugaut et al.
NUCLEIC ACIDS RESEARCH (2012)
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
Nicholas T. Ingolia et al.
CELL (2011)
Integrative genomics viewer
James T. Robinson et al.
NATURE BIOTECHNOLOGY (2011)
SignalP 4.0: discriminating signal peptides from transmembrane regions
Thomas Nordahl Petersen et al.
NATURE METHODS (2011)
Detection of nonneutral substitution rates on mammalian phylogenies
Katherine S. Pollard et al.
GENOME RESEARCH (2010)
5'-UTR G-quadruplex structures acting as translational repressors
Jean-Denis Beaudoin et al.
NUCLEIC ACIDS RESEARCH (2010)
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
Sarah E. Calvo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
Peng Lu et al.
NATURE BIOTECHNOLOGY (2007)
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
A Siepel et al.
GENOME RESEARCH (2005)
The Ensembl genome database project
T Hubbard et al.
NUCLEIC ACIDS RESEARCH (2002)
Upstream open reading frames as regulators of mRNA translation
DR Morris et al.
MOLECULAR AND CELLULAR BIOLOGY (2000)
dbSNP: a database of single nucleotide polymorphisms
EM Smigielski et al.
NUCLEIC ACIDS RESEARCH (2000)