Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover

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

(2018) Jorge Ruiz-Orera et al.   Nature Ecology & Evolution

New Genes and Functional Innovation in Mammals

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

Random protein sequences can form defined secondary structures and are well-tolerated in vivo

(2017) Vyacheslav Tretyachenko et al.   Scientific Reports

High GC content causes orphan proteins to be intrinsically disordered

(2017) Walter Basile et al.   PLoS Computational 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

The Nuanced Interplay of Intrinsic Disorder and Other Structural Properties Driving Protein Evolution

(2016) Joseph Ahrens et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Rafik Neme et al.   eLife

Emergence of de novo proteins from 'dark genomic matter' by 'grow slow and moult'

(2015) E. Bornberg-Bauer et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Intrinsically disordered proteins in cellular signalling and regulation

(2015) Peter E. Wright et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Death of a dogma: eukaryotic mRNAs can code for more than one protein

(2015) Hélène Mouilleron et al.   NUCLEIC ACIDS RESEARCH

Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates

(2015) Jia-Yu Chen et al.   PLoS Genetics

Origins of De Novo Genes in Human and Chimpanzee

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

(2014) B. A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

The life cycle of Drosophila orphan genes

(2014) Nicola Palmieri et al.   eLife

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

Dynamics and adaptive benefits of modular protein evolution

(2013) Erich Bornberg-Bauer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Integration of New Genes into Cellular Networks, and Their Structural Maturation

(2013) G. Abrusan   GENETICS

Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes

(2013) Lothar Wissler et al.   Genome Biology and Evolution

Chaperone machines for protein folding, unfolding and disaggregation

(2013) Helen Saibil   NATURE REVIEWS MOLECULAR CELL BIOLOGY

GWIPS-viz: development of a ribo-seq genome browser

(2013) Audrey M. Michel et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Repertoire of Foldable Regions within Whole Genomes

(2013) Guilhem Faure et al.   PLoS Computational Biology

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

Estimating intrinsic structural preferences of de novo emerging random-sequence proteins: Is aggregation the main bottleneck?

(2012) Annamária F. Ángyán et al.   FEBS LETTERS

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Exonization of transposed elements: A challenge and opportunity for evolution

(2011) Jürgen Schmitz et al.   BIOCHIMIE

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

(2011) Mark TA Donoghue et al.   BMC EVOLUTIONARY BIOLOGY

Unstructural biology coming of age

(2011) Peter Tompa   CURRENT OPINION IN STRUCTURAL BIOLOGY

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

De Novo Origin of Human Protein-Coding Genes

(2011) Dong-Dong Wu et al.   PLoS Genetics

Bringing order to protein disorder through comparative genomics and genetic interactions

(2011) Jeremy Bellay et al.   GENOME BIOLOGY

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be

(2010) Christian Schaefer et al.   BIOINFORMATICS

Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast

(2010) K. A. Geiler-Samerotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Emergence of a New Gene from an Intergenic Region

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

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

More than just orphans: are taxonomically-restricted genes important in evolution?

(2009) Konstantin Khalturin et al.   TRENDS IN GENETICS