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

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

(2017) Ramunas Stepanauskas et al.   Nature Communications

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

SAR11 bacteria linked to ocean anoxia and nitrogen loss

(2016) Despina Tsementzi et al.   NATURE

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

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

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines

(2015) David Kamanda Ngugi et al.   ISME Journal

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genusNitrospira

(2015) Hanna Koch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres

(2014) Brandon K. Swan et al.   PLoS One

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

(2014) A. K. Hawley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

(2014) W. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of a new marine nitrite oxidizing bacterium, Nitrospina watsonii sp. nov., a member of the newly proposed phylum “Nitrospinae”

(2014) Eva Spieck et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Nitrospina-like bacteria are the main drivers of nitrite oxidation in the seasonal upwelling area of the Eastern South Pacific (Central Chile ∼36°S)

(2014) Héctor A. Levipan et al.   Environmental Microbiology Reports

Chromatographic Determination of Nanomolar Cyanate Concentrations in Estuarine and Sea Waters by Precolumn Fluorescence Derivatization

(2013) Brittany Widner et al.   ANALYTICAL CHEMISTRY

Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics

(2013) Cody S. Sheik et al.   ENVIRONMENTAL MICROBIOLOGY

Nitrite oxidation in the upper water column and oxygen minimum zone of the eastern tropical North Pacific Ocean

(2013) J Michael Beman et al.   ISME Journal

Quantitative Assessment of In-solution Digestion Efficiency Identifies Optimal Protocols for Unbiased Protein Analysis

(2013) Ileana R. León et al.   MOLECULAR & CELLULAR PROTEOMICS

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

(2013) B. K. Swan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer

(2013) Sebastian Lücker et al.   Frontiers in Microbiology

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Microbial ecology of expanding oxygen minimum zones

(2012) Jody J. Wright et al.   NATURE REVIEWS MICROBIOLOGY

CREST – Classification Resources for Environmental Sequence Tags

(2012) Anders Lanzén et al.   PLoS One

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Contribution ofCrenarchaeotaandBacteriato autotrophy in the North Atlantic interior

(2011) Marta M. Varela et al.   ENVIRONMENTAL MICROBIOLOGY

Relevance of Nitrospira for nitrite oxidation in a marine recirculation aquaculture system and physiological features of a Nitrospira marina-like isolate

(2011) Sabine Keuter et al.   ENVIRONMENTAL MICROBIOLOGY

Chemoautotrophy in the ocean

(2011) Jack J. Middelburg   GEOPHYSICAL RESEARCH LETTERS

Nitrite oxidation in the Namibian oxygen minimum zone

(2011) Jessika Füssel et al.   ISME Journal

A survey of carbon fixation pathways through a quantitative lens

(2011) Arren Bar-Even et al.   JOURNAL OF EXPERIMENTAL BOTANY

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Refinements to Label Free Proteome Quantitation: How to Deal with Peptides Shared by Multiple Proteins

(2010) Ying Zhang et al.   ANALYTICAL CHEMISTRY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   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

A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria

(2010) S. Lucker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

(2009) D. A. Walsh et al.   SCIENCE

Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation

(2008) Courtney E. Jahn et al.   JOURNAL OF MICROBIOLOGICAL METHODS

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION