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

CRISPR germline engineering—the community speaks

(2015) Katrine S Bosley et al.   NATURE BIOTECHNOLOGY

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

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

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

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

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

(2014) A. Pauli et al.   SCIENCE

The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes

(2014) Leng Han et al.   Nature Communications

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

(2014) Nicholas T. Ingolia 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

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

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

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

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

(2013) E. G. Magny et al.   SCIENCE

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

(2012) Shanker Kalyana-Sundaram et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

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

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena 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

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

A Transcriptional Signature and Common Gene Networks Link Cancer with Lipid Metabolism and Diverse Human Diseases

(2010) Heather A. Hirsch et al.   CANCER CELL

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

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

(2010) Andrew J Oler et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells

(2010) Zarmik Moqtaderi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

An Epigenetic Switch Involving NF-κB, Lin28, Let-7 MicroRNA, and IL6 Links Inflammation to Cell Transformation

(2009) Dimitrios Iliopoulos et al.   CELL

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH