Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

(2017) Simon Roux et al.   Nature Communications

Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions

(2017) Jordan C. Angle et al.   Nature Communications

Microbial distribution and variation in produced water from separators to storage tanks of shale gas wells in Sichuan Basin, China

(2017) Yimeng Zhang et al.   Environmental Science-Water Research & Technology

Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome

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Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

(2017) Anne E. Booker et al.   mSphere

Biogenic methane production from coal: A review on recent research and development on microbially enhanced coalbed methane (MECBM)

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New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11

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Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

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Metabolic Capability of a Predominant Halanaerobium sp. in Hydraulically Fractured Gas Wells and Its Implication in Pipeline Corrosion

(2016) Renxing Liang et al.   Frontiers in Microbiology

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

(2016) Rebecca A. Daly et al.   Nature Microbiology

Organic and inorganic composition and microbiology of produced waters from Pennsylvania shale gas wells

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Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal

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VirSorter: mining viral signal from microbial genomic data

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Temporal Changes in Microbial Ecology and Geochemistry in Produced Water from Hydraulically Fractured Marcellus Shale Gas Wells

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The Functional Potential of Microbial Communities in Hydraulic Fracturing Source Water and Produced Water from Natural Gas Extraction Characterized by Metagenomic Sequencing

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A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase

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MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

Microbial Community Changes in Hydraulic Fracturing Fluids and Produced Water from Shale Gas Extraction

(2013) Arvind Murali Mohan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Predominant archaea in marine sediments degrade detrital proteins

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Choline andN,N-Dimethylethanolamine as Direct Substrates for Methanogens

(2012) Andrew J. Watkins et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

New gas material balance to quantify biogenic gas generation rates from shallow organic-matter-rich shales

(2012) M. Cokar et al.   FUEL

Bacterial Communities Associated with Production Facilities of Two Newly Drilled Thermogenic Natural Gas Wells in the Barnett Shale (Texas, USA)

(2012) James P. Davis et al.   MICROBIAL ECOLOGY

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

Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme

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Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

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Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

(2011) Michael A. Fischbach et al.   Cell Host & Microbe

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence

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Thermodynamic limits to microbial life at high salt concentrations

(2010) Aharon Oren   ENVIRONMENTAL MICROBIOLOGY

A Sparse PLS for Variable Selection when Integrating Omics Data

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Sparse principal component analysis via regularized low rank matrix approximation

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