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

Stepwise Evolution of a Buried Inhibitor Peptide over 45 My

(2017) Achala S. Jayasena et al.   MOLECULAR BIOLOGY AND EVOLUTION

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

(2017) Jia-Xing Yue et al.   NATURE GENETICS

Ribosome Footprint Profiling of Translation throughout the Genome

(2016) Nicholas T. Ingolia   CELL

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

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

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

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting

(2015) Lea Fellner et al.   BMC EVOLUTIONARY BIOLOGY

The 100-genomes strains, anS. cerevisiaeresource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

(2015) Pooja K. Strope et al.   GENOME RESEARCH

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

(2015) Alexander P. Fields et al.   MOLECULAR CELL

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Expression Profile and Gene Age Jointly Shaped the Genome-Wide Distribution of Premature Termination Codons in a Drosophila melanogaster Population

(2014) Haiwang Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

The life cycle of Drosophila orphan genes

(2014) Nicola Palmieri 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

Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes

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

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses

(2013) Angelo Pavesi et al.   PLoS Computational Biology

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

Evolution of cis-regulatory elements in yeast de novo and duplicated new genes

(2012) Zing Tsung-Yeh Tsai et al.   BMC GENOMICS

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

De Novo Origin of Protein-Coding Genes in Murine Rodents

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

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

(2012) Chen Xie et al.   PLoS Genetics

Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments

(2011) Seán S ÓhÉigeartaigh et al.   BMC GENOMICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational 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

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

Evolutionary Roles of Upstream Open Reading Frames in Mediating Gene Regulation in Fungi

(2009) Heather M. Hood et al.   Annual Review of Microbiology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation

(2009) C. Rancurel et al.   JOURNAL OF VIROLOGY

A Rice Gene of De Novo Origin Negatively Regulates Pathogen-Induced Defense Response

(2009) Wenfei Xiao et al.   PLoS One

Identification and Gene Expression Analysis of a Taxonomically Restricted Cysteine-Rich Protein Family in Reef-Building Corals

(2009) Shinichi Sunagawa et al.   PLoS One

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

(2009) N. T. Ingolia et al.   SCIENCE

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

(2009) Konstantin Khalturin et al.   TRENDS IN GENETICS

Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome

(2009) Jonathan L. Gordon et al.   PLoS 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

Revisiting the Saccharomyces cerevisiae predicted ORFeome

(2008) Q.-R. Li et al.   GENOME RESEARCH

Origin of Primate Orphan Genes: A Comparative Genomics Approach

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

Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites

(2008) R. Egea et al.   NUCLEIC ACIDS RESEARCH