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

Newly evolved genes: Moving from comparative genomics to functional studies in model systems

(2012) José M. Ranz et al.   BIOESSAYS

The Fetal Brain Provides a Raison d’être for the Evolution of New Human Genes

(2012) Genevieve Konopka   BRAIN BEHAVIOR AND EVOLUTION

Inhibition of SRGAP2 Function by Its Human-Specific Paralogs Induces Neoteny during Spine Maturation

(2012) Cécile Charrier et al.   CELL

Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication

(2012) Megan Y. Dennis et al.   CELL

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Frequent Recent Origination of Brain Genes Shaped the Evolution of Foraging Behavior in Drosophila

(2012) Sidi Chen et al.   Cell Reports

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

When orthologs diverge between human and mouse

(2011) W. H. Gharib et al.   BRIEFINGS IN BIOINFORMATICS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster

(2011) D. R. Schrider et al.   GENOME RESEARCH

Identification of Novel GDNF Isoforms andcis-Antisense GDNFOS Gene and Their Regulation in Human Middle Temporal Gyrus of Alzheimer Disease

(2011) Mikko Airavaara et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2011) Kerstin Lindblad-Toh et al.   NATURE

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Translation Goes Global

(2011) R. B. Weiss et al.   SCIENCE

Accelerated Recruitment of New Brain Development Genes into the Human Genome

(2011) Yong E. Zhang et al.   PLOS BIOLOGY

De Novo Origin of Human Protein-Coding Genes

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

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

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

Age-dependent chromosomal distribution of male-biased genes in Drosophila

(2010) Y. E. Zhang et al.   GENOME RESEARCH

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Proteogenomics to discover the full coding content of genomes: A computational perspective

(2010) Natalie Castellana et al.   Journal of Proteomics

Mass spectrometry at the interface of proteomics and genomics

(2010) Karsten Krug et al.   Molecular BioSystems

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Mutational effects and the evolution of new protein functions

(2010) Misha Soskine et al.   NATURE REVIEWS GENETICS

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

(2010) Yong E. Zhang et al.   PLOS BIOLOGY

A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions

(2010) Chuan-Yun Li et al.   PLoS Computational Biology

Positive selection for the male functionality of a co-retroposed gene in the hominoids

(2009) Yong Zhang et al.   BMC EVOLUTIONARY BIOLOGY

Emergence of a New Gene from an Intergenic Region

(2009) Tobias J.A.J. Heinen et al.   CURRENT BIOLOGY

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

Human-specific transcriptional regulation of CNS development genes by FOXP2

(2009) Genevieve Konopka et al.   NATURE

Database resources of the National Center for Biotechnology Information

(2009) Eric W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Genomic Clues to DNA Treasure Sometimes Lead Nowhere

(2009) D. Monroe   SCIENCE

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

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

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

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

On the origin of new genes in Drosophila

(2008) Q. Zhou et al.   GENOME RESEARCH

On the origin and evolution of new genes—a genomic and experimental perspective

(2008) Qi Zhou et al.   Journal of Genetics and Genomics

PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution

(2008) J. J. Cai   JOURNAL OF HEREDITY

The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression

(2008) Jacob L Mueller et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The evolution of courtship behaviors through the origination of a new gene in Drosophila

(2008) H. Dai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Null mutations in human and mouse orthologs frequently result in different phenotypes

(2008) B.-Y. Liao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Steady progress and recent breakthroughs in the accuracy of automated genome annotation

(2007) Michael R. Brent   NATURE REVIEWS GENETICS