How Clonal Is Clonal? Genome Plasticity across Multicellular Segments of a “Candidatus Marithrix sp.” Filament from Sulfidic, Briny Seafloor Sediments in the Gulf of Mexico

Patterns and variability in geochemical signatures and microbial activity within and between diverse cold seep habitats along the lower continental slope, Northern Gulf of Mexico

(2016) Marshall Bowles et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island

(2016) Eduard Fadeev et al.   Frontiers in Microbiology

Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions

(2016) Matthias Winkel et al.   Frontiers in Microbiology

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

(2016) Beverly E. Flood et al.   Frontiers in Microbiology

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

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

Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh

(2015) Verena Salman et al.   ISME Journal

In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella

(2015) Abdul R Sheik et al.   ISME Journal

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Compartmentalization and organelle formation in bacteria

(2014) Elias Cornejo et al.   CURRENT OPINION IN CELL BIOLOGY

Microevolution of Burkholderia pseudomallei during an Acute Infection

(2014) Direk Limmathurotsakul et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Phylogenetic and morphologic complexity of giant sulphur bacteria

(2013) Verena Salman et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

(2013) Barbara J. MacGregor et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament

(2013) Barbara J. MacGregor et al.   Marine Genomics

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

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

(2012) M. Kearse et al.   BIOINFORMATICS

Spatial heterogeneity and underlying geochemistry of phylogenetically diverse orange and white Beggiatoa mats in Guaymas Basin hydrothermal sediments

(2012) Luke J. McKay et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

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

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

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

(2012) V. Salman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Unusual polyphosphate inclusions observed in a marine Beggiatoa strain

(2011) Jörg Brock et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Ploidy and gene conversion in Archaea

(2011) Jörg Soppa   BIOCHEMICAL SOCIETY TRANSACTIONS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Vacuolated Beggiatoa-like filaments from different hypersaline environments form a novel genus

(2011) Susanne Hinck et al.   ENVIRONMENTAL MICROBIOLOGY

Niche differentiation among mat-forming, sulfide-oxidizing bacteria at cold seeps of the Nile Deep Sea Fan (Eastern Mediterranean Sea)

(2011) S. GRÜNKE et al.   Geobiology

Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria

(2011) Jake V Bailey et al.   ISME Journal

Rapid and precise δ13C measurement of dissolved inorganic carbon in natural waters using liquid chromatography coupled to an isotope-ratio mass spectrometer

(2011) Jay A. Brandes   LIMNOLOGY AND OCEANOGRAPHY-METHODS

DNA Replication and Genomic Architecture of Very Large Bacteria

(2010) Esther R. Angert   Annual Review of Microbiology

Biogeochemical signatures and microbial activity of different cold-seep habitats along the Gulf of Mexico deep slope

(2010) Samantha B. Joye et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Filamentous sulfur bacteria, Beggiatoa spp., in arctic marine sediments (Svalbard, 79°N)

(2010) Bo Barker Jørgensen et al.   FEMS MICROBIOLOGY ECOLOGY

The energetics of genome complexity

(2010) Nick Lane et al.   NATURE

Multiple displacement amplification compromises quantitative analysis of metagenomes

(2010) Suzan Yilmaz et al.   NATURE METHODS

Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep

(2010) Karen G. Lloyd et al.   PLoS One

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Temporal separation of cell division and diazotrophy in the marine diazotrophic cyanobacteriumTrichodesmium erythraeumIMS101

(2009) Gustaf Sandh et al.   FEMS MICROBIOLOGY LETTERS

Vacuolate-attached filaments: highly productive Ridgeia piscesae epibionts at the Juan de Fuca hydrothermal vents

(2009) Karen M. Kalanetra et al.   MARINE BIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS

Extreme polyploidy in a large bacterium

(2008) J. E. Mendell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA