Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing

Plasmid and clonal interference during post horizontal gene transfer evolution

(2017) S. Bedhomme et al.   MOLECULAR ECOLOGY

Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution

(2017) Tatiana Giraud et al.   MOLECULAR ECOLOGY

Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria

(2017) James P. J. Hall et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

(2016) Kathleen Sprouffske et al.   BMC BIOINFORMATICS

Flexible genomic islands as drivers of genome evolution

(2016) Francisco Rodriguez-Valera et al.   CURRENT OPINION IN MICROBIOLOGY

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering

(2016) Andrew D Garst et al.   NATURE BIOTECHNOLOGY

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Condition-dependent sex: who does it, when and why?

(2016) Yoav Ram et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria

(2016) Eva C. Boritsch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

(2016) Christopher L. Hemme et al.   mBio

Not So Simple After All: Bacteria, Their Population Genetics, and Recombination

(2016) William P. Hanage   Cold Spring Harbor Perspectives in Biology

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

(2016) Jan-Hendrik Hehemann et al.   Nature Communications

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict

(2016) Nicholas J. Croucher et al.   PLOS BIOLOGY

Computational methods for predicting genomic islands in microbial genomes

(2016) Bingxin Lu et al.   Computational and Structural Biotechnology Journal

Multicopy plasmids potentiate the evolution of antibiotic resistance in bacteria

(2016) Alvaro San Millan et al.   Nature Ecology & Evolution

The Characterization of Escherichia coli CpdB as a Recombinant Protein Reveals that, besides Having the Expected 3´-Nucleotidase and 2´,3´-Cyclic Mononucleotide Phosphodiesterase Activities, It Is Also Active as Cyclic Dinucleotide Phosphodiesterase

(2016) Iralis López-Villamizar et al.   PLoS One

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community

(2016) Stephan Thies et al.   Scientific Reports

Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP

(2016) Anat Bren et al.   Scientific Reports

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature?

(2015) Susan F. Bailey et al.   MOLECULAR ECOLOGY

Recombinant transfer in the basic genome ofEscherichia coli

(2015) Purushottam D. Dixit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche

(2015) M. J. Rosen et al.   SCIENCE

Rates of Lateral Gene Transfer in Prokaryotes: High but Why?

(2015) Michiel Vos et al.   TRENDS IN MICROBIOLOGY

Success in incorporating horizontally transferred genes: the H-NS protein

(2015) Mario Hüttener et al.   TRENDS IN MICROBIOLOGY

Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa

(2015) Alvaro San Millan et al.   Nature Communications

Inferring Horizontal Gene Transfer

(2015) Matt Ravenhall et al.   PLoS Computational Biology

The chromosomal accommodation and domestication of mobile genetic elements

(2014) Marie Touchon et al.   CURRENT OPINION IN MICROBIOLOGY

Extensive Horizontal Gene Transfer during Staphylococcus aureus Co-colonization In Vivo

(2014) Alex J. McCarthy et al.   Genome Biology and Evolution

Minor Fitness Costs in an Experimental Model of Horizontal Gene Transfer in Bacteria

(2014) Anna Knöppel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial transformation: distribution, shared mechanisms and divergent control

(2014) Calum Johnston et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic Identification of a Novel Salt Tolerance Gene from the Human Gut Microbiome Which Encodes a Membrane Protein with Homology to a brp/blh-Family β-Carotene 15,15′-Monooxygenase

(2014) Eamonn P. Culligan et al.   PLoS One

Multiple Phenotypic Changes Associated with Large-Scale Horizontal Gene Transfer

(2014) Kevin Dougherty et al.   PLoS One

Network-level architecture and the evolutionary potential of underground metabolism

(2014) R. A. Notebaart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Erosion Primarily Through Mutation Accumulation, and Not Tradeoffs, Drives Limited Evolution of Substrate Specificity in Escherichia coli

(2014) Nicholas Leiby et al.   PLOS BIOLOGY

Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli

(2013) M. Dragosits et al.   Molecular Systems Biology

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

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

Exploring the costs of horizontal gene transfer

(2013) David A. Baltrus   TRENDS IN ECOLOGY & EVOLUTION

Statistical Mechanics of Modularity and Horizontal Gene Transfer

(2013) Michael W. Deem   Annual Review of Condensed Matter Physics

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

(2012) Xavier Didelot et al.   BMC GENOMICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

High Expression Hampers Horizontal Gene Transfer

(2012) Chungoo Park et al.   Genome Biology and Evolution

Harnessing recombination to speed adaptive evolution in Escherichia coli

(2012) James Winkler et al.   METABOLIC ENGINEERING

Yeast Adapts to a Changing Stressful Environment by Evolving Cross-Protection and Anticipatory Gene Regulation

(2012) Riddhiman Dhar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Gene transfer agents: phage-like elements of genetic exchange

(2012) Andrew S. Lang et al.   NATURE REVIEWS MICROBIOLOGY

Crosstalk of Escherichia coli FadR with Global Regulators in Expression of Fatty Acid Transport Genes

(2012) Youjun Feng et al.   PLoS One

Enhancing E. coli Tolerance towards Oxidative Stress via Engineering Its Global Regulator cAMP Receptor Protein (CRP)

(2012) Souvik Basak et al.   PLoS One

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

Genetic adaptation to high altitude in the Ethiopian highlands

(2012) Laura B Scheinfeldt et al.   GENOME BIOLOGY

Membrane Stresses Induced by Overproduction of Free Fatty Acids in Escherichia coli

(2011) Rebecca M. Lennen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

(2011) Colin T Archer et al.   BMC GENOMICS

The evolution of metabolic networks of E. coli

(2011) David J Baumler et al.   BMC Systems Biology

Biased gene transfer in microbial evolution

(2011) Cheryl P. Andam et al.   NATURE REVIEWS MICROBIOLOGY

Microbial degradation of aromatic compounds — from one strategy to four

(2011) Georg Fuchs et al.   NATURE REVIEWS MICROBIOLOGY

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

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

The RpoS-Mediated General Stress Response inEscherichia coli

(2010) Aurelia Battesti et al.   Annual Review of Microbiology

Acetate accumulation through alternative metabolic pathways in ackA − pta − poxB − triple mutant in E. coli B (BL21)

(2010) Je-Nie Phue et al.   BIOTECHNOLOGY LETTERS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Compensatory gene amplification restores fitness after inter-species gene replacements

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

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow

(2010) Rachel A. F. Wozniak et al.   NATURE REVIEWS MICROBIOLOGY

Understanding the Differences between Genome Sequences of Escherichia coli B Strains REL606 and BL21(DE3) and Comparison of the E. coli B and K-12 Genomes

(2009) F. William Studier et al.   JOURNAL OF MOLECULAR BIOLOGY

Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)

(2009) Haeyoung Jeong et al.   JOURNAL OF MOLECULAR BIOLOGY

Interplay of cellular cAMP levels,  S activity and oxidative stress resistance in Escherichia coli

(2009) E. Barth et al.   MICROBIOLOGY-SGM

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

(2008) M. S. Dillingham et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Construction and Characterization of ack Deleted Mutant of Clostridium tyrobutyricum for Enhanced Butyric Acid and Hydrogen Production

(2006) Xiaoguang Liu et al.   BIOTECHNOLOGY PROGRESS