Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

The Definition of Open Reading Frame Revisited

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

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

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

Genetic dissection of interspecific differences in yeast thermotolerance

(2018) Carly V. Weiss et al.   NATURE GENETICS

From de novo to ‘de nono’: The majority of novel protein coding genes identified with phylostratigraphy are old genes or recent duplicates

(2018) Claudio Casola   Genome Biology and Evolution

A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology

(2018) Clara Bleuven et al.   MicrobiologyOpen

The Rapid Evolution of an Ohnolog Contributes to the Ecological Specialization of Incipient Yeast Species

(2017) Chris Eberlein et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Comprehensive Analysis of Transcript-Supported De Novo Genes in Saccharomyces sensu stricto Yeasts

(2017) Tzu-Chiao Lu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The goddard and saturn genes are essential for Drosophila male fertility and may have arisen de novo

(2017) Anna M. Gubala et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Molecular Portrait of De Novo Genes in Yeasts

(2017) Nikolaos Vakirlis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mitochondrial Recombination and Introgression during Speciation by Hybridization

(2017) Jean-Baptiste Leducq et al.   MOLECULAR BIOLOGY AND EVOLUTION

SMS: Smart Model Selection in PhyML

(2017) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ensembl 2018

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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

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data

(2016) Joshua G. Dunn et al.   BMC GENOMICS

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

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

Speciation driven by hybridization and chromosomal plasticity in a wild yeast

(2016) Jean-Baptiste Leducq et al.   Nature Microbiology

Found in translation: functions and evolution of a recently discovered alternative proteome

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Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

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Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation

(2015) Santiago Naranjo et al.   PLoS Genetics

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

(2015) Zhe Ji et al.   eLife

Effects of new mutations on fitness: insights from models and data

(2014) Thomas Bataillon et al.   Annals of the New York Academy of Sciences

Chromosomal variation segregates within incipient species and correlates with reproductive isolation

(2014) Guillaume Charron et al.   MOLECULAR ECOLOGY

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

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes

(2014) Guénola Drillon et al.   PLoS One

Long non-coding RNAs as a source of new peptides

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Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast

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Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

New genes as drivers of phenotypic evolution

(2013) Sidi Chen et al.   NATURE REVIEWS GENETICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

qPCA: a scalable assay to measure the perturbation of protein–protein interactions in living cells

(2012) Luca Freschi et al.   Molecular BioSystems

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

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

(2012) Chen Xie et al.   PLoS Genetics

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

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

The Mutational Profile of the Yeast Genome Is Shaped by Replication

(2011) N. Agier et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

(2011) Devin R. Scannell et al.   G3-Genes Genomes Genetics

The Reality of Pervasive Transcription

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

BEDTools: a flexible suite of utilities for comparing genomic features

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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

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A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions

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ABACAS: algorithm-based automatic contiguation of assembled sequences

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Recent de novo origin of human protein-coding genes

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

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

(2009) Y. I. Wolf 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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae

(2008) J. Cai et al.   GENETICS

On the origin of new genes in Drosophila

(2008) Q. Zhou et al.   GENOME RESEARCH

An in Vivo Map of the Yeast Protein Interactome

(2008) K. Tarassov et al.   SCIENCE