A de novo approach to disentangle partner identity and function in holobiont systems

Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network

(2018) Arnaud Meng et al.   MOLECULAR ECOLOGY

More protist genomes needed

(2017) Shannon J. Sibbald et al.   Nature Ecology & Evolution

Challenges and advances for transcriptome assembly in non-model species

(2017) Arnaud Ungaro et al.   PLoS One

SAMSA: a comprehensive metatranscriptome analysis pipeline

(2016) Samuel T. Westreich et al.   BMC BIOINFORMATICS

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

In situ imaging reveals the biomass of giant protists in the global ocean

(2016) Tristan Biard et al.   NATURE

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

Comparative transcriptome analysis reveals insights into the streamlined genomes of haplosclerid demosponges

(2016) Christine Guzman et al.   Scientific Reports

MetaTrans: an open-source pipeline for metatranscriptomics

(2016) Xavier Martinez et al.   Scientific Reports

Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica

(2015) Selene L Fernandez-Valverde et al.   BMC GENOMICS

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

(2015) Noan Le Bescot et al.   ENVIRONMENTAL MICROBIOLOGY

The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.)

(2015) Solenn Mordret et al.   ISME Journal

Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus)

(2015) Nguyen Minh Thanh et al.   Marine Genomics

High-Throughput Sequencing Technologies

(2015) Jason A. Reuter et al.   MOLECULAR CELL

Towards an Integrative Morpho-molecular Classification of the Collodaria (Polycystinea, Radiolaria)

(2015) Tristan Biard et al.   PROTIST

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Microbes in the coral holobiont: partners through evolution, development, and ecological interactions

(2015) Janelle R. Thompson et al.   Frontiers in Cellular and Infection Microbiology

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

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

Open science resources for the discovery and analysis of Tara Oceans data

(2015) Stéphane Pesant et al.   Scientific Data

Whole transcriptome analysis reveals changes in expression of immune-related genes during and after bleaching in a reef-building coral

(2015) J. H. Pinzon et al.   Royal Society Open Science

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Brandtodiniumgen. nov. andB. nutriculacomb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians

(2014) Ian Probert et al.   JOURNAL OF PHYCOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

A Snapshot of a Coral “Holobiont”: A Transcriptome Assembly of the Scleractinian Coral, Porites, Captures a Wide Variety of Genes from Both the Host and Symbiotic Zooxanthellae

(2014) Chuya Shinzato et al.   PLoS One

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

DSK: k-mer counting with very low memory usage

(2013) G. Rizk et al.   BIOINFORMATICS

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

A NGS approach to the encrusting Mediterranean spongeCrella elegans(Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages

(2013) A. R. Pérez-Porro et al.   Molecular Ecology Resources

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Same, same but different: symbiotic bacterial associations in GBR sponges

(2013) N. S. Webster et al.   Frontiers in Microbiology

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

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Cell Biology of Cnidarian-Dinoflagellate Symbiosis

(2012) S. K. Davy et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

An original mode of symbiosis in open ocean plankton

(2012) J. Decelle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple microalgal partners in symbiosis with the acantharian Acanthochiasma sp. (Radiolaria)

(2012) Johan Decelle et al.   SYMBIOSIS

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

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

Marine sponges and their microbial symbionts: love and other relationships

(2011) Nicole S. Webster et al.   ENVIRONMENTAL MICROBIOLOGY

Using the Acropora digitifera genome to understand coral responses to environmental change

(2011) Chuya Shinzato et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Molecular Phylogeny and Morphological Evolution of the Acantharia (Radiolaria)

(2011) Johan Decelle et al.   PROTIST

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

(2010) Alexander Siegl et al.   ISME Journal

Coral Life History and Symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata

(2008) Jodi A Schwarz et al.   BMC GENOMICS