New Genes and Functional Innovation in Mammals

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

The life history of retrocopies illuminates the evolution of new mammalian genes

(2016) Francesco Nicola Carelli 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

Recent evolution of the salivary mucin MUC7

(2016) Duo Xu et al.   Scientific Reports

AP-57/C10orf99 is a new type of mutifunctional antimicrobial peptide

(2015) Meijia Yang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The Recent De Novo Origin of Protein C-Termini

(2015) Matthew E. Andreatta et al.   Genome Biology and Evolution

Structural Dissection of Crotalicidin, a Rattlesnake Venom Cathelicidin, Retrieves a Fragment with Antimicrobial and Antitumor Activity

(2015) Claudio Borges Falcao et al.   JOURNAL OF MEDICINAL CHEMISTRY

2016 update of the PRIDE database and its related tools

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

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression

(2015) Dmitri D. Pervouchine et al.   Nature Communications

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

Evolution: Dynamics of De Novo Gene Emergence

(2014) Rafik Neme et al.   CURRENT BIOLOGY

New genes contribute to genetic and phenotypic novelties in human evolution

(2014) Yong E Zhang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication

(2014) Oriol Pich i Roselló et al.   Genome Biology and Evolution

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

(2014) Iakes Ezkurdia et al.   HUMAN MOLECULAR GENETICS

Evolutionary Origin and Diversification of Epidermal Barrier Proteins in Amniotes

(2014) Bettina Strasser et al.   MOLECULAR BIOLOGY AND EVOLUTION

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

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

Emergence of novel domains in proteins

(2013) Macarena Toll-Riera et al.   BMC EVOLUTIONARY BIOLOGY

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

(2013) Rafik Neme et al.   BMC GENOMICS

Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes

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

Accelerated Evolution after Gene Duplication: A Time-Dependent Process Affecting Just One Copy

(2013) Cinta Pegueroles et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

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

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

New genes expressed in human brains: Implications for annotating evolving genomes

(2012) Yong E. Zhang et al.   BIOESSAYS

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

De Novo Origin of Protein-Coding Genes in Murine Rodents

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

Structure and Age Jointly Influence Rates of Protein Evolution

(2012) Macarena Toll-Riera et al.   PLoS Computational Biology

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

(2012) Chen Xie et al.   PLoS Genetics

Characterization of taxonomically restricted genes in a phylum-restricted cell type

(2012) Sabine Milde et al.   GENOME BIOLOGY

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

AMPA: an automated web server for prediction of protein antimicrobial regions

(2011) Marc Torrent et al.   BIOINFORMATICS

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

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

Taxonomically restricted genes are associated with the evolution of sociality in the honey bee

(2011) Brian R Johnson et al.   BMC GENOMICS

The Evolution of Milk Casein Genes from Tooth Genes before the Origin of Mammals

(2011) K. Kawasaki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Role of Low-Complexity Sequences in the Formation of Novel Protein Coding Sequences

(2011) M. Toll-Riera et al.   MOLECULAR BIOLOGY AND EVOLUTION

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

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

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

De Novo Origin of Human Protein-Coding Genes

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

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Lineage-Specific Variation in Intensity of Natural Selection in Mammals

(2010) M. Toll-Riera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Quantifying the mechanisms of domain gain in animal proteins

(2010) Marija Buljan et al.   GENOME 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

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Human IgA-Inducing Protein from Dendritic Cells Induces IgA Production by Naive IgD+ B Cells

(2009) M. A. Endsley et al.   JOURNAL OF IMMUNOLOGY

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

(2009) Konstantin Khalturin et al.   TRENDS IN GENETICS

Prm3, the Fourth Gene in the Mouse Protamine Gene Cluster, Encodes a Conserved Acidic Protein That Affects Sperm Motility1

(2008) Pawel Grzmil et al.   BIOLOGY OF REPRODUCTION

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

(2008) J. Cai et al.   GENETICS