Copy number change: evolving views on gene amplification

Dynamic Large-Scale Chromosomal Rearrangements Fuel Rapid Adaptation in Yeast Populations

(2013) Shang-Lin Chang et al.   PLoS Genetics

PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants

(2012) Yue Jiang et al.   BIOINFORMATICS

Poxvirus Use a “Gene Accordion” to Tune Out Host Defenses

(2012) John R. Roth et al.   CELL

Poxviruses Deploy Genomic Accordions to Adapt Rapidly against Host Antiviral Defenses

(2012) Nels C. Elde et al.   CELL

Differential Occurrence of Streptococcus pneumoniae Serotype 11E Between Asymptomatic Carriage and Invasive Pneumococcal Disease Isolates Reflects a Unique Model of Pathogen Microevolution

(2012) J. J. Calix et al.   CLINICAL INFECTIOUS DISEASES

Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences

(2012) Josephine Bryant et al.   Future Microbiology

Multiple Pathways of Duplication Formation with and Without Recombination (RecA) in Salmonella enterica

(2012) A. B. Reams et al.   GENETICS

Analysis of IS1236-Mediated Gene Amplification Events in Acinetobacter baylyi ADP1

(2012) L. E. Cuff et al.   JOURNAL OF BACTERIOLOGY

Estimated copy number of Bacillus anthracis plasmids pXO1 and pXO2 using digital PCR

(2012) Timothy Straub et al.   JOURNAL OF MICROBIOLOGICAL METHODS

A strategy of gene overexpression based on tandem repetitive promoters in Escherichia coli

(2012) Mingji Li et al.   Microbial Cell Factories

Genomic analysis of a key innovation in an experimental Escherichia coli population

(2012) Zachary D. Blount et al.   NATURE

Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation

(2012) Alexandra S. Whale et al.   NUCLEIC ACIDS RESEARCH

Independent Large Scale Duplications in Multiple M. tuberculosis Lineages Overlapping the Same Genomic Region

(2012) Brian Weiner et al.   PLoS One

Genome-Wide Detection of Spontaneous Chromosomal Rearrangements in Bacteria

(2012) Song Sun 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

Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence

(2012) J. Nasvall et al.   SCIENCE

Expression of a Cryptic Secondary Sigma Factor Gene Unveils Natural Competence for DNA Transformation in Staphylococcus aureus

(2012) Kazuya Morikawa et al.   PLoS Pathogens

Whack-an-E. coli with the morbidostat

(2012) Ofer Fridman et al.   GENOME BIOLOGY

Dynamics of Gene Duplication in the Genomes of Chlorophyll d-Producing Cyanobacteria: Implications for the Ecological Niche

(2011) Scott R. Miller et al.   Genome Biology and Evolution

Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing

(2011) Ole Skovgaard et al.   GENOME RESEARCH

ZouA, a Putative Relaxase, Is Essential for DNA Amplification in Streptomyces kanamyceticus

(2011) T. Murakami et al.   JOURNAL OF BACTERIOLOGY

Genome-wide selection for increased copy number in Acinetobacter baylyi ADP1: locus and context-dependent variation in gene amplification

(2011) Sarah C. Seaton et al.   MOLECULAR MICROBIOLOGY

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments

(2011) Yong Wang et al.   PLoS One

A system for the targeted amplification of bacterial gene clusters multiplies antibiotic yield in Streptomyces coelicolor

(2011) T. Murakami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolving promiscuously

(2011) D. I. Andersson   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Chromosomal Structural Instability in a Subpopulation of Starving Escherichia coli Cells

(2011) Dongxu Lin et al.   PLoS Genetics

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Quantifying EGFR Alterations in the Lung Cancer Genome with Nanofluidic Digital PCR Arrays

(2010) J. Wang et al.   CLINICAL CHEMISTRY

Amplification of the Gene for Isoleucyl-tRNA Synthetase Facilitates Adaptation to the Fitness Cost of Mupirocin Resistance in Salmonella enterica

(2010) W. Paulander et al.   GENETICS

Duplication Frequency in a Population of Salmonella enterica Rapidly Approaches Steady State With or Without Recombination

(2010) A. B. Reams et al.   GENETICS

The Tandem Inversion Duplication in Salmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types

(2010) E. Kugelberg et al.   GENETICS

Novel genetic context of multiple blaOXA-58 genes in Acinetobacter genospecies 3

(2010) B. A. Evans et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Massive Gene Duplication Event among Clinical Isolates of the Mycobacterium tuberculosis W/Beijing Family

(2010) P. Domenech et al.   JOURNAL OF BACTERIOLOGY

Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution

(2010) Suzanne Weaver et al.   METHODS

Duplication of the chromosomal blaSHV-11 gene in a clinical hypermutable strain of Klebsiella pneumoniae

(2010) C. Duvernay et al.   MICROBIOLOGY-SGM

The joys and terrors of fast adaptation: new findings elucidate antibiotic resistance and natural selection

(2010) John R. Roth   MOLECULAR MICROBIOLOGY

Escape from growth restriction in small colony variants of Salmonella typhimurium by gene amplification and mutation

(2010) Maria Pränting et al.   MOLECULAR MICROBIOLOGY

Compensatory gene amplification restores fitness after inter-species gene replacements

(2010) Peter A. Lind et al.   MOLECULAR MICROBIOLOGY

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

Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli

(2010) V. W. C. Soo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward a General Theory of Adaptive Radiation

(2009) Rees Kassen   Annals of the New York Academy of Sciences

Gene Amplification and Adaptive Evolution in Bacteria

(2009) Dan I. Andersson et al.   Annual Review of Genetics

The life and death of gene families

(2009) Jeffery P. Demuth et al.   BIOESSAYS

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

(2009) Chao Xie et al.   BMC BIOINFORMATICS

Genomic island excisions in Bordetella petrii

(2009) Melanie Lechner et al.   BMC MICROBIOLOGY

Expansion of a chromosomal repeat in Escherichia coli: roles of replication, repair, and recombination functions

(2009) Anthony R Poteete   BMC MOLECULAR BIOLOGY

The blaSHV-5 gene is encoded in a compound transposon duplicated in tandem in Enterobacter cloacae

(2009) U. Garza-Ramos et al.   CLINICAL MICROBIOLOGY AND INFECTION

Fast, adaptive evolution at a bacterial host-resistance locus: The PFam54 gene array in Borrelia burgdorferi

(2009) Ewa Wywial et al.   GENE

Contribution of Gene Amplification to Evolution of Increased Antibiotic Resistance in Salmonella typhimurium

(2009) Song Sun et al.   GENETICS

Rapid identification of homologous recombinants and determination of gene copy number with reference/query pyrosequencing (RQPS)

(2009) Z. Liu et al.   GENOME RESEARCH

Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates

(2009) M. W. Hahn   JOURNAL OF HEREDITY

Stabilized gene duplication enables long-term selection-free heterologous pathway expression

(2009) Keith E J Tyo et al.   NATURE BIOTECHNOLOGY

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

Bacterial gene amplification: implications for the evolution of antibiotic resistance

(2009) Linus Sandegren et al.   NATURE REVIEWS MICROBIOLOGY

Microarray-based DNA profiling to study genomic aberrations

(2008) Nic Waddell   IUBMB LIFE

Ohno's Model Revisited: Measuring the Frequency of Potentially Adaptive Mutations under Various Mutational Drifts

(2008) Shimon Bershtein et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention

(2008) Niyaz Ahmed et al.   NATURE REVIEWS MICROBIOLOGY

Studying copy number variations using a nanofluidic platform

(2008) Jian Qin et al.   NUCLEIC ACIDS RESEARCH

High Throughput Gene Expression Measurement with Real Time PCR in a Microfluidic Dynamic Array

(2008) Sandra L. Spurgeon et al.   PLoS One

Secondary Chromosomal Attachment Site and Tandem Integration of the Mobilizable Salmonella Genomic Island 1

(2008) Benoît Doublet et al.   PLoS One

Small-scale copy number variation and large-scale changes in gene expression

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

Complete Genome Sequence of the N2-Fixing Broad Host Range Endophyte Klebsiella pneumoniae 342 and Virulence Predictions Verified in Mice

(2008) Derrick E. Fouts et al.   PLoS Genetics