Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates

Evolution: Dynamics of De Novo Gene Emergence

(2014) Rafik Neme et al.   CURRENT BIOLOGY

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

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

Evolutionary Interrogation of Human Biology in Well-Annotated Genomic Framework of Rhesus Macaque

(2014) Shi-Jian Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

RNA Editome in Rhesus Macaque Shaped by Purifying Selection

(2014) Jia-Yu Chen et al.   PLoS Genetics

The life cycle of Drosophila orphan genes

(2014) Nicola Palmieri et al.   eLife

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera 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

Divergent Transcription: A Driving Force for New Gene Origination?

(2013) Xuebing Wu et al.   CELL

Primate genome architecture influences structural variation mechanisms and functional consequences

(2013) O. Gokcumen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The rhesus macaque is three times as diverse but more closely equivalent in damaging coding variation as compared to the human

(2012) Qiaoping Yuan et al.   BMC GENETICS

CLLU1 expression has prognostic value in chronic lymphocytic leukemia after first-line therapy in younger patients and in those with mutated IGHV genes

(2012) D. Gonzalez et al.   HAEMATOLOGICA

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

RhesusBase: a knowledgebase for the monkey research community

(2012) Shi-Jian Zhang et al.   NUCLEIC ACIDS RESEARCH

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Chen Xie et al.   PLoS Genetics

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

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

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

(2011) Guangmei Yan et al.   NATURE BIOTECHNOLOGY

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Preventing Dangerous Nonsense: Selection for Robustness to Transcriptional Error in Human Genes

(2011) Brian P. Cusack et al.   PLoS Genetics

De Novo Origin of Human Protein-Coding Genes

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

Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque

(2011) Xiaodong Fang et al.   GENOME BIOLOGY

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

MYEOV is a prognostic factor in multiple myeloma

(2010) Jerome Moreaux et al.   EXPERIMENTAL HEMATOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq

(2010) Yi Liu et al.   NUCLEIC ACIDS RESEARCH

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(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

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

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS 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

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

Origin of Primate Orphan Genes: A Comparative Genomics Approach

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

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE