Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus

(2015) Praveen Baskaran et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptomic characterisation and genomic glimps into the toxigenic dinoflagellate Azadinium spinosum, with emphasis on polykeitde synthase genes

(2015) Jan M Meyer et al.   BMC GENOMICS

Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis)

(2015) Yuantao Xu et al.   BMC GENOMICS

Identification and evolution of the orphan genes in the domestic silkworm,Bombyx mori

(2015) Wei Sun et al.   FEBS LETTERS

Genome-wide identification of lineage-specific genes within Caenorhabditis elegans

(2015) Kun Zhou et al.   GENOMICS

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation

(2015) Melanie G. Mayer et al.   PLoS Genetics

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

(2015) Philine G. D. Feulner et al.   PLoS Genetics

Genomics of Ecological Adaptation in Cactophilic Drosophila

(2015) Yolanda Guillén et al.   Genome Biology and Evolution

Microevolution of Duplications and Deletions and Their Impact on Gene Expression in the Nematode Pristionchus pacificus

(2015) Praveen Baskaran et al.   PLoS One

Characterization of Genetic Diversity in the NematodePristionchus pacificusfrom Population-Scale Resequencing Data

(2014) Christian Rödelsperger et al.   GENETICS

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

Comparative RNAi Screens in C. elegans and C. briggsae Reveal the Impact of Developmental System Drift on Gene Function

(2014) Adrian J. Verster et al.   PLoS Genetics

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

(2014) Frédéric J. J. Chain et al.   PLoS Genetics

The life cycle of Drosophila orphan genes

(2014) Nicola Palmieri et al.   eLife

Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish

(2013) Liandong Yang et al.   BMC GENOMICS

A Developmental Switch Coupled to the Evolution of Plasticity Acts through a Sulfatase

(2013) Erik J. Ragsdale et al.   CELL

Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes

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

Cryptic variation in vulva development by cis-regulatory evolution of a HAIRY-binding site

(2013) Simone Kienle et al.   Nature Communications

Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans

(2012) Amit Sinha et al.   BMC GENOMICS

Expressional and functional variation of horizontally acquired cellulases in the nematode Pristionchus pacificus

(2012) Lisa N. Schuster et al.   GENE

The importance of being regular: Caenorhabditis elegans and Pristionchus pacificus defecation mutants are hypersusceptible to bacterial pathogens

(2012) Robbie Rae et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Phosphoproteome ofPristionchus pacificusProvides Insights into Architecture of Signaling Networks in Nematode Models

(2012) Nadine Borchert et al.   MOLECULAR & CELLULAR PROTEOMICS

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

System Wide Analysis of the Evolution of Innate Immunity in the Nematode Model Species Caenorhabditis elegans and Pristionchus pacificus

(2012) Amit Sinha et al.   PLoS One

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Computational archaeology of the Pristionchus pacificus genome reveals evidence of horizontal gene transfers from insects

(2011) Christian Rödelsperger et al.   BMC EVOLUTIONARY BIOLOGY

Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover

(2011) Werner E Mayer et al.   BMC EVOLUTIONARY BIOLOGY

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Genome-wide patterns of divergence during speciation: the lake whitefish case study

(2011) S. Renaut et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models

(2010) N. Borchert et al.   GENOME RESEARCH

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

Functional annotations improve the predictive score of human disease-related mutations in proteins

(2009) Remo Calabrese et al.   HUMAN MUTATION

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

(2009) Konstantin Khalturin et al.   TRENDS IN GENETICS

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Origin of Primate Orphan Genes: A Comparative Genomics Approach

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

Comparative genomics and the study of evolution by natural selection

(2008) HANS ELLEGREN   MOLECULAR ECOLOGY

The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

(2008) Christoph Dieterich et al.   NATURE GENETICS