Expression of eukaryotic-like protein in the microbiome of sponges

Hologenome analysis of two marine sponges with different microbiomes

(2016) Taewoo Ryu et al.   BMC GENOMICS

Evolution and function of eukaryotic-like proteins from sponge symbionts

(2016) David Reynolds et al.   MOLECULAR ECOLOGY

Sample Processing Impacts the Viability and Cultivability of the Sponge Microbiome

(2016) Ana I. S. Esteves et al.   Frontiers in Microbiology

Detection of Prokaryotic Genes in the Amphimedon queenslandica Genome

(2016) Cecilia Conaco et al.   PLoS One

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

(2015) Detmer Sipkema et al.   ENVIRONMENTAL MICROBIOLOGY

The art of destruction: revealing the proteolytic capacity of bacterial caspase homologs

(2015) Johannes Asplund-Samuelsson   MOLECULAR MICROBIOLOGY

Secretion systems in Gram-negative bacteria: structural and mechanistic insights

(2015) Tiago R. D. Costa et al.   NATURE REVIEWS MICROBIOLOGY

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

(2015) Ilia Burgsdorf et al.   mBio

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

(2015) Dennis Versluis et al.   Scientific Reports

Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange

(2015) Cara L. Fiore et al.   Frontiers in Microbiology

Genome evolution in an ancient bacteria-ant symbiosis: parallel gene loss amongBlochmanniaspanning the origin of the ant tribe Camponotini

(2015) Laura E. Williams et al.   PeerJ

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data

(2015) Gordon M. Daly et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

(2014) Adriana Alberti et al.   BMC GENOMICS

Bacterial secreted effectors and caspase-3 interactions

(2014) Daniel M. Wall et al.   CELLULAR MICROBIOLOGY

Revealing microbial functional activities in the Red Sea spongeStylissa carteriby metatranscriptomics

(2014) Lucas Moitinho-Silva et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Rfam 12.0: updates to the RNA families database

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

The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features

(2014) Janine Kamke et al.   PLoS One

Symbiotic Adaptation Drives Genome Streamlining of the Cyanobacterial Sponge Symbiont "Candidatus Synechococcus spongiarum"

(2014) Z.-M. Gao et al.   mBio

Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation

(2014) Albi Celaj et al.   Microbiome

Infernal 1.1: 100-fold faster RNA homology searches

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

Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts

(2013) J G Sanders et al.   ISME Journal

Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress

(2013) Lu Fan et al.   ISME Journal

Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis

(2013) Mary T. H. D. Nguyen et al.   MOLECULAR ECOLOGY

Cellular microbiology and molecular ecology ofLegionella–amoeba interaction

(2013) Ashley M. Richards et al.   Virulence

Augmenting transcriptome assembly by combiningde novoand genome-guided tools

(2013) Prachi Jain et al.   PeerJ

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Classification of metagenomic sequences: methods and challenges

(2012) S. S. Mande et al.   BRIEFINGS IN BIOINFORMATICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community

(2012) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

Tetratricopeptide Repeat Motifs in the World of Bacterial Pathogens: Role in Virulence Mechanisms

(2012) Lukas Cerveny et al.   INFECTION AND IMMUNITY

Metaproteogenomic analysis of a community of sponge symbionts

(2012) Michael Liu et al.   ISME Journal

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

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

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Iron transporters in marine prokaryotic genomes and metagenomes

(2011) Brian M. Hopkinson et al.   ENVIRONMENTAL MICROBIOLOGY

Eu-Detect: An algorithm for detecting eukaryotic sequences in metagenomic data sets

(2011) Monzoorul Haque Mohammed et al.   JOURNAL OF BIOSCIENCES

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq

(2011) Hana Yi et al.   NUCLEIC ACIDS RESEARCH

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

The Sensitivity of Massively Parallel Sequencing for Detecting Candidate Infectious Agents Associated with Human Tissue

(2011) Richard A. Moore et al.   PLoS One

Type IV Pili in Francisella – A Virulence Trait in an Intracellular Pathogen

(2011) Emelie Näslund Salomonsson et al.   Frontiers in Microbiology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu et al.   BMC BIOINFORMATICS

The cell envelope subtilisin-like proteinase is a virulence determinant for Streptococcus suis

(2010) Laetitia Bonifait et al.   BMC MICROBIOLOGY

The origins of eukaryotic-like proteins in Legionella pneumophila

(2010) Mor N. Lurie-Weinberger et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

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

(2010) Torsten Thomas et al.   ISME Journal

Structural Basis of Chaperone Recognition of Type III Secretion System Minor Translocator Proteins

(2010) Viviana Job et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

(2010) Shaomei He et al.   NATURE METHODS

Inhibition of pathogen-induced apoptosis by a Coxiella burnetii type IV effector protein

(2010) A. Luhrmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Subtilisin-Like Protease AprV2 Is Required for Virulence and Uses a Novel Disulphide-Tethered Exosite to Bind Substrates

(2010) Ruth M. Kennan et al.   PLoS Pathogens

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Peptidoglycan-associated lipoprotein (Pal) of Gram-negative bacteria: function, structure, role in pathogenesis and potential application in immunoprophylaxis

(2009) Renata Godlewska et al.   FEMS MICROBIOLOGY LETTERS

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

The Coxiella burnetii Ankyrin Repeat Domain-Containing Protein Family Is Heterogeneous, with C-Terminal Truncations That Influence Dot/Icm-Mediated Secretion

(2009) D. E. Voth et al.   JOURNAL OF BACTERIOLOGY

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

Role for the Ankyrin eukaryotic-like genes of Legionella pneumophila in parasitism of protozoan hosts and human macrophages

(2008) Fabien Habyarimana et al.   ENVIRONMENTAL MICROBIOLOGY

The functional roles of marine sponges

(2008) James J. Bell   ESTUARINE COASTAL AND SHELF SCIENCE

Type IV Pili in Francisella tularensis: Roles of pilF and pilT in Fiber Assembly, Host Cell Adherence, and Virulence

(2008) S. Chakraborty et al.   INFECTION AND IMMUNITY

Molecular Control of Bacterial Death and Lysis

(2008) K. C. Rice et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ankyrin Repeat Proteins Comprise a Diverse Family of Bacterial Type IV Effectors

(2008) X. Pan et al.   SCIENCE

New substrates for TonB-dependent transport: do we only see the ‘tip of the iceberg’?

(2008) Kristine Schauer et al.   TRENDS IN BIOCHEMICAL SCIENCES

Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes

(2008) Jon Bohlin et al.   PLoS Computational Biology

Structure of the Yersinia enterocolitica Type III Secretion Translocator Chaperone SycD

(2007) Carina R. Büttner et al.   JOURNAL OF MOLECULAR BIOLOGY