Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

The deep-sea glass sponge L ophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur

(2016) Ren-Mao Tian et al.   ENVIRONMENTAL MICROBIOLOGY

PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity

(2016) N. Ricker et al.   GENE

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

(2016) Yu-Chih Tsai et al.   mBio

The Sponge Hologenome

(2016) Nicole S. Webster et al.   mBio

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

(2016) J. A. Frank et al.   Scientific Reports

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Paenibacillus larvae-Directed Bacteriophage HB10c2 and Its Application in American Foulbrood-Affected Honey Bee Larvae

(2015) Hannes Beims et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart

(2015) Gaetano Malgieri et al.   FEBS Journal

Carnitine in bacterial physiology and metabolism

(2015) Jamie A. Meadows et al.   MICROBIOLOGY-SGM

Restriction-Modification Systems as Mobile Genetic Elements in the Evolution of an Intracellular Symbiont

(2015) Hao Zheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

(2015) Ilia Burgsdorf et al.   mBio

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

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

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

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

(2014) T.B.K. Reddy et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Cell Turnover and Detritus Production in Marine Sponges from Tropical and Temperate Benthic Ecosystems

(2014) Brittany E. Alexander et al.   PLoS One

Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges

(2014) Cole G. Easson et al.   Frontiers in Microbiology

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

(2013) Janine Kamke et al.   ISME Journal

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

(2013) K. Vasu et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Discovery of Functional Toxin/Antitoxin Systems in Bacteria by Shotgun Cloning

(2013) Hila Sberro et al.   MOLECULAR CELL

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

PBSIM: PacBio reads simulator—toward accurate genome assembly

(2012) Yukiteru Ono et al.   BIOINFORMATICS

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts

(2012) L. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Deep sequencing reveals diversity and community structure of complex microbiota in five Mediterranean sponges

(2011) Susanne Schmitt et al.   HYDROBIOLOGIA

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

(2011) Susanne Schmitt et al.   ISME Journal

IMG/M: the integrated metagenome data management and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

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

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

(2010) Alexander Siegl et al.   ISME Journal

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

(2009) Kira S Makarova et al.   Biology Direct

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Sulfated polysaccharides from marine sponges (Porifera): an ancestor cell-cell adhesion event based on the carbohydrate-carbohydrate interaction

(2009) E. Vilanova et al.   GLYCOBIOLOGY

Comparative proteomic analysis of passagedHelicobacter pylori

(2009) Mao-Jun Zhang et al.   JOURNAL OF BASIC MICROBIOLOGY

Cell kinetics of the marine sponge Halisarca caerulea reveal rapid cell turnover and shedding

(2009) J. M. De Goeij et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

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

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

Fossil steroids record the appearance of Demospongiae during the Cryogenian period

(2009) Gordon D. Love et al.   NATURE

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS