Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones

GToTree: a user-friendly workflow for phylogenomics

(2019) Michael D Lee   BIOINFORMATICS

Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus “Candidatus Fonsibacter” and proposal of Ca. Fonsibacter lacus sp. nov

(2019) Despina Tsementzi et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Magic-BLAST, an accurate RNA-seq aligner for long and short reads

(2019) Grzegorz M. Boratyn et al.   BMC BIOINFORMATICS

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

(2019) Dongwan D. Kang et al.   PeerJ

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

(2019) Takuya Aramaki et al.   BIOINFORMATICS

Marine Proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle

(2019) Lennart Schada von Borzyskowski et al.   NATURE

Ecogenomics of the SAR11 clade

(2019) Jose M. Haro‐Moreno et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

(2019) Qiyun Zhu et al.   Nature Communications

MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes

(2018) Wataru Arai et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

(2018) Michael W. Henson et al.   ISME Journal

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

(2018) Luis M Rodriguez-R et al.   NUCLEIC ACIDS RESEARCH

Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation

(2018) Xian Zhang et al.   Frontiers in Microbiology

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient

(2018) Alexandra Meziti et al.   ISME Journal

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

imGLAD: accurate detection and quantification of target organisms in metagenomes

(2018) Juan C. Castro et al.   PeerJ

Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column

(2017) Anthony D. Bertagnolli et al.   ENVIRONMENTAL MICROBIOLOGY

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

SWORD—a highly efficient protein database search

(2016) Robert Vaser et al.   BIOINFORMATICS

In situ quantification of ultra-low O2 concentrations in oxygen minimum zones: Application of novel optodes

(2016) Morten Larsen et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

SAR11 bacteria linked to ocean anoxia and nitrogen loss

(2016) Despina Tsementzi et al.   NATURE

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol

(2016) Jing Sun et al.   Nature Microbiology

Proteome Remodeling in Response to Sulfur Limitation in “ Candidatus Pelagibacter ubique”

(2016) Daniel P. Smith et al.   mSystems

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

(2015) Sangita Ganesh et al.   ISME Journal

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal

(2015) Konstantinos T. Konstantinidis et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution

(2015) Dominique Boeuf et al.   Database-The Journal of Biological Databases and Curation

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

(2015) Jennifer B. Glass et al.   Frontiers in Microbiology

Pathways and Bioenergetics of Anaerobic Carbon Monoxide Fermentation

(2015) Martijn Diender et al.   Frontiers in Microbiology

Transcriptomic evidence for microbial sulfur cycling in the eastern tropical North Pacific oxygen minimum zone

(2015) Molly T. Carolan et al.   Frontiers in Microbiology

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

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

(2015) A. Murat Eren et al.   PeerJ

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Rapid evaluation and quality control of next generation sequencing data with FaQCs

(2014) Chien-Chi Lo et al.   BMC BIOINFORMATICS

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea

(2014) Ian Salter et al.   ISME Journal

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

(2014) J Cameron Thrash et al.   ISME Journal

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

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

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Prochlorococcus: the structure and function of collective diversity

(2014) Steven J. Biller et al.   NATURE REVIEWS MICROBIOLOGY

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Diversity and abundance of “Pelagibacterales” (SAR11) in the Baltic Sea salinity gradient

(2014) Daniel P.R. Herlemann et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

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

High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences

(2013) Kevin L Vergin et al.   ISME Journal

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

(2013) Sangita Ganesh et al.   ISME Journal

The unique metabolism of SAR11 aquatic bacteria

(2013) H. James Tripp   JOURNAL OF MICROBIOLOGY

Comparative and Phylogenomic Evidence That the Alphaproteobacterium HIMB59 Is Not a Member of the Oceanic SAR11 Clade

(2013) Johan Viklund et al.   PLoS One

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters

(2012) Timothy J Williams et al.   ISME Journal

Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium

(2012) Paul Carini et al.   ISME Journal

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

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

Global biogeography of SAR11 marine bacteria

(2012) Mark V Brown et al.   Molecular Systems Biology

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

Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade

(2012) J. Grote et al.   mBio

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Bacterial species may exist, metagenomics reveal

(2011) Alejandro Caro-Quintero et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Complete Genome Sequence of Strain IMCC9063, Belonging to SAR11 Subgroup 3, Isolated from the Arctic Ocean

(2011) H.-M. Oh et al.   JOURNAL OF BACTERIOLOGY

Going Deeper: Metagenome of a Hadopelagic Microbial Community

(2011) Emiley A. Eloe et al.   PLoS One

One Carbon Metabolism in SAR11 Pelagic Marine Bacteria

(2011) Jing Sun et al.   PLoS One

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?

(2010) Georg Fuchs   Annual Review of 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

Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing

(2010) Rohit Ghai et al.   ISME Journal

Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara

(2010) Achim Quaiser et al.   ISME Journal

Ecosystem-specific selection pressures revealed through comparative population genomics

(2010) M. L. Coleman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast

(2010) D. E. Canfield et al.   SCIENCE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean

(2009) Martha Schattenhofer et al.   ENVIRONMENTAL MICROBIOLOGY

The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity

(2009) M. S. Schwalbach et al.   ENVIRONMENTAL MICROBIOLOGY

Revising the nitrogen cycle in the Peruvian oxygen minimum zone

(2009) P. Lam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Genomic patterns of recombination, clonal divergence and environment in marine microbial populations

(2008) Konstantinos T Konstantinidis et al.   ISME Journal

Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea

(2008) Craig A Carlson et al.   ISME Journal

SAR11 marine bacteria require exogenous reduced sulphur for growth

(2008) H. James Tripp et al.   NATURE

The prokaryotic complex iron–sulfur molybdoenzyme family

(2007) Richard A. Rothery et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES