Integrative and conjugative elements and their hosts: composition, distribution and organization

Identification and analysis of integrons and cassette arrays in bacterial genomes

(2016) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

Biology of ICE Bs1 , an integrative and conjugative element in Bacillus subtilis

(2016) Jennifer M. Auchtung et al.   PLASMID

Regulation of genetic flux between bacteria by restriction–modification systems

(2016) Pedro H. Oliveira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of protein secretion systems in bacterial genomes

(2016) Sophie S. Abby et al.   Scientific Reports

Integrative and Conjugative Elements (ICEs): What They Do and How They Work

(2015) Christopher M. Johnson et al.   Annual Review of Genetics

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner

(2015) Nicolas Carraro et al.   PLoS Genetics

The chromosomal accommodation and domestication of mobile genetic elements

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

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

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

The Diversity of Prokaryotic DDE Transposases of the Mutator Superfamily, Insertion Specificity, and Association with Conjugation Machineries

(2014) Romain Guérillot 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

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

(2014) Julien Guglielmini et al.   NUCLEIC ACIDS RESEARCH

The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts

(2014) Pedro H. Oliveira et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

Pervasive domestication of defective prophages by bacteria

(2014) L.-M. Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

(2014) Val F. Lanza et al.   PLoS Genetics

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

The Xer/dif site-specific recombination system of Campylobacter jejuni

(2013) Maxime Leroux et al.   MOLECULAR GENETICS AND GENOMICS

ICEA ofMycoplasma agalactiae: a new family of self-transmissible integrative elements that confers conjugative properties to the recipient strain

(2013) Emilie Dordet Frisoni et al.   MOLECULAR MICROBIOLOGY

Conjugative type IV secretion systems in Gram-positive bacteria

(2013) Nikolaus Goessweiner-Mohr et al.   PLASMID

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

A Conserved Helicase Processivity Factor Is Needed for Conjugation and Replication of an Integrative and Conjugative Element

(2013) Jacob Thomas et al.   PLoS Genetics

Evolution of Conjugation and Type IV Secretion Systems

(2012) Julien Guglielmini et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Adaptation of Temperate Bacteriophages to Their Host Genomes

(2012) Louis-Marie Bobay et al.   MOLECULAR BIOLOGY AND EVOLUTION

DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes

(2012) Feng Gao et al.   NUCLEIC ACIDS RESEARCH

Site-Specific Integration of Foreign DNA into Minimal Bacterial and Human Target Sequences Mediated by a Conjugative Relaxase

(2012) Leticia Agúndez et al.   PLoS One

Xer Recombinase and Genome Integrity in Helicobacter pylori, a Pathogen without Topoisomerase IV

(2012) Aleksandra W. Debowski et al.   PLoS One

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Trends and barriers to lateral gene transfer in prokaryotes

(2011) Ovidiu Popa et al.   CURRENT OPINION IN MICROBIOLOGY

Site-specific accretion of an integrative conjugative element together with a related genomic island leads to cis mobilization and gene capture

(2011) Xavier Bellanger et al.   MOLECULAR MICROBIOLOGY

Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria

(2011) Mariana Gabriela Ghinet et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

(2011) Julien Guglielmini et al.   PLoS Genetics

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis

(2010) Maarten J Schijffelen et al.   BMC GENOMICS

Mobility of Plasmids

(2010) C. Smillie et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Origins and Evolution of Antibiotic Resistance

(2010) J. Davies et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Evolution in Quantum Leaps: Multiple Combinatorial Transfers of HPI and Other Genetic Modules in Enterobacteriaceae

(2010) Armand Paauw et al.   PLoS One

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

(2010) Zasha Weinberg et al.   GENOME BIOLOGY

Genomic island excisions in Bordetella petrii

(2009) Melanie Lechner et al.   BMC MICROBIOLOGY

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Autonomous plasmid-like replication ofBacillusICEBs1: a general feature of integrative conjugative elements?

(2009) Elisabeth Grohmann   MOLECULAR MICROBIOLOGY

Autonomous plasmid-like replication of a conjugative transposon

(2009) Catherine A. Lee et al.   MOLECULAR MICROBIOLOGY

Genomic islands are dynamic, ancient integrative elements in bacterial evolution

(2009) E. Fidelma Boyd et al.   TRENDS IN MICROBIOLOGY

Mobile Antibiotic Resistance Encoding Elements Promote Their Own Diversity

(2009) Geneviève Garriss et al.   PLoS Genetics

A Toxin–Antitoxin System Promotes the Maintenance of an Integrative Conjugative Element

(2009) Rachel A. F. Wozniak et al.   PLoS Genetics

Atypical association of DDE transposition with conjugation specifies a new family of mobile elements

(2008) Mathieu Brochet et al.   MOLECULAR MICROBIOLOGY

Why is entry exclusion an essential feature of conjugative plasmids?

(2008) M. Pilar Garcillán-Barcia et al.   PLASMID