Identifying (non-)coding RNAs and small peptides: Challenges and opportunities

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

(2014) A. A. Bazzini et al.   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

Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue

(2014) Jiao Ma et al.   JOURNAL OF PROTEOME RESEARCH

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Central Cell-Derived Peptides Regulate Early Embryo Patterning in Flowering Plants

(2014) L. M. Costa et al.   SCIENCE

Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors

(2014) A. Pauli et al.   SCIENCE

A Peptide Hormone and Its Receptor Protein Kinase Regulate Plant Cell Expansion

(2014) M. Haruta et al.   SCIENCE

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

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

(2014) Julie L Aspden et al.   eLife

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

“Dark matter” worlds of unstable RNA and protein

(2014) Sabyasachi Baboo et al.   Nucleus

Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)

(2013) Peng Zhou et al.   BMC BIOINFORMATICS

Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish

(2013) Håvard Aanes et al.   BMC GENOMICS

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

(2013) Mitchell Guttman et al.   CELL

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

ELABELA: A Hormone Essential for Heart Development Signals via the Apelin Receptor

(2013) Serene C. Chng et al.   DEVELOPMENTAL CELL

Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing

(2013) J. A. Arribere et al.   GENOME RESEARCH

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

The RNA Degradation Pathway Regulates the Function of GAS5 a Non-Coding RNA in Mammalian Cells

(2013) Hidenori Tani et al.   PLoS One

Small open reading frames associated with morphogenesis are hidden in plant genomes

(2013) K. Hanada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) E. G. Magny et al.   SCIENCE

Maternal Control of Nutrient Allocation in Plant Seeds by Genomic Imprinting

(2012) Liliana M. Costa et al.   CURRENT BIOLOGY

Extensive alternative polyadenylation during zebrafish development

(2012) I. Ulitsky et al.   GENOME RESEARCH

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

Observation of dually decoded regions of the human genome using ribosome profiling data

(2012) A. M. Michel et al.   GENOME RESEARCH

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

(2012) C. Fritsch et al.   GENOME RESEARCH

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

(2012) Chen Xie et al.   PLoS Genetics

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

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

Identification of prokaryotic small proteins using a comparative genomic approach

(2011) Josue Samayoa et al.   BIOINFORMATICS

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

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

(2011) Nicholas T. Ingolia et al.   CELL

Peptide Signaling in Plant Development

(2011) Leron Katsir et al.   CURRENT BIOLOGY

An expanding universe of small proteins

(2011) Errett C Hobbs et al.   CURRENT OPINION IN MICROBIOLOGY

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

(2011) Håvard Aanes et al.   GENOME RESEARCH

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

Expression of two novel transcripts in the mouse definitive endoderm

(2010) Ali S. Hassan et al.   GENE EXPRESSION PATTERNS

C/EBP  uORF mice--a genetic model for uORF-mediated translational control in mammals

(2010) K. Wethmar et al.   GENES & DEVELOPMENT

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

sORF finder: a program package to identify small open reading frames with high coding potential

(2009) Kousuke Hanada et al.   BIOINFORMATICS

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

(2009) N. T. Ingolia et al.   SCIENCE

Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells

(2008) Kazuko Hanyu-Nakamura et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The EPIP Peptide of INFLORESCENCE DEFICIENT IN ABSCISSION Is Sufficient to Induce Abscission in Arabidopsis through the Receptor-Like Kinases HAESA and HAESA-LIKE2

(2008) G.-E. Stenvik et al.   PLANT CELL

Repression of RNA Polymerase II Transcription by a Drosophila Oligopeptide

(2008) Gyula Timinszky et al.   PLoS One

Regulation of floral organ abscission in Arabidopsis thaliana

(2008) S. K. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology