A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila

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

(2020) Nikolaos Vakirlis et al.   eLife

Rapid evolution of protein diversity by de novo origination in Oryza

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

iMKT: the integrative McDonald and Kreitman test

(2019) Jesús Murga-Moreno et al.   NUCLEIC ACIDS RESEARCH

De novo gene birth

(2019) Stephen Branden Van Oss et al.   PLoS Genetics

Differences Between the Raw Material and the Products of de Novo Gene Birth Can Result from Mutational Biases

(2019) Lou Nielly-Thibault et al.   GENETICS

Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila

(2019) Evan Witt et al.   eLife

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

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

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

Tracing the De Novo Origin of Protein-Coding Genes in Yeast

(2018) Baojun Wu et al.   mBio

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

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

From de novo to ‘de nono’: The majority of novel protein coding genes identified with phylostratigraphy are old genes or recent duplicates

(2018) Claudio Casola   Genome Biology and Evolution

FlyBase 2.0: the next generation

(2018) Jim Thurmond et al.   NUCLEIC ACIDS RESEARCH

Further Simulations and Analyses Demonstrate Open Problems of Phylostratigraphy

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

The developmental proteome of Drosophila melanogaster

(2017) Nuria Casas-Vila et al.   GENOME RESEARCH

A Molecular Portrait of De Novo Genes in Yeasts

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

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

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

Simultaneous gene finding in multiple genomes

(2016) Stefanie König et al.   BIOINFORMATICS

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

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

(2015) Tristan Bitard-Feildel et al.   BIOCHIMIE

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

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

(2015) Alexander Kanitz et al.   GENOME BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition

(2014) Iva Kronja et al.   Cell Reports

Dopamine drives Drosophila sechellia adaptation to its toxic host

(2014) Sofía Lavista-Llanos et al.   eLife

The life cycle of Drosophila orphan genes

(2014) Nicola Palmieri et al.   eLife

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

(2014) Julie L Aspden et al.   eLife

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes

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

GWIPS-viz: development of a ribo-seq genome browser

(2013) Audrey M. Michel et al.   NUCLEIC ACIDS RESEARCH

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Genome-scale prediction of proteins with long intrinsically disordered regions

(2013) Zhenling Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

(2013) Joshua G Dunn et al.   eLife

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

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

The Many Landscapes of Recombination in Drosophila melanogaster

(2012) Josep M. Comeron et al.   PLoS Genetics

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Drosophila melanogaster recombination rate calculator

(2010) Anna-Sophie Fiston-Lavier et al.   GENE

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Identifying and Quantifying Orphan Protein Sequences in Fungi

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

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

Pervasive Natural Selection in the Drosophila Genome?

(2009) Guy Sella et al.   PLoS Genetics

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

(2008) J. Cai et al.   GENETICS

Analysis of the Drosophila melanogaster Testes Transcriptome Reveals Coordinate Regulation of Paralogous Genes

(2008) L. M. Mikhaylova et al.   GENETICS

On the origin of new genes in Drosophila

(2008) Q. Zhou et al.   GENOME RESEARCH