A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean

Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf

(2022) Clara Martínez-Pérez et al.   Nature Communications

Phylogeny and Metabolic Potential of the Candidate Phylum SAR324

(2022) Lukas Malfertheiner et al.   Biology-Basel

Prokaryotic Life in the Deep Ocean's Water Column

(2022) Gerhard J. Herndl et al.   Annual Review of Marine Science

Biosynthetic potential of the global ocean microbiome

(2022) Lucas Paoli et al.   NATURE

The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

(2022) Yosuke Nishimura et al.   Scientific Data

Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny

(2022) Robert C. Edgar   Nature Communications

clinker & clustermap.js: automatic generation of gene cluster comparison figures

(2021) Cameron L M Gilchrist et al.   BIOINFORMATICS

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Sulfur cycling in oceanic oxygen minimum zones

(2021) Cameron M. Callbeck et al.   LIMNOLOGY AND OCEANOGRAPHY

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Microbes mediating the sulfur cycle in the Atlantic Ocean and their link to chemolithoautotrophy

(2021) Daniele De Corte et al.   ENVIRONMENTAL MICROBIOLOGY

Structural and Mechanistic Insights Into Dimethylsulfoxide Formation Through Dimethylsulfide Oxidation

(2021) Xiu-Juan Wang et al.   Frontiers in Microbiology

Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

(2020) Lucas Czech et al.   BIOINFORMATICS

Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean

(2020) Yao Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics

(2020) Shunan Cao et al.   Microbiome

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

(2020) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Sulfur metabolites that facilitate oceanic phytoplankton–bacteria carbon flux

(2019) Marine Landa et al.   ISME Journal

Bacteria are important dimethylsulfoniopropionate producers in coastal sediments

(2019) Beth T. Williams et al.   Nature Microbiology

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

(2019) Guillem Salazar et al.   CELL

OUP accepted manuscript

(2018)   BIOINFORMATICS

A novel bacterial sulfur oxidation pathway provides a new link between the cycles of organic and inorganic sulfur compounds

(2018) Tobias Koch et al.   ISME Journal

Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria

(2018) Cameron M. Callbeck et al.   Nature Communications

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

(2018) Pierre Barbera et al.   SYSTEMATIC BIOLOGY

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents

(2017) Dimitri V Meier et al.   ISME Journal

Crustacean zooplankton release copious amounts of dissolved organic matter as taurine in the ocean

(2017) Elisabeth L. Clifford et al.   LIMNOLOGY AND OCEANOGRAPHY

The MAR databases: development and implementation of databases specific for marine metagenomics

(2017) Terje Klemetsen et al.   NUCLEIC ACIDS RESEARCH

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation

(2017) Maria G. Pachiadaki et al.   SCIENCE

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

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

Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic

(2016) Federico Baltar et al.   Frontiers in Microbiology

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Tara Oceans studies plankton at planetary scale

(2015) P. Bork et al.   SCIENCE

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Infernal 1.1: 100-fold faster RNA homology searches

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

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial control of the dark end of the biological pump

(2013) Gerhard J. Herndl et al.   Nature Geoscience

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Microbial oceanography of anoxic oxygen minimum zones

(2012) O. Ulloa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Carboxylases in Natural and Synthetic Microbial Pathways

(2011) Tobias J. Erb   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

(2011) Frank J. Stewart et al.   ENVIRONMENTAL MICROBIOLOGY

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Mechanisms and Evolution of Oxidative Sulfur Metabolism in Green Sulfur Bacteria

(2011) Lea H. Gregersen et al.   Frontiers in Microbiology

mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models forIn SilicoEvaluation of Oligonucleotide Probes for FluorescenceIn SituHybridization

(2010) L. Safak Yilmaz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic’s interior

(2010) Thomas Reinthaler et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Significance of non-sinking particulate organic carbon and dark CO2fixation to heterotrophic carbon demand in the mesopelagic northeast Atlantic

(2010) Federico Baltar et al.   GEOPHYSICAL RESEARCH LETTERS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

(2009) D. A. Walsh et al.   SCIENCE

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

(2008) Sean R. Eddy   PLoS Computational Biology