Settling Down: The Genome of Serratia symbiotica from the Aphid Cinara tujafilina Zooms in on the Process of Accommodation to a Cooperative Intracellular Life

Genome Degeneration and Adaptation in a Nascent Stage of Symbiosis

(2014) Kelly F. Oakeson et al.   Genome Biology and Evolution

Phenotypic Effect of “Candidatus Rickettsiella viridis,” a Facultative Symbiont of the Pea Aphid (Acyrthosiphon pisum), and Its Interaction with a Coexisting Symbiont

(2013) Tsutomu Tsuchida et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Shared Metabolic Pathways in a Coevolved Insect-Bacterial Symbiosis

(2013) Calum W. Russell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

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

Maintenance of essential amino acid synthesis pathways in the Blattabacterium cuenoti symbiont of a wood-feeding cockroach

(2013) G. Tokuda et al.   Biology Letters

Horizontally Transmitted Symbionts and Host Colonization of Ecological Niches

(2013) Lee M. Henry et al.   CURRENT BIOLOGY

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

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

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov et al.   BIOINFORMATICS

Domain enhanced lookup time accelerated BLAST

(2012) Grzegorz M Boratyn et al.   Biology Direct

Endosymbiotic bacteria as a source of carotenoids in whiteflies

(2012) D. B. Sloan et al.   Biology Letters

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

Proteomic Analysis of an Unculturable Bacterial Endosymbiont (Blochmannia) Reveals High Abundance of Chaperonins and Biosynthetic Enzymes

(2012) Yongliang Fan et al.   JOURNAL OF PROTEOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Comparative Genomics of Serratia spp.: Two Paths towards Endosymbiotic Life

(2012) Alejandro Manzano-Marín et al.   PLoS One

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

New Clues about the Evolutionary History of Metabolic Losses in Bacterial Endosymbionts, Provided by the Genome of Buchnera aphidicola from the Aphid Cinara tujafilina

(2011) Araceli Lamelas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont

(2011) Shuji Shigenobu et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Massive Genomic Decay in Serratia symbiotica, a Recently Evolved Symbiont of Aphids

(2011) Gaelen R. Burke et al.   Genome Biology and Evolution

Genomic basis of endosymbiont-conferred protection against an insect parasitoid

(2011) A. K. Hansen et al.   GENOME RESEARCH

Large-Scale Label-Free Quantitative Proteomics of the Pea aphid-BuchneraSymbiosis

(2011) Anton Poliakov et al.   MOLECULAR & CELLULAR PROTEOMICS

Genetic and metabolic determinants of nutritional phenotype in an insect-bacterial symbiosis

(2011) S. J. MACDONALD et al.   MOLECULAR ECOLOGY

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Aphid genome expression reveals host-symbiont cooperation in the production of amino acids

(2011) A. K. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of the amoeba symbiont "CandidatusAmoebophilus asiaticus" encodes an afp-like prophage possibly used for protein secretion

(2011) Thomas Penz et al.   Virulence

Sequence Conservation and Functional Constraint on Intergenic Spacers in Reduced Genomes of the Obligate Symbiont Buchnera

(2011) Patrick H. Degnan et al.   PLoS Genetics

Serratia symbiotica from the Aphid Cinara cedri: A Missing Link from Facultative to Obligate Insect Endosymbiont

(2011) Araceli Lamelas et al.   PLoS Genetics

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies

(2010) Eugeni Belda et al.   BMC GENOMICS

Correlations Between Bacterial Ecology and Mobile DNA

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

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

(2010) E. F. Kirkness et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

webMGR: an online tool for the multiple genome rearrangement problem

(2009) Chi Ho Lin et al.   BIOINFORMATICS

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Effects of facultative symbionts and heat stress on the metabolome of pea aphids

(2009) Gaelen Burke et al.   ISME Journal

Endosymbiotic Bacteria in Insects: Their Diversity and Culturability

(2009) Yoshitomo Kikuchi   MICROBES AND ENVIRONMENTS

Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors

(2009) P. H. Degnan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

Evolution of the Secondary Symbiont "Candidatus Serratia symbiotica" in Aphid Species of the Subfamily Lachninae

(2008) A. Lamelas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Striking Case of Tryptophan Provision in the Cedar Aphid Cinara cedri

(2008) M. J. Gosalbes et al.   JOURNAL OF BACTERIOLOGY

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

(2008) Andrés Moya et al.   NATURE REVIEWS GENETICS