Translation of neutrally evolving peptides provides a basis for de novo gene evolution

New Genes and Functional Innovation in Mammals

(2017) José Luis Villanueva-Cañas et al.   Genome Biology and Evolution

Classification and function of small open reading frames

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

Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth

(2017) Benjamin A. Wilson et al.   Nature Ecology & Evolution

Random sequences are an abundant source of bioactive RNAs or peptides

(2017) Rafik Neme et al.   Nature Ecology & Evolution

Open questions in the study of de novo genes: what, how and why

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

Hemotin, a Regulator of Phagocytosis Encoded by a Small ORF and Conserved across Metazoans

(2016) José I. Pueyo et al.   PLOS BIOLOGY

Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence

(2016) Rafik Neme et al.   eLife

Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus

(2016) Bettina Harr et al.   Scientific Data

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

(2015) R. Axel W. Wiberg et al.   Genome Biology and Evolution

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding

(2015) Chien-Hung Yu et al.   MOLECULAR CELL

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The RNA-binding protein HuR is essential for the B cell antibody response

(2015) Manuel D Diaz-Muñoz et al.   NATURE IMMUNOLOGY

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Multiple repressive mechanisms in the hippocampus during memory formation

(2015) J. Cho et al.   SCIENCE

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

Origins of De Novo Genes in Human and Chimpanzee

(2015) Jorge Ruiz-Orera et al.   PLoS Genetics

Uncovering adaptive evolution in the human lineage

(2014) Magdalena Gayà-Vidal et al.   BMC GENOMICS

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

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

Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice

(2014) J. Castaneda et al.   EMBO JOURNAL

Ribosome Profiling Reveals a Cell-Type-Specific Translational Landscape in Brain Tumors

(2014) C. Gonzalez et al.   JOURNAL OF NEUROSCIENCE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

The effect of tRNA levels on decoding times of mRNA codons

(2014) Alexandra Dana et al.   NUCLEIC ACIDS RESEARCH

Evolutionary meandering of intermolecular interactions along the drift barrier

(2014) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

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

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences

(2013) Josephine A. Reinhardt et al.   PLoS Genetics

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

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

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

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

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

(2011) Nicholas T. Ingolia et al.   CELL

Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

(2011) Benjamin A. Wilson et al.   Genome Biology and Evolution

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

ConDeTri - A Content Dependent Read Trimmer for Illumina Data

(2011) Linnéa Smeds et al.   PLoS One

Relaxed Purifying Selection and Possibly High Rate of Adaptation in Primate Lineage-Specific Genes

(2010) James J. Cai et al.   Genome Biology and Evolution

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

Emergence of a New Gene from an Intergenic Region

(2009) Tobias J.A.J. Heinen et al.   CURRENT BIOLOGY

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

(2009) N. T. Ingolia et al.   SCIENCE

Origin of Primate Orphan Genes: A Comparative Genomics Approach

(2008) M. Toll-Riera et al.   MOLECULAR BIOLOGY AND EVOLUTION