Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms

(2019) Matthew R. Olm et al.   Microbiome

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

Tracing the Evolution of the Plastome and Mitogenome in the Chloropicophyceae Uncovered Convergent tRNA Gene Losses and a Variant Plastid Genetic Code

(2019) Monique Turmel et al.   Genome Biology and Evolution

Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean

(2019) Dominique Boeuf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Genome-reconstruction for eukaryotes from complex natural microbial communities

(2018) Patrick T. West et al.   GENOME RESEARCH

Impacts of Shifts in Phytoplankton Community on Clouds and Climate via the Sulfur Cycle

(2018) Shanlin Wang et al.   GLOBAL BIOGEOCHEMICAL CYCLES

The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean

(2018) Flora J. Vincent et al.   ISME Journal

A global ocean atlas of eukaryotic genes

(2018) Quentin Carradec et al.   Nature Communications

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton

(2018) Andrew R. J. Curson et al.   Nature Microbiology

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data

(2018) Florian Plaza Oñate et al.   BIOINFORMATICS

Quantitative biogeography of picoprasinophytes establishes ecotype distributions and significant contributions to marine phytoplankton

(2017) Alexander J. Limardo et al.   ENVIRONMENTAL MICROBIOLOGY

Distinct ecological niches of marine symbiotic N2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa sublineages

(2017) Kendra A. Turk-Kubo et al.   JOURNAL OF PHYCOLOGY

First observations of living sea-ice diatom agglomeration to tintinnid loricae in East Antarctica

(2017) Linda H. Armbrecht et al.   JOURNAL OF PLANKTON RESEARCH

New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona

(2017) Mohammed-Amin Madoui et al.   MOLECULAR ECOLOGY

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Chloropicophyceae, a new class of picophytoplanktonic prasinophytes

(2017) Adriana Lopes dos Santos et al.   Scientific Reports

Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria

(2017) Hannah A. Bullock et al.   Frontiers in Microbiology

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

(2017) Adriana Alberti et al.   Scientific Data

Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process

(2017) Andrew R. J. Curson et al.   Nature Microbiology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

More protist genomes needed

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

New insights into the ecology of the globally significant uncultured nitrogen-fixing symbiont UCYN-A

(2016) H Farnelid et al.   AQUATIC MICROBIAL ECOLOGY

Enzymatic breakage of dimethylsulfoniopropionate—a signature molecule for life at sea

(2016) Andrew WB Johnston et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP

(2016) Winifred M Johnson et al.   ISME Journal

Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

(2016) Adriana Lopes dos Santos et al.   ISME Journal

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Unusual marine unicellular symbiosis with the nitrogen-fixing cyanobacterium UCYN-A

(2016) Jonathan P. Zehr et al.   Nature Microbiology

Survey of the green picoalga Bathycoccus genomes in the global ocean

(2016) Thomas Vannier et al.   Scientific Reports

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Next-generation sequencing propels environmental genomics to the front line of research

(2015) D Joly et al.   HEREDITY

Identification of the algal dimethyl sulfide-releasing enzyme: A missing link in the marine sulfur cycle

(2015) U. Alcolombri et al.   SCIENCE

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

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

(2015) Stéphane Pesant et al.   Scientific Data

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Genetic diversity of the unicellular nitrogen-fixing cyanobacteria UCYN-A and its prymnesiophyte host

(2014) Anne Thompson et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria

(2014) Deniz Bombar et al.   ISME Journal

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

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

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

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Discovery of an Endosymbiotic Nitrogen-Fixing Cyanobacterium UCYN-A in Braarudosphaera bigelowii (Prymnesiophyceae)

(2013) Kyoko Hagino et al.   PLoS One

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Global distribution of a wild alga revealed by targeted metagenomics

(2012) Alexandra Z. Worden et al.   CURRENT BIOLOGY

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Zooplankton population connections, community dynamics, and climate variability

(2012) J. E. Keister et al.   ICES JOURNAL OF MARINE SCIENCE

Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling

(2012) Daniel Vaulot et al.   PLoS One

Unicellular Cyanobacterium Symbiotic with a Single-Celled Eukaryotic Alga

(2012) A. W. Thompson et al.   SCIENCE

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

Nitrogen fixation and transfer in open ocean diatom–cyanobacterial symbioses

(2011) Rachel A Foster et al.   ISME Journal

Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria

(2011) Chris R. Reisch et al.   NATURE

Nitrogen Cycle of the Open Ocean: From Genes to Ecosystems

(2010) Jonathan P. Zehr et al.   Annual Review of Marine Science

Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium

(2010) H. James Tripp et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

(2009) Daniel R. Zerbino et al.   PLoS One

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Protists are microbes too: a perspective

(2008) David A Caron et al.   ISME Journal

Globally Distributed Uncultivated Oceanic N2-Fixing Cyanobacteria Lack Oxygenic Photosystem II

(2008) J. P. Zehr et al.   SCIENCE