Mixed transmission modes and dynamic genome evolution in an obligate animal–bacterial symbiosis

Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission

(2015) Detmer Sipkema et al.   ENVIRONMENTAL MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

An out-of-body experience: the extracellular dimension for the transmission of mutualistic bacteria in insects

(2015) H. Salem et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Tiniest Tiny Genomes

(2014) Nancy A. Moran et al.   Annual Review of Microbiology

Evidence of Environmental and Vertical Transmission of Burkholderia Symbionts in the Oriental Chinch Bug, Cavelerius saccharivorus (Heteroptera: Blissidae)

(2014) Hideomi Itoh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis

(2014) Oleg Dmytrenko et al.   BMC GENOMICS

Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis

(2014) Douglas Gomes et al.   BMC GENOMICS

Genetic conflict, kin and the origins of novel genetic systems

(2014) B. B. Normark et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Epidemiology and Evolution of Symbionts with Mixed-Mode Transmission

(2013) Dieter Ebert   Annual Review of Ecology Evolution and Systematics

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with Conchifera

(2013) Federico Plazzi et al.   BMC GENOMICS

Into the deep: A phylogenetic approach to the bivalve subclass Protobranchia

(2013) Prashant P. Sharma et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Multiple Symbiont Acquisition Strategies as an Adaptive Mechanism in the Coral Stylophora pistillata

(2013) Kristen A. Byler et al.   PLoS One

Physical Proximity May Promote Lateral Acquisition of Bacterial Symbionts in Vesicomyid Clams

(2013) Carole Decker et al.   PLoS One

Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts

(2013) M. Kleiner et al.   mBio

A Single-Cell Genome for Thiovulum sp.

(2012) Ian P. G. Marshall et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

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

(2012) M. Kearse et al.   BIOINFORMATICS

Evidence of diversity and recombination in Arsenophonus symbionts of the Bemisia tabaci species complex

(2012) Laurence Mouton et al.   BMC MICROBIOLOGY

Diversity and recombination in Wolbachia and Cardinium from Bryobia spider mites

(2012) Vera I D Ros et al.   BMC MICROBIOLOGY

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

(2012) Pablo Cingolani et al.   FLY

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs

(2011) John P. McCutcheon et al.   CURRENT BIOLOGY

Horizontal Transmission Rapidly Erodes Disequilibria Between Organelle and Symbiont Genomes

(2011) Yaniv Brandvain et al.   GENETICS

Short- and Long-term Evolutionary Dynamics of Bacterial Insertion Sequences: Insights from Wolbachia Endosymbionts

(2011) Nicolas Cerveau et al.   Genome Biology and Evolution

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria

(2011) Dexi Bi et al.   NUCLEIC ACIDS RESEARCH

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Chemosymbiotic bivalves from the mud volcanoes of the Gulf of Cadiz, NE Atlantic, with descriptions of new species of Solemyidae, Lucinidae and Vesicomyidae

(2011) Graham Oliver et al.   ZooKeys

Metatranscriptomic Analysis of Sulfur Oxidation Genes in the Endosymbiont of Solemya Velum

(2011) Frank J. Stewart et al.   Frontiers in Microbiology

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Correlations Between Bacterial Ecology and Mobile DNA

(2010) Irene L. G. Newton et al.   CURRENT MICROBIOLOGY

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

A complex journey: transmission of microbial symbionts

(2010) Monika Bright et al.   NATURE REVIEWS MICROBIOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Detection and correction of false segmental duplications caused by genome mis-assembly

(2010) David R Kelley et al.   GENOME BIOLOGY

Reordering contigs of draft genomes using the Mauve Aligner

(2009) Anna I. Rissman et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

Molecular Microbial Diversity Survey of Sponge Reproductive Stages and Mechanistic Insights into Vertical Transmission of Microbial Symbionts

(2008) S. Schmitt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Coalescence Times and FST Under a Skewed Offspring Distribution Among Individuals in a Population

(2008) B. Eldon et al.   GENETICS

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

Lateral Symbiont Acquisition in a Maternally Transmitted Chemosynthetic Clam Endosymbiosis

(2008) F. J. Stewart et al.   MOLECULAR BIOLOGY AND EVOLUTION

Learning how to live together: genomic insights into prokaryote–animal symbioses

(2008) Andrés Moya et al.   NATURE REVIEWS GENETICS

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY