A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting

The combinatorics of overlapping genes

(2017) Sophie Lèbre et al.   JOURNAL OF THEORETICAL BIOLOGY

N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana

(2017) Patrick Willems et al.   MOLECULAR & CELLULAR PROTEOMICS

Programmed Ribosomal Frameshifting Generates a Copper Transporter and a Copper Chaperone from the Same Gene

(2017) Sezen Meydan et al.   MOLECULAR CELL

Identification of Unannotated Small Genes in Salmonella

(2017) Jonghwan Baek et al.   G3-Genes Genomes Genetics

Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome

(2017) Sarah M. Hücker et al.   PLoS One

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

(2016) Klaus Neuhaus et al.   BMC GENOMICS

Unusually Situated Binding Sites for Bacterial Transcription Factors Can Have Hidden Functionality

(2016) James R. J. Haycocks et al.   PLoS One

TMSEG: Novel prediction of transmembrane helices

(2016) Michael Bernhofer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

(2016) Joana Carlevaro-Fita et al.   RNA

The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)

(2016) Yujin Jeong et al.   Nature Communications

Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling

(2016) Hadas Zur et al.   Scientific Reports

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

(2015) Lea Fellner et al.   BMC EVOLUTIONARY BIOLOGY

sORFs.org: a repository of small ORFs identified by ribosome profiling

(2015) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

The EMBL-EBI bioinformatics web and programmatic tools framework

(2015) Weizhong Li et al.   NUCLEIC ACIDS RESEARCH

Small membrane proteins – elucidating the function of the needle in the haystack

(2014) Grant Kemp et al.   BIOLOGICAL CHEMISTRY

A versatile and highly efficient method for scarless genome editing in Escherichia coli and Salmonella enterica

(2014) Juhan Kim et al.   BMC BIOTECHNOLOGY

Overlapping genes: a window on gene evolvability

(2014) Maxime Huvet et al.   BMC GENOMICS

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

Programmed –1 Frameshifting by Kinetic Partitioning during Impeded Translocation

(2014) Neva Caliskan et al.   CELL

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

SearchDOGS Bacteria, Software That Provides Automated Identification of Potentially Missed Genes in Annotated Bacterial Genomes

(2014) S. S. OhEigeartaigh et al.   JOURNAL OF BACTERIOLOGY

LocTree3 prediction of localization

(2014) Tatyana Goldberg et al.   NUCLEIC ACIDS RESEARCH

PredictProtein—an open resource for online prediction of protein structural and functional features

(2014) Guy Yachdav et al.   NUCLEIC ACIDS RESEARCH

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

(2014) Julie L Aspden et al.   eLife

Regulation of Bacterial Metabolism by Small RNAs Using Diverse Mechanisms

(2013) Maksym Bobrovskyy et al.   Annual Review of Genetics

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

Origin and Length Distribution of Unidirectional Prokaryotic Overlapping Genes

(2013) Miguel M. Fonseca et al.   G3-Genes Genomes Genetics

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

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

Predicting Statistical Properties of Open Reading Frames in Bacterial Genomes

(2012) Katharina Mir 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

A Pilot Study of Bacterial Genes with Disrupted ORFs Reveals a Surprising Profusion of Protein Sequence Recoding Mediated by Ribosomal Frameshifting and Transcriptional Realignment

(2011) V. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

Towards the integration of genomics, epidemiological and clinical data

(2011) Victor V Solovyev et al.   Genome Medicine

Missing genes in the annotation of prokaryotic genomes

(2010) Andrew S Warren et al.   BMC BIOINFORMATICS

Why genes overlap in viruses

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

Widespread Antisense Transcription in Escherichia coli

(2010) J. E. Dornenburg et al.   mBio

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

Dissection of recognition determinants ofEscherichia coliσ32suggests a composite −10 region with an ‘extended −10’ motif and a core −10 element

(2009) Byoung-Mo Koo et al.   MOLECULAR MICROBIOLOGY

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

The origin of a novel gene through overprinting in Escherichia coli

(2008) Luis Delaye et al.   BMC EVOLUTIONARY BIOLOGY

An Ancient Evolutionary Origin of Genes Associated with Human Genetic Diseases

(2008) T. Domazet-Loso et al.   MOLECULAR BIOLOGY AND EVOLUTION

Small membrane proteins found by comparative genomics and ribosome binding site models

(2008) Matthew R. Hemm et al.   MOLECULAR MICROBIOLOGY

Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1

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