Identification and analysis of integrons and cassette arrays in bacterial genomes

The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences

(2014) Marie Touchon et al.   Genome Biology and Evolution

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

(2014) Michael R Gillings et al.   ISME Journal

Integrons: Past, Present, and Future

(2014) Michael R. Gillings   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exploring the costs of horizontal gene transfer

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

Integrons and gene cassettes: hotspots of diversity in bacterial genomes

(2012) Ruth M. Hall   Annals of the New York Academy of Sciences

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

(2012) M. Kearse et al.   BIOINFORMATICS

Integron Involvement in Environmental Spread of Antibiotic Resistance

(2012) Thibault Stalder et al.   Frontiers in Microbiology

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Natural transformation with synthetic gene cassettes: new tools for integron research and biotechnology

(2011) A. M. Gestal et al.   MICROBIOLOGY-SGM

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons

(2011) Guillaume Cambray et al.   Mobile DNA

Integrons

(2010) Guillaume Cambray et al.   Annual Review of Genetics

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Gene cassette transcription in a large integron-associated array

(2010) Carolyn A Michael et al.   BMC GENETICS

Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths

(2010) T. Kloesges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mobyle: a new full web bioinformatics framework

(2009) B. Neron et al.   BIOINFORMATICS

INTEGRALL: a database and search engine for integrons, integrases and gene cassettes

(2009) A. Moura et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Context-driven discovery of gene cassettes in mobile integrons using a computational grammar

(2009) Guy Tsafnat et al.   BMC BIOINFORMATICS

ACID: annotation of cassette and integron data

(2009) Michael J Joss et al.   BMC BIOINFORMATICS

Genome sequence ofVibrio splendidus: an abundant planctonic marine species with a large genotypic diversity

(2009) Frédérique Le Roux et al.   ENVIRONMENTAL MICROBIOLOGY

Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis

(2009) Philippe Salah et al.   NUCLEIC ACIDS RESEARCH

The relaxed requirements of the integron cleavage site allow predictable changes in integron target specificity

(2009) C. Frumerie et al.   NUCLEIC ACIDS RESEARCH

The impact of long-distance horizontal gene transfer on prokaryotic genome size

(2009) O. X. Cordero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Features of Single-Stranded Integron Cassette attC Sites and Their Role in Strand Selection

(2009) Marie Bouvier et al.   PLoS Genetics

Insights and inferences about integron evolution from genomic data

(2008) Diana R Nemergut et al.   BMC GENOMICS

The Evolution of Class 1 Integrons and the Rise of Antibiotic Resistance

(2008) M. Gillings et al.   JOURNAL OF BACTERIOLOGY

An analysis of the evolutionary relationships of integron integrases, with emphasis on the prevalence of class 1 integrons in Escherichia coli isolates from clinical and environmental origins

(2008) J. J. Diaz-Mejia et al.   MICROBIOLOGY-SGM