Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

(2016) Ping Hu et al.   mBio

Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents

(2016) Begüm D. Topçuoğlu et al.   Frontiers in Microbiology

Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis

(2016) Lukas Kohl et al.   Journal of Geophysical Research-Biogeosciences

Endolithic microbial communities in carbonate precipitates from serpentinite-hosted hyperalkaline springs of the Voltri Massif (Ligurian Alps, Northern Italy)

(2015) Marianne Quéméneur et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

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

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

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Nonequilibrium clumped isotope signals in microbial methane

(2015) D. T. Wang et al.   SCIENCE

Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines)

(2015) Kristin M. Woycheese et al.   Frontiers in Microbiology

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

(2015) William C. Nelson et al.   Frontiers in Microbiology

Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome

(2015) Vímac Nolla-Ardèvol et al.   Frontiers in Microbiology

Record of archaeal activity at the serpentinite-hosted Lost City Hydrothermal Field

(2015) S. Méhay et al.   Geobiology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

VAMPS: a website for visualization and analysis of microbial population structures

(2014) Susan M Huse et al.   BMC BIOINFORMATICS

Geochemical evidence for active tropical serpentinization in the Santa Elena Ophiolite, Costa Rica: An analog of a humid early Earth?

(2014) Ricardo Sánchez-Murillo et al.   GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS

Fermentative hydrogen production by a new alkaliphilic Clostridium sp. (strain PROH2) isolated from a shallow submarine hydrothermal chimney in Prony Bay, New Caledonia

(2014) Nan Mei et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus

(2014) Emmanuel Prestat et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys

(2014) Michael C. Nelson et al.   PLoS One

Deciphering the Prokaryotic Community and Metabolisms in South African Deep-Mine Biofilms through Antibody Microarrays and Graph Theory

(2014) Yolanda Blanco et al.   PLoS One

Spatial distribution of microbial communities in the shallow submarine alkaline hydrothermal field of the Prony Bay, New Caledonia

(2014) Marianne Quéméneur et al.   Environmental Microbiology Reports

Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site

(2014) Shino Suzuki et al.   Nature Communications

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Investigations of potential microbial methanogenic and carbon monoxide utilization pathways in ultra-basic reducing springs associated with present-day continental serpentinization: the Tablelands, NL, CAN

(2014) Penny L. Morrill et al.   Frontiers in Microbiology

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach

(2014) Melitza Crespo-Medina et al.   Frontiers in Microbiology

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

(2014) Susan M Huse et al.   Microbiome

Bacterial Communities Associated with Subsurface Geochemical Processes in Continental Serpentinite Springs

(2013) William J. Brazelton et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Geochemistry and geobiology of a present-day serpentinization site in California: The Cedars

(2013) Penny L. Morrill et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Sources and cycling of carbon in continental, serpentinite-hosted alkaline springs in the Voltri Massif, Italy

(2013) Esther M. Schwarzenbach et al.   LITHOS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem

(2013) S. Suzuki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Serpentinization, Carbon, and Deep Life

(2013) M. O. Schrenk et al.   Reviews in Mineralogy & Geochemistry

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization

(2012) Igor Tiago et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial utilization of abiogenic carbon and hydrogen in a serpentinite-hosted system

(2012) Susan Q. Lang et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

The role of serpentinites in cycling of carbon and sulfur: Seafloor serpentinization and subduction metamorphism

(2012) Jeffrey C. Alt et al.   LITHOS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Metagenomic Evidence for H2 Oxidation and H2 Production by Serpentinite-Hosted Subsurface Microbial Communities

(2012) William J. Brazelton et al.   Frontiers in Microbiology

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Physiological Differentiation within a Single-Species Biofilm Fueled by Serpentinization

(2011) W. J. Brazelton et al.   mBio

How to Make a Living by Exhaling Methane

(2010) James G. Ferry   Annual Review of Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

(2009) Yuzhen Ye et al.   PLoS Computational Biology

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Extraordinary 13C enrichment of diether lipids at the Lost City Hydrothermal Field indicates a carbon-limited ecosystem

(2008) Alexander S. Bradley et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

An alkaline spring system within the Del Puerto Ophiolite (California, USA): A Mars analog site

(2008) J.G. Blank et al.   PLANETARY AND SPACE SCIENCE

Abiogenic Hydrocarbon Production at Lost City Hydrothermal Field

(2008) G. Proskurowski et al.   SCIENCE