Metatranscriptomics by In Situ RNA Stabilization Directly and Comprehensively Revealed Episymbiotic Microbial Communities of Deep-Sea Squat Lobsters

Dual energy metabolism of the Campylobacterota endosymbiont in the chemosynthetic snail Alviniconcha marisindica

(2020) Junichi Miyazaki et al.   ISME Journal

The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally

(2019) Gregory J. Dick   NATURE REVIEWS MICROBIOLOGY

Highly variable mRNA half‐life time within marine bacterial taxa and functional genes

(2019) Paul A. Steiner et al.   ENVIRONMENTAL MICROBIOLOGY

Methanotrophy across a natural permafrost thaw environment

(2018) Caitlin M Singleton et al.   ISME Journal

Addendum: Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

(2018) David W. Waite et al.   Frontiers in Microbiology

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

(2017) David W. Waite et al.   Frontiers in Microbiology

Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals

(2017) Lauren K. Yum et al.   Scientific Reports

Biometric assessment of deep-sea vent megabenthic communities using multi-resolution 3D image reconstructions

(2016) Blair Thornton et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Comparison of Niskin vs. in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples

(2016) V.P. Edgcomb et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes

(2016) Sherry L. Seston et al.   Frontiers in Microbiology

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

(2016) Jillian M. Petersen et al.   Nature Microbiology

Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data

(2015) Amin Allam et al.   BIOINFORMATICS

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center

(2015) Karthik Anantharaman et al.   ISME Journal

Cytoplasmic sulfur trafficking in sulfur-oxidizing prokaryotes

(2015) Christiane Dahl   IUBMB LIFE

Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples

(2015) Violetta La Cono et al.   Environmental Microbiology Reports

Diversity and methane oxidation of active epibiotic methanotrophs on live Shinkaia crosnieri

(2014) Tomo-o Watsuji et al.   ISME Journal

Molecular evidence of digestion and absorption of epibiotic bacterial community by deep-sea crab Shinkaia crosnieri

(2014) Tomo-o Watsuji et al.   ISME Journal

New Proteins Involved in Sulfur Trafficking in the Cytoplasm ofAllochromatium vinosum

(2014) Yvonne Stockdreher et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts

(2013) J G Sanders et al.   ISME Journal

Bacterial Intracellular Sulfur Globules: Structure and Function

(2013) James S. Maki   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Effects of Hydrogen Sulfide on Bacterial Communities on the Surface of Galatheid Crab, Shinkaia crosnieri, and in a Bacterial Mat Cultured in Rearing Tanks

(2012) Masaaki Konishi et al.   MICROBES AND ENVIRONMENTS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Cell-Specific Thioautotrophic Productivity of Epsilon-Proteobacterial Epibionts Associated with Shinkaia crosnieri

(2012) Tomo-o Watsuji et al.   PLoS One

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system

(2011) Janie Feike et al.   ISME Journal

Hydrogen is an energy source for hydrothermal vent symbioses

(2011) Jillian M. Petersen et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Sulfur Metabolisms in Epsilon- and Gamma-Proteobacteria in Deep-Sea Hydrothermal Fields

(2011) Masahiro Yamamoto et al.   Frontiers in Microbiology

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Epibiotic association between filamentous bacteria and the vent-associated galatheid crab, Shinkaia crosnieri (Decapoda: Anomura)

(2010) Shinji Tsuchida et al.   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM

Diversity and Function of Epibiotic Microbial Communities on the Galatheid Crab, Shinkaia crosnieri

(2010) Tomo-o Watsuji et al.   MICROBES AND ENVIRONMENTS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Indigenous ectosymbiotic bacteria associated with diverse hydrothermal vent invertebrates

(2010) Shana K. Goffredi   Environmental Microbiology Reports

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance

(2008) Satoshi Nakagawa et al.   FEMS MICROBIOLOGY ECOLOGY

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

(2008) Nicole Dubilier et al.   NATURE REVIEWS MICROBIOLOGY