De novo gene birth

Rapid evolution of protein diversity by de novo origination in Oryza

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

Inferring synteny between genome assemblies: a systematic evaluation

(2018) Dang Liu et al.   BMC BIOINFORMATICS

Origins and structural properties of novel and de novo protein domains during insect evolution

(2018) Steffen Klasberg et al.   FEBS Journal

Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes

(2018) Sara Willis et al.   GENETICS

Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes

(2018) Sara Willis et al.   GENETICS

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

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

Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences

(2018) Cemalettin Bekpen et al.   BMC EVOLUTIONARY BIOLOGY

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

(2018) Michael S Werner et al.   GENOME RESEARCH

Deep taxon sampling reveals the evolutionary dynamics of novel gene families in ​Pristionchus nematodes

(2018) Neel Prabh et al.   GENOME RESEARCH

Exosome-mediated transfer of lncRNA PART1 induces gefitinib resistance in esophageal squamous cell carcinoma via functioning as a competing endogenous RNA

(2018) Min Kang et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

Robustness by intrinsically disordered C-termini and translational readthrough

(2018) April Snofrid Kleppe et al.   NUCLEIC ACIDS RESEARCH

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

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

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

A Molecular Portrait of De Novo Genes in Yeasts

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

Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants

(2017) Polly Yingshan Hsu et al.   PROTEOMICS

Foldability of a Natural De Novo Evolved Protein

(2017) Dixie Bungard et al.   STRUCTURE

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

Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

(2017) Sondos Samandi et al.   eLife

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

Benchmarking the next generation of homology inference tools

(2016) Ganapathi Varma Saripella et al.   BIOINFORMATICS

De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting

(2016) Daniele Guerzoni et al.   Genome Biology and Evolution

On the Origin of De Novo Genes inArabidopsis thalianaPopulations

(2016) Zi-Wen Li et al.   Genome Biology and Evolution

Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution

(2016) Bryan A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

(2016) B. R. Nelson et al.   SCIENCE

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

(2016) Rafik Neme et al.   eLife

Expression of evolutionarily novel genes in tumors

(2016) A. P. Kozlov   Infectious Agents and Cancer

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

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

Detection of orphan domains in Drosophila using “hydrophobic cluster analysis”

(2015) Tristan Bitard-Feildel et al.   BIOCHIMIE

Proteny: discovering and visualizing statistically significant syntenic clusters at the proteome level

(2015) Thies Gehrmann et al.   BIOINFORMATICS

Elucidating evolutionary features and functional implications of orphan genes in Leishmania major

(2015) Sumit Mukherjee et al.   INFECTION GENETICS AND EVOLUTION

Intrinsically disordered proteins in cellular signalling and regulation

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

New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation

(2015) Aoife McLysaght et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

Evolution of New Functions De Novo and from Preexisting Genes

(2015) Dan I. Andersson et al.   Cold Spring Harbor Perspectives in Biology

Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae

(2015) Junhyun Jeon et al.   Scientific Reports

Origins of De Novo Genes in Human and Chimpanzee

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

Evaluating synteny for improved comparative studies

(2014) C. G. Ghiurcuta et al.   BIOINFORMATICS

Distinguishing between "Function" and "Effect" in Genome Biology

(2014) W. F. Doolittle et al.   Genome Biology and Evolution

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

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

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

Emerging evidence for functional peptides encoded by short open reading frames

(2014) Shea J. Andrews et al.   NATURE REVIEWS GENETICS

Defining functional DNA elements in the human genome

(2014) M. Kellis 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

Pleiotropy of the de novo-originated gene MDF1

(2014) Dan Li et al.   Scientific Reports

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

(2014) Nicholas T. Ingolia et al.   Cell Reports

NCYM, a Cis-Antisense Gene of MYCN, Encodes a De Novo Evolved Protein That Inhibits GSK3β Resulting in the Stabilization of MYCN in Human Neuroblastomas

(2014) Yusuke Suenaga et al.   PLoS Genetics

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

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

New genes as drivers of phenotypic evolution

(2013) Sidi Chen et al.   NATURE REVIEWS GENETICS

PBOV1 Is a Human De Novo Gene with Tumor-Specific Expression That Is Associated with a Positive Clinical Outcome of Cancer

(2013) Nikolay Samusik et al.   PLoS One

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

Extensive Natural Epigenetic Variation at a De Novo Originated Gene

(2013) Amanda Bortolini Silveira et al.   PLoS Genetics

Evolution of Viral Proteins Originated De Novo by Overprinting

(2012) Niv Sabath et al.   MOLECULAR BIOLOGY AND EVOLUTION

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

De Novo Origin of Protein-Coding Genes in Murine Rodents

(2012) Daniel N. Murphy et al.   PLoS One

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

(2012) Claudia Kutter et al.   PLoS Genetics

Pervasive transcription – Lessons from yeast

(2011) Mathieu Tisseur et al.   BIOCHIMIE

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

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

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

Evolution of molecular error rates and the consequences for evolvability

(2011) E. Rajon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unique Aspects of Transcription Regulation in Male Germ Cells

(2011) H. White-Cooper et al.   Cold Spring Harbor Perspectives in Biology

Accelerated Recruitment of New Brain Development Genes into the Human Genome

(2011) Yong E. Zhang et al.   PLOS BIOLOGY

The Reality of Pervasive Transcription

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

De Novo Origin of Human Protein-Coding Genes

(2011) Dong-Dong Wu et al.   PLoS 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

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

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

(2010) Chuan-Yun Li et al.   PLoS Computational Biology

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

Identifying and Quantifying Orphan Protein Sequences in Fungi

(2009) Diana Ekman et al.   JOURNAL OF MOLECULAR BIOLOGY

Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves

(2009) Ling Li et al.   PLANT JOURNAL

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

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

(2009) Konstantin Khalturin et al.   TRENDS IN GENETICS

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

Origin of Primate Orphan Genes: A Comparative Genomics Approach

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

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

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