Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Environmental controls on intragroup diversity of the uncultured benthicarchaeaof the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA)

(2015) Cassandre Sara Lazar et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

(2015) Jimmy H. Saw et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria

(2015) Brett J Baker et al.   Microbiome

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Archaea in Biogeochemical Cycles

(2013) Pierre Offre et al.   Annual Review of Microbiology

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

(2013) Jeremy A. Dodsworth et al.   Nature Communications

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

(2012) Y. Peng et al.   BIOINFORMATICS

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

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

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

(2012) K. C. Wrighton et al.   SCIENCE

The Emergence and Early Evolution of Biological Carbon-Fixation

(2012) Rogier Braakman et al.   PLoS Computational Biology

Evidence for Horizontal Gene Transfer of Anaerobic Carbon Monoxide Dehydrogenases

(2012) Stephen M. Techtmann et al.   Frontiers in Microbiology

The origin of NO3− and N2 in deep subsurface fracture water of South Africa

(2011) Bianca J. Silver et al.   CHEMICAL GEOLOGY

Anaerobic transformation of carbon monoxide by microbial communities of Kamchatka hot springs

(2011) Tatiana V. Kochetkova et al.   EXTREMOPHILES

Distinct Physiological Roles of the Three [NiFe]-Hydrogenase Orthologs in the Hyperthermophilic Archaeon Thermococcus kodakarensis

(2011) T. Kanai et al.   JOURNAL OF BACTERIOLOGY

Identification of a Novel Class of Membrane-Bound [NiFe]-Hydrogenases in Thermococcus onnurineus NA1 by In Silico Analysis

(2010) J. K. Lim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Enigmatic, ultrasmall, uncultivated Archaea

(2010) B. J. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Diversity and ecophysiological features of thermophilic carboxydotrophic anaerobes

(2009) Tatyana G. Sokolova et al.   FEMS MICROBIOLOGY ECOLOGY

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

A comparison of methods for total community DNA preservation and extraction from various thermal environments

(2008) Kendra R. Mitchell et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY