Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents

(2017) Dimitri V Meier et al.   ISME Journal

Microbial community assembly and evolution in subseafloor sediment

(2017) Piotr Starnawski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How clonal are bacteria over time?

(2016) B Jesse Shapiro   CURRENT OPINION IN MICROBIOLOGY

Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise

(2016) Julie Reveillaud et al.   ENVIRONMENTAL MICROBIOLOGY

Pathways for abiotic organic synthesis at submarine hydrothermal fields

(2015) Jill M. McDermott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring deep microbial life in coal-bearing sediment down to  2.5 km below the ocean floor

(2015) F. Inagaki et al.   SCIENCE

ITEP: An integrated toolkit for exploration of microbial pan-genomes

(2014) Matthew N Benedict et al.   BMC GENOMICS

The origin of methanethiol in midocean ridge hydrothermal fluids

(2014) E. P. Reeves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano

(2013) Julie L Meyer et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids

(2013) Nancy H. Akerman et al.   Frontiers in Microbiology

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

(2013) Katarzyna Zaremba-Niedzwiedzka et al.   GENOME BIOLOGY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

A precision multi-sampler for deep-sea hydrothermal microbial mat studies

(2012) J.A. Breier et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

In situchemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field

(2012) Mirjam Perner et al.   ENVIRONMENTAL MICROBIOLOGY

Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin

(2012) G. E. FLORES et al.   Geobiology

Draft Genome Sequence of the Sulfur-Oxidizing Bacterium "Candidatus Sulfurovum sediminum" AR, Which Belongs to the Epsilonproteobacteria

(2012) S.-J. Park et al.   JOURNAL OF BACTERIOLOGY

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

Prospects for the study of evolution in the deep biosphere

(2012) Jennifer F. Biddle   Frontiers in Microbiology

Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge

(2011) Gilberto E. Flores et al.   ENVIRONMENTAL MICROBIOLOGY

Catabolic and anabolic energy for chemolithoautotrophs in deep-sea hydrothermal systems hosted in different rock types

(2011) Jan P. Amend et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

(2010) Arantxa Peña et al.   ISME Journal

Metagenomic Comparison of Two Thiomicrospira Lineages Inhabiting Contrasting Deep-Sea Hydrothermal Environments

(2010) William J. Brazelton et al.   PLoS One

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

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A suspended-particle rosette multi-sampler for discrete biogeochemical sampling in low-particle-density waters

(2009) J.A. Breier et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm

(2009) William J Brazelton et al.   ISME Journal

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Genome Rearrangements and Multiple Horizontal Gene Transfers in a Population of Pyrococcus Isolates from Vulcano Island, Italy

(2008) J. R. White et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Variability in the microbial communities and hydrothermal fluid chemistry at the newly discovered Mariner hydrothermal field, southern Lau Basin

(2008) Ken Takai et al.   JOURNAL OF GEOPHYSICAL RESEARCH