Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation

The LINC00961 transcript and its encoded micropeptide, small regulatory polypeptide of amino acid response, regulate endothelial cell function

(2020) Helen L Spencer et al.   CARDIOVASCULAR RESEARCH

Long non‐coding RNAs in development and disease: conservation to mechanisms

(2020) Ioannis Tsagakis et al.   JOURNAL OF PATHOLOGY

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

The Proteomic Landscape of Cysteine Oxidation That Underpins Retinoic Acid-Induced Neuronal Differentiation

(2020) Katrin Brenig et al.   JOURNAL OF PROTEOME RESEARCH

The micropeptide LEMP plays an evolutionarily conserved role in myogenesis

(2020) Lantian Wang et al.   Cell Death & Disease

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

(2020) Chloe Chong et al.   Nature Communications

Functional annotation of human long noncoding RNAs via molecular phenotyping

(2020) Jordan A. Ramilowski et al.   GENOME RESEARCH

Translation of upstream open reading frames in a model of neuronal differentiation

(2019) Caitlin M. Rodriguez et al.   BMC GENOMICS

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Developmental dynamics of lncRNAs across mammalian organs and species

(2019) Ioannis Sarropoulos et al.   NATURE

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

HuR interacts with lincBRN1a and lincBRN1b during neuronal stem cells differentiation

(2019) Stephana Carelli et al.   RNA Biology

LncRNA LINC01116 Promotes Cancer Cell Proliferation, Migration And Invasion In Gastric Cancer By Positively Interacting With lncRNA CASC11

(2019) Xiaohui Su et al.   OncoTargets and Therapy

ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

(2019) Niels Hulstaert et al.   JOURNAL OF PROTEOME RESEARCH

Heterochromatin protein 1α interacts with parallel RNA and DNA G-quadruplexes

(2019) Ruby J Roach et al.   NUCLEIC ACIDS RESEARCH

The long noncoding RNA lncR492 inhibits neural differentiation of murine embryonic stem cells

(2018) Maria Winzi et al.   PLoS One

The Long Non-coding RNA lnc-31 Interacts with Rock1 mRNA and Mediates Its YB-1-Dependent Translation

(2018) Dacia Dimartino et al.   Cell Reports

Downregulation of ribosome biogenesis during early forebrain development

(2018) Kevin F Chau et al.   eLife

Mass spectrometry evaluation of a neuroblastoma SH-SY5Y cell culture protocol

(2018) Jimmy Rodriguez Murillo et al.   ANALYTICAL BIOCHEMISTRY

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

UniProt: a worldwide hub of protein knowledge

(2018)   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

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pervasive translational regulation of the cell signalling circuitry underlies mammalian development

(2017) Kotaro Fujii et al.   Nature Communications

The novel long non-coding RNA TALNEC2, regulates tumor cell growth and the stemness and radiation response of glioma stem cells

(2017) Shlomit Brodie et al.   Oncotarget

Widespread Translational Remodeling during Human Neuronal Differentiation

(2017) John D. Blair et al.   Cell Reports

MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search

(2016) Noa Rappaport et al.   NUCLEIC ACIDS RESEARCH

RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data

(2016) Audrey M. Michel et al.   RNA Biology

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

(2016) Joana Carlevaro-Fita et al.   RNA

HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development

(2016) Susan J. Lindsay et al.   Frontiers in Neuroanatomy

msa: an R package for multiple sequence alignment

(2015) Ulrich Bodenhofer et al.   BIOINFORMATICS

protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences

(2015) Nan Xiao et al.   BIOINFORMATICS

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

(2015) Douglas M. Anderson et al.   CELL

Discovery and characterization of smORF-encoded bioactive polypeptides

(2015) Alan Saghatelian et al.   Nature Chemical Biology

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells

(2015) Jian-Rong Li et al.   NUCLEIC ACIDS RESEARCH

The Novel Gene CRNDE Encodes a Nuclear Peptide (CRNDEP) Which Is Overexpressed in Highly Proliferating Tissues

(2015) Lukasz Michal Szafron et al.   PLoS One

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

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

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

The translational landscape of fission-yeast meiosis and sporulation

(2014) Caia D S Duncan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

(2014) Julie L Aspden et al.   eLife

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

(2013) Per Johnsson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Phenotypic Characterization of Retinoic Acid Differentiated SH-SY5Y Cells by Transcriptional Profiling

(2013) Joanna A. Korecka et al.   PLoS One

Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames

(2013) E. G. Magny et al.   SCIENCE

MalaCards: an integrated compendium for diseases and their annotation

(2013) Noa Rappaport et al.   Database-The Journal of Biological Databases and Curation

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

LncRNADisease: a database for long-non-coding RNA-associated diseases

(2012) Geng Chen et al.   NUCLEIC ACIDS RESEARCH

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Metastats: an improved statistical method for analysis of metagenomic data

(2012)   GENOME BIOLOGY

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

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

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Widespread establishment and regulatory impact of Alu exons in human genes

(2011) S. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

(2010) Rebecca A Chodroff et al.   GENOME BIOLOGY

Evidence for natural antisense transcript-mediated inhibition of microRNA function

(2010) Mohammad Ali Faghihi et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

The 11-aminoacid long Tarsal-less peptides trigger a cell signal in Drosophila leg development

(2008) Jose Ignacio Pueyo et al.   DEVELOPMENTAL BIOLOGY