Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics

Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume

(2013) Meng Li et al.   ENVIRONMENTAL MICROBIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

(2012) Ryan A Lesniewski et al.   ISME Journal

Sizing up metatranscriptomics

(2012) Mary Ann Moran et al.   ISME Journal

Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume

(2012) Brett J Baker et al.   ISME Journal

Biogeochemical Processes at Hydrothermal Vents: Microbes and Minerals, Bioenergetics, and Carbon Fluxes

(2012) James Holden et al.   OCEANOGRAPHY

Cytoplasmic Sulfurtransferases in the Purple Sulfur Bacterium Allochromatium vinosum: Evidence for Sulfur Transfer from DsrEFH to DsrC

(2012) Yvonne Stockdreher et al.   PLoS One

Pole-to-pole biogeography of surface and deep marine bacterial communities

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

Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria

(2012) K. Anantharaman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modularity of methylotrophy, revisited

(2011) Ludmila Chistoserdova   ENVIRONMENTAL MICROBIOLOGY

Metabolic strategies of free-living and aggregate-associated bacterial communities inferred from biologic and chemical profiles in the Black Sea suboxic zone

(2011) Clara A. Fuchsman et al.   FEMS MICROBIOLOGY ECOLOGY

Quantitative proteomics of Chlorobaculum tepidum: insights into the sulfur metabolism of a phototrophic green sulfur bacterium

(2011) Lasse G. Falkenby et al.   FEMS MICROBIOLOGY LETTERS

Microbial oceanography of the dark ocean's pelagic realm

(2011) Javier Arístegui et al.   LIMNOLOGY AND OCEANOGRAPHY

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

(2011) B. N. Orcutt et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacteriumNocardioidessp. strain CF8 is a novel member of the AMO/PMO family

(2011) Luis A. Sayavedra-Soto et al.   Environmental Microbiology Reports

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

(2010) Michael Hügler et al.   Annual Review of Marine Science

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li 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

Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume

(2010) Gregory J. Dick et al.   ENVIRONMENTAL MICROBIOLOGY

Time-series analyses of Monterey Bay coastal microbial picoplankton using a ‘genome proxy’ microarray

(2010) Virginia I. Rich et al.   ENVIRONMENTAL MICROBIOLOGY

Diverse styles of submarine venting on the ultraslow spreading Mid-Cayman Rise

(2010) C. R. German et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untangling the multiple monooxygenases ofMycobacterium chubuensestrain NBB4, a versatile hydrocarbon degrader

(2010) Nicholas V. Coleman et al.   Environmental Microbiology Reports

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

Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia

(2009) Elena Zaikova et al.   ENVIRONMENTAL MICROBIOLOGY

Enzymatic microbial Mn(II) oxidation and Mn biooxide production in the Guaymas Basin deep-sea hydrothermal plume

(2009) Gregory J. Dick et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Elevated concentrations of formate, acetate and dissolved organic carbon found at the Lost City hydrothermal field

(2009) Susan Q. Lang et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column

(2009) Yanmei Shi et al.   NATURE

Preservation of iron(II) by carbon-rich matrices in a hydrothermal plume

(2009) Brandy M. Toner et al.   Nature Geoscience

Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

(2009) D. A. Walsh et al.   SCIENCE

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Genomic Insights into Mn(II) Oxidation by the Marine Alphaproteobacterium Aurantimonas sp. Strain SI85-9A1

(2008) G. J. Dick et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre

(2008) Vinh D. Pham et al.   ENVIRONMENTAL MICROBIOLOGY

Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes

(2008) Alexander Loy et al.   ENVIRONMENTAL MICROBIOLOGY

Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle

(2008) Murray Ronald Badger et al.   JOURNAL OF EXPERIMENTAL BOTANY

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY