Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis

Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge

(2014) Ren-Mao Tian et al.   ENVIRONMENTAL MICROBIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Complete Genome Sequence of Marinomonas Bacteriophage P12026

(2012) Ilnam Kang et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Pyrosequencing of Bacterial Symbionts within Axinella corrugata Sponges: Diversity and Seasonal Variability

(2012) James R. White et al.   PLoS One

Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms

(2011) Rachel L. Simister et al.   ENVIRONMENTAL MICROBIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Copper toxicity and the origin of bacterial resistance—new insights and applications

(2011) Christopher L. Dupont et al.   Metallomics

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Life in blue: Copper resistance mechanisms of bacteria and Archaea used in industrial biomining of minerals

(2010) Alvaro Orell et al.   BIOTECHNOLOGY ADVANCES

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis

(2010) Torsten Thomas et al.   ISME Journal

Copper Homeostasis inSalmonellaIs Atypical and Copper-CueP Is a Major Periplasmic Metal Complex

(2010) Deenah Osman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CtpV: a putative copper exporter required for full virulence of Mycobacterium tuberculosis

(2010) Sarah K. Ward et al.   MOLECULAR MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Inter- and Intraspecific Variations of Bacterial Communities Associated with Marine Sponges from San Juan Island, Washington

(2009) O. O. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing

(2009) Daniel N Frank   BMC BIOINFORMATICS

Sponge-associated marine bacteria as indicators of heavy metal pollution

(2007) Joseph Selvin et al.   MICROBIOLOGICAL RESEARCH