Rapid evolution of protein diversity by de novo origination in Oryza

Origins and structural properties of novel and de novo protein domains during insect evolution

(2018) Steffen Klasberg et al.   FEBS Journal

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

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

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

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Functional horizontal gene transfer from bacteria to eukaryotes

(2017) Filip Husnik et al.   NATURE REVIEWS MICROBIOLOGY

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

Random sequences are an abundant source of bioactive RNAs or peptides

(2017) Rafik Neme et al.   Nature Ecology & Evolution

Functional innovation from changes in protein domains and their combinations

(2016) Jonathan G Lees et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Comprehensive Investigation toward the Indicative Proteins of Bladder Cancer in Urine: From Surveying Cell Secretomes to Verifying Urine Proteins

(2016) Jiao Guo et al.   JOURNAL OF PROTEOME RESEARCH

Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution

(2016) Bryan A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptomics resources of human tissues and organs

(2016) M. Uhlen et al.   Molecular Systems Biology

A multicenter study benchmarks software tools for label-free proteome quantification

(2016) Pedro Navarro et al.   NATURE BIOTECHNOLOGY

Open questions in the study of de novo genes: what, how and why

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

High-precision iRT prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation

(2016) Roland Bruderer et al.   PROTEOMICS

Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation

(2016) Dongyan Zhao et al.   G3-Genes Genomes Genetics

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

(2015) Tristan Bitard-Feildel et al.   BIOCHIMIE

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics

(2015) Yi Zhao et al.   BMC EVOLUTIONARY BIOLOGY

The potential clinical impact of the tissue-based map of the human proteome

(2015) Cecilia Lindskog   Expert Review of Proteomics

Biomarker Discovery and Verification of Esophageal Squamous Cell Carcinoma Using Integration of SWATH/MRM

(2015) Guixue Hou et al.   JOURNAL OF PROTEOME RESEARCH

A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery

(2015) Martin Sjöström et al.   JOURNAL OF PROTEOME RESEARCH

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome

(2015) Xiao Cui et al.   Molecular Plant

IPeak: An open source tool to combine results from multiple MS/MS search engines

(2015) Bo Wen et al.   PROTEOMICS

Applications of targeted proteomics in systems biology and translational medicine

(2015) H. Alexander Ebhardt et al.   PROTEOMICS

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

“Out of Pollen” Hypothesis for Origin of New Genes in Flowering Plants: Study from Arabidopsis thaliana

(2014) Dong-Dong Wu et al.   Genome Biology and Evolution

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

(2014) Muhua Wang et al.   NATURE GENETICS

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

New Gene Evolution: Little Did We Know

(2013) Manyuan Long et al.   Annual Review of Genetics

Dynamics and adaptive benefits of modular protein evolution

(2013) Erich Bornberg-Bauer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

High Occurrence of Functional New Chimeric Genes in Survey of Rice Chromosome 3 Short Arm Genome Sequences

(2013) Chengjun Zhang et al.   Genome Biology and Evolution

Quantitative Analysis of the Human AKR Family Members in Cancer Cell Lines Using the mTRAQ/MRM Approach

(2013) Shenyan Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Western BlotsversusSelected Reaction Monitoring Assays: Time to Turn the Tables?

(2013) Ruedi Aebersold et al.   MOLECULAR & CELLULAR PROTEOMICS

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

(2013) Hiroaki Sakai et al.   PLANT AND CELL PHYSIOLOGY

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

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

(2012) Yong E. Zhang et al.   BIOESSAYS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes

(2012) Florent Murat et al.   Genome Biology and Evolution

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

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

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

(2011) Mark TA Donoghue et al.   BMC EVOLUTIONARY BIOLOGY

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

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

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

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

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

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen 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

Emergence of a New Gene from an Intergenic Region

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

Pervasive transcription constitutes a new level of eukaryotic genome regulation

(2009) Julia Berretta et al.   EMBO REPORTS

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

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

(2009) Wenfei Xiao et al.   PLoS One

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

Origin of Primate Orphan Genes: A Comparative Genomics Approach

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

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH