Adaptations to high pressure of Nautilia sp. strain PV ‐1, a piezophilic Campylobacterium (aka Epsilonproteobacterium) isolated from a deep‐sea hydrothermal vent

Metaproteogenomic Profiling of Chemosynthetic Microbial Biofilms Reveals Metabolic Flexibility During Colonization of a Shallow-Water Gas Vent

(2021) Sushmita Patwardhan et al.   Frontiers in Microbiology

Genus-Specific Carbon Fixation Activity Measurements Reveal Distinct Responses to Oxygen among Hydrothermal Vent Campylobacteria

(2021) Jesse McNichol et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial single-cell omics: the crux of the matter

(2020) Anne-Kristin Kaster et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The effect of O 2 and pressure on thiosulfate oxidation by Thiomicrospira thermophila

(2019) Jennifer L. Houghton et al.   Geobiology

Single Cell Genomics-Based Analysis of Gene Content and Expression of Prophages in a Diffuse-Flow Deep-Sea Hydrothermal System

(2019) Jessica M. Labonté et al.   Frontiers in Microbiology

Mechanisms of DNA Uptake by Naturally Competent Bacteria

(2019) David Dubnau et al.   Annual Review of Genetics

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

(2019) James J Davis et al.   NUCLEIC ACIDS RESEARCH

Elemental sulfur reduction in the deep-sea vent thermophile, Thermovibrio ammonificans

(2018) Benjamin Jelen et al.   ENVIRONMENTAL MICROBIOLOGY

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

(2018) Jongsik Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Primary productivity below the seafloor at deep-sea hot springs

(2018) Jesse McNichol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure

(2017) Melvin F. Siliakus et al.   EXTREMOPHILES

Biogeochemical N signatures from rate-yield trade-offs during in vitro chemosynthetic NO 3 − reduction by deep-sea vent ε-Proteobacteria and Aquificae growing at different temperatures

(2017) Ileana Pérez-Rodríguez et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

(2017) Claire Bertelli et al.   NUCLEIC ACIDS RESEARCH

Lebetimonas natsushimae sp. nov., a novel strictly anaerobic, moderately thermophilic chemoautotroph isolated from a deep-sea hydrothermal vent polychaete nest in the Mid-Okinawa Trough

(2017) Ryousuke Nagata et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans

(2017) Donato Giovannelli et al.   eLife

The Type IV Pilus Assembly ATPase PilB ofMyxococcus xanthusInteracts with the Inner Membrane Platform Protein PilC and the Nucleotide-binding Protein PilM

(2016) Lisa Franziska Bischof et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Homeoviscous Adaptation and the Regulation of Membrane Lipids

(2016) Robert Ernst et al.   JOURNAL OF MOLECULAR BIOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification

(2016) Olivier Langella et al.   JOURNAL OF PROTEOME RESEARCH

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii

(2016) Grégoire Michoud et al.   Scientific Reports

A Continuous Culture System for Assessing Microbial Activities in the Piezosphere

(2015) Dionysis I. Foustoukos et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial diversity and adaptation to high hydrostatic pressure in deep-sea hydrothermal vents prokaryotes

(2015) Mohamed Jebbar et al.   EXTREMOPHILES

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

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

Cetia pacifica gen. nov., sp. nov., a chemolithoautotrophic, thermophilic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent

(2015) Ashley Grosche et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics

(2015) Hyungwon Choi et al.   Journal of Proteomics

Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics

(2015) Sarah R. Langley et al.   Journal of Proteomics

Genome expression of Thermococcus barophilus and Thermococcus kodakarensis in response to different hydrostatic pressure conditions

(2015) Pauline Vannier et al.   RESEARCH IN MICROBIOLOGY

Membrane homeoviscous adaptation in the piezo-hyperthermophilic archaeon Thermococcus barophilus

(2015) Anaïs Cario et al.   Frontiers in Microbiology

Measuring fluid flow and heat output in seafloor hydrothermal environments

(2015) Leonid N. Germanovich et al.   JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap)

(2014) Costantino Vetriani et al.   ISME Journal

Transcriptomics Reveal Several Gene Expression Patterns in the Piezophile Desulfovibrio hydrothermalis in Response to Hydrostatic Pressure

(2014) Amira Amrani et al.   PLoS One

Genome sequence of a novel deep-sea vent epsilonproteobacterial phage provides new insight into the co-evolution of Epsilonproteobacteria and their phages

(2013) Yukari Yoshida-Takashima et al.   EXTREMOPHILES

Photobacterium profundum under Pressure: A MS-Based Label-Free Quantitative Proteomics Study

(2013) Thierry Le Bihan et al.   PLoS One

Nitrate ammonification by Nautilia profundicola AmH: experimental evidence consistent with a free hydroxylamine intermediate

(2013) Thomas E. Hanson et al.   Frontiers in Microbiology

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

High-pressure tolerance in Halobacterium salinarum NRC-1 and other non-piezophilic prokaryotes

(2012) Adrienne Kish et al.   EXTREMOPHILES

Chemoautotrophy at Deep-Sea Vents: Past, Present, and Future

(2012) Stefan Sievert et al.   OCEANOGRAPHY

Complete genome sequence of Thermovibrio ammonificans HB-1T, a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent

(2012) Donato Giovannelli et al.   Standards in Genomic Sciences

Kinetics of H2–O2–H2O redox equilibria and formation of metastable H2O2 under low temperature hydrothermal conditions

(2011) Dionysis I. Foustoukos et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Bacillus subtilis CinA is a stationary phase–induced protein that localizes to the nucleoid and plays a minor role in competent cells

(2010) Christine Kaimer et al.   ARCHIVES OF MICROBIOLOGY

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Molecular characterization of inorganic sulfur-compound metabolism in the deep-sea epsilonproteobacterium Sulfurovum sp. NBC37-1

(2010) Masahiro Yamamoto et al.   ENVIRONMENTAL MICROBIOLOGY

Architecture of the type II secretion and type IV pilus machineries

(2010) Melissa Ayers et al.   Future Microbiology

The many ways of coping with pressure

(2010) Philippe M. Oger et al.   RESEARCH IN MICROBIOLOGY

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

Nautilia abyssi sp. nov., a thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific Rise hydrothermal vent

(2009) K. Alain et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola

(2009) Barbara J. Campbell et al.   PLoS Genetics

The Deep-Sea Bacterium Photobacterium profundum SS9 Utilizes Separate Flagellar Systems for Swimming and Swarming under High-Pressure Conditions

(2008) E. A. Eloe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Sequence variability of Campylobacter temperate bacteriophages

(2008) Clifford G Clark et al.   BMC MICROBIOLOGY

Culture dependent and independent analyses of 16S rRNA and ATP citrate lyase genes: a comparison of microbial communities from different black smoker chimneys on the Mid-Atlantic Ridge

(2008) James W. Voordeckers et al.   EXTREMOPHILES

Nautilia profundicola sp. nov., a thermophilic, sulfur-reducing epsilonproteobacterium from deep-sea hydrothermal vents

(2008) J. L. Smith et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics

(2008) Hyungwon Choi et al.   MOLECULAR & CELLULAR PROTEOMICS

Cell proliferation at 122 C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation

(2008) K. Takai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA