A Molecular Portrait of De Novo Genes in Yeasts

Further Simulations and Analyses Demonstrate Open Problems of Phylostratigraphy

(2017) Bryan A. Moyers et al.   Genome Biology and Evolution

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

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

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

(2016) Nikolaos Vakirlis et al.   GENOME RESEARCH

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

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

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar 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

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

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

Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast

(2015) I. Lam et al.   SCIENCE

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

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

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

(2015) Marina Marcet-Houben et al.   PLOS BIOLOGY

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

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

(2015) Zhe Ji et al.   eLife

Remote homology and the functions of metagenomic dark matter

(2015) Briallen Lobb et al.   Frontiers in Genetics

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

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

Estimating the Phanerozoic history of the Ascomycota lineages: Combining fossil and molecular data

(2014) Christina Beimforde et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

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

(2013) Rafik Neme et al.   BMC GENOMICS

Divergent Transcription: A Driving Force for New Gene Origination?

(2013) Xuebing Wu et al.   CELL

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

(2013) G. Abrusan   GENETICS

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution and function of de novo originated genes

(2013) Dong-Dong Wu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Arabidopsis meiotic crossover hot spots overlap with H2A.Z nucleosomes at gene promoters

(2013) Kyuha Choi et al.   NATURE GENETICS

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Bidirectional Promoters as Important Drivers for the Emergence of Species-Specific Transcripts

(2013) Valer Gotea et al.   PLoS One

Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs

(2013) Adam Auton 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

Estimating divergence times in large molecular phylogenies

(2012) K. Tamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Chen Xie et al.   PLoS Genetics

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

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

A Hierarchical Combination of Factors Shapes the Genome-wide Topography of Yeast Meiotic Recombination Initiation

(2011) Jing Pan et al.   CELL

De novo origin of new genes with introns inPlasmodium vivax

(2011) Zefeng Yang et al.   FEBS LETTERS

Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

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

An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework

(2011) J.-P Doyon et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2011) M. Toll-Riera 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

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

How do new proteins arise?

(2010) Erich Bornberg-Bauer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Relaxed Purifying Selection and Possibly High Rate of Adaptation in Primate Lineage-Specific Genes

(2010) James J. Cai et al.   Genome Biology and Evolution

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast

(2010) Michael D. Barton et al.   PLoS One

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

Darwinian alchemy: Human genes from noncoding DNA

(2009) A. Siepel   GENOME RESEARCH

Recent de novo origin of human protein-coding genes

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

Comparative genomics of protoploid Saccharomycetaceae

(2009) et al.   GENOME RESEARCH

A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae

(2009) L. E. Berchowitz et al.   GENOME RESEARCH

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

(2009) Helen Neil et al.   NATURE

Insertion of Horizontally Transferred Genes within Conserved Syntenic Regions of Yeast Genomes

(2009) Thomas Rolland et al.   PLoS One

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

(2009) Konstantin Khalturin et al.   TRENDS IN GENETICS

Acquisition of prokaryotic genes by fungal genomes

(2009) Marina Marcet-Houben 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

High-resolution mapping of meiotic crossovers and non-crossovers in yeast

(2008) Eugenio Mancera et al.   NATURE

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Conservation of divergent transcription in fungi

(2008) Philip R. Kensche et al.   TRENDS IN GENETICS