Uncovering de novo gene birth in yeast using deep transcriptomics

De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

(2020) Nikolaos Vakirlis et al.   Nature Communications

Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes

(2020) Nikolaos Vakirlis et al.   eLife

Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids

(2019) Xuan Zhuang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid evolution of protein diversity by de novo origination in Oryza

(2019) Li Zhang et al.   Nature Ecology & Evolution

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

(2019) Éléonore Durand et al.   GENOME RESEARCH

Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker’s yeast

(2019) William R. Blevins et al.   Scientific Reports

Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory Networks

(2019) Paco Majic et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation

(2018) Michael S Werner et al.   GENOME RESEARCH

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

(2018) Jonathan F. Schmitz et al.   Nature Ecology & Evolution

Translation of Small Open Reading Frames: Roles in Regulation and Evolutionary Innovation

(2018) Jorge Ruiz-Orera et al.   TRENDS IN GENETICS

New Genes and Functional Innovation in Mammals

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

De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data

(2017) Helle Tessand Baalsrud et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Molecular Portrait of De Novo Genes in Yeasts

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

Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale

(2017) Marcel Morgenstern et al.   Cell Reports

TransRate: reference-free quality assessment of de novo transcriptome assemblies

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

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

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

Protein Abundance Control by Non-coding Antisense Transcription

(2016) Florian Huber et al.   Cell Reports

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

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

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

Coming of age: orphan genes in plants

(2014) Zebulun W. Arendsee et al.   TRENDS IN PLANT SCIENCE

Pleiotropy of the de novo-originated gene MDF1

(2014) Dan Li et al.   Scientific Reports

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

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

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

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

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

(2012) Cole Trapnell et al.   Nature Protocols

Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

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

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

(2011) E. L. van Dijk et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

(2010) Dan Li et al.   CELL RESEARCH

The Role of Nucleosome Positioning in the Evolution of Gene Regulation

(2010) Alexander M. Tsankov et al.   PLOS BIOLOGY

Recent de novo origin of human protein-coding genes

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

Climate change: Snakes tell a torrid tale

(2009) Matthew Huber   NATURE

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

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

(2009) N. T. Ingolia et al.   SCIENCE

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

(2008) J. Cai et al.   GENETICS

Origin of Primate Orphan Genes: A Comparative Genomics Approach

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

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

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