Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting

The Recent De Novo Origin of Protein C-Termini

(2015) Matthew E. Andreatta et al.   Genome Biology and Evolution

Studying protein fold evolution with hybrids of differently folded homologs

(2015) Karen V. Eaton et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Gene duplication and the evolution of moonlighting proteins

(2015) Adriana Espinosa-Cantú et al.   Frontiers in Genetics

Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces

(2014) Richard Landstorfer et al.   BMC GENOMICS

Overlapping transcription and bacterial RNA removal

(2014) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

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

Phenotype ofhtgA(mbiA), a recently evolved orphan gene ofEscherichia coliandShigella, completely overlapping in antisense toyaaW

(2013) Lea Fellner et al.   FEMS MICROBIOLOGY LETTERS

Identification of the Set of Genes, Including Nonannotated morA, under the Direct Control of ModE in Escherichia coli

(2013) T. Kurata et al.   JOURNAL OF BACTERIOLOGY

The Effect of Gene Overlapping on the Rate of RNA Virus Evolution

(2013) Etienne Simon-Loriere et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Scalable web services for the PSIPRED Protein Analysis Workbench

(2013) Daniel W. A. Buchan et al.   NUCLEIC ACIDS RESEARCH

Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes

(2013) J. J. Carter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous prediction of protein secondary structure and transmembrane spans

(2013) Julia Koehler Leman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses

(2013) Angelo Pavesi et al.   PLoS Computational Biology

Thousands of missed genes found in bacterial genomes and their analysis with COMBREX

(2012) Derrick E Wood et al.   Biology Direct

A novel gene,ardD, determines antirestriction activity of the non-conjugative transposon Tn5053and is located antisense within thetniAgene

(2012) Vladimir P. Balabanov et al.   FEMS MICROBIOLOGY LETTERS

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

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

MassTRIX Reloaded: Combined Analysis and Visualization of Transcriptome and Metabolome Data

(2012) Brigitte Wägele et al.   PLoS One

Gene duplication as a mechanism of genomic adaptation to a changing environment

(2012) F. A. Kondrashov   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

An effort to make sense of antisense transcription in bacteria

(2012) Iñigo Lasa et al.   RNA Biology

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

(2011) Benjamin A. Wilson et al.   Genome Biology and Evolution

CitA/CitB Two-Component System Regulating Citrate Fermentation in Escherichia coli and Its Relation to the DcuS/DcuR System In Vivo

(2011) P. D. Scheu et al.   JOURNAL OF BACTERIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

(2011) Adam Deutschbauer et al.   PLoS Genetics

Bacterial Antisense RNAs: How Many Are There, and What Are They Doing?

(2010) Maureen Kiley Thomason et al.   Annual Review of Genetics

WebGeSTer DB—a transcription terminator database

(2010) Anirban Mitra et al.   NUCLEIC ACIDS RESEARCH

Metabolomics Unravel Contrasting Effects of Biodiversity on the Performance of Individual Plant Species

(2010) Christian Scherling et al.   PLoS One

NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features

(2010) Bent Petersen et al.   PLoS One

Why genes overlap in viruses

(2010) N. Chirico et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Neural networks for secondary structure and structural class predictions

(2010) John-Marc Chandonia et al.   PROTEIN SCIENCE

Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations

(2010) S. Gottesman et al.   Cold Spring Harbor Perspectives in Biology

Two overlapping antiparallel genes encoding the iron regulator DmdR1 and the Adm proteins control sidephore and antibiotic biosynthesis in Streptomyces coelicolor A3(2)

(2009) Sedef Tunca et al.   FEBS Journal

Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation

(2009) C. Rancurel et al.   JOURNAL OF VIROLOGY

Improved Disorder Prediction by Combination of Orthogonal Approaches

(2009) Avner Schlessinger et al.   PLoS One

The origin of a novel gene through overprinting in Escherichia coli

(2008) Luis Delaye et al.   BMC EVOLUTIONARY BIOLOGY

The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli

(2008) Mark W. J. van Passel et al.   PLoS Computational Biology

Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1

(2008) Mark W. Silby et al.   PLoS Genetics