Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures

MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes

(2018) Wataru Arai et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Microbial biogeography of 925 geothermal springs in New Zealand

(2018) Jean F. Power et al.   Nature Communications

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota

(2018) Zheng-Shuang Hua et al.   Nature Communications

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs

(2017) Eric D. Becraft et al.   Frontiers in Microbiology

Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities

(2017) Ryan de Montmollin Jennings et al.   Frontiers in Microbiology

Tracking microbial interactions with NanoSIMS

(2016) Niculina Musat et al.   CURRENT OPINION IN BIOTECHNOLOGY

An automated system for evaluation of the potential functionome: MAPLE version 2.1.0

(2016) Hideto Takami et al.   DNA RESEARCH

Phylogenetic organization of bacterial activity

(2016) Ember M Morrissey et al.   ISME Journal

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Communications

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

(2016) Marcel Huntemann et al.   Standards in Genomic Sciences

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes

(2015) Eric D. Becraft et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative Microbial Ecology through Stable Isotope Probing

(2015) Bruce A. Hungate et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’

(2015) Brian P Hedlund et al.   CURRENT OPINION IN MICROBIOLOGY

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

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

Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer’ community

(2015) Jacob P Beam et al.   ISME Journal

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

(2015) Sonia Tarazona et al.   NUCLEIC ACIDS RESEARCH

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

High carbon use efficiency in soil microbial communities is related to balanced growth, not storage compound synthesis

(2015) Paul Dijkstra et al.   SOIL BIOLOGY & BIOCHEMISTRY

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

(2015) Young-Mo Kim et al.   Frontiers in Microbiology

Stable isotope labeling confirms mixotrophic nature of streamer biofilm communities at alkaline hot springs

(2015) Florence Schubotz et al.   Frontiers in Microbiology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

NCBI BLAST+ integrated into Galaxy

(2015) Peter J. A. Cock et al.   GigaScience

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

(2015) Brett J Baker et al.   Microbiome

Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.

(2014) J. A. Dodsworth et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments

(2014) Christine E Sharp et al.   ISME Journal

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

(2014) C. Brasen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Accelerated microbial turnover but constant growth efficiency with warming in soil

(2014) Shannon B. Hagerty et al.   Nature Climate Change

Community Microrespirometry and Molecular Analyses Reveal a Diverse Energy Economy in Great Boiling Spring and Sandy's Spring West in the U.S. Great Basin

(2013) Caitlin N. Murphy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Archaeal and bacterial diversity in acidic to circumneutral hot springs in the Philippines

(2013) Qiuyuan Huang et al.   FEMS MICROBIOLOGY ECOLOGY

Cultivation and characterization of thermophilicNitrospiraspecies from geothermal springs in the US Great Basin, China, and Armenia

(2013) Tara A. Edwards et al.   FEMS MICROBIOLOGY ECOLOGY

Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining During Thermal Adaptation

(2013) Niv Sabath et al.   Genome Biology and Evolution

Spatial and temporal variability of biomarkers and microbial diversity reveal metabolic and community flexibility in Streamer Biofilm Communities in the Lower Geyser Basin, Yellowstone National Park

(2013) F. Schubotz et al.   Geobiology

Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring

(2013) Christian G Klatt et al.   ISME Journal

COMPLETE-MFA: Complementary parallel labeling experiments technique for metabolic flux analysis

(2013) Robert W. Leighty et al.   METABOLIC ENGINEERING

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

(2013) Weiguo Hou et al.   PLoS One

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

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

Glycolytic strategy as a tradeoff between energy yield and protein cost

(2013) A. Flamholz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using metabolic tracer techniques to assess the impact of tillage and straw management on microbial carbon use efficiency in soil

(2013) Kees Jan van Groenigen et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Evaluation method for the potential functionome harbored in the genome and metagenome

(2012) Hideto Takami et al.   BMC GENOMICS

Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs

(2012) Jeremy A. Dodsworth et al.   FEMS MICROBIOLOGY ECOLOGY

Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

(2012) Jessica K Cole et al.   ISME Journal

Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

(2012) Dimitry Y Sorokin et al.   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

(2012) Hideto Takami et al.   PLoS One

Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem

(2012) Wesley D. Swingley et al.   PLoS One

Modeling the Habitat Range of Phototrophs in Yellowstone National Park: Toward the Development of a Comprehensive Fitness Landscape

(2012) Eric S. Boyd et al.   Frontiers in Microbiology

Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea

(2011) Jeremy A. Dodsworth et al.   ENVIRONMENTAL MICROBIOLOGY

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

An actin-based cytoskeleton in archaea

(2011) Thijs J. G. Ettema et al.   MOLECULAR MICROBIOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Modeling soil metabolic processes using isotopologue pairs of position-specific 13C-labeled glucose and pyruvate

(2011) Paul Dijkstra et al.   SOIL BIOLOGY & BIOCHEMISTRY

Effect of temperature on metabolic activity of intact microbial communities: Evidence for altered metabolic pathway activity but not for increased maintenance respiration and reduced carbon use efficiency

(2011) Paul Dijkstra et al.   SOIL BIOLOGY & BIOCHEMISTRY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The transition to microbial photosynthesis in hot spring ecosystems

(2010) Alysia Cox et al.   CHEMICAL GEOLOGY

Thermodynamic limits to microbial life at high salt concentrations

(2010) Aharon Oren   ENVIRONMENTAL MICROBIOLOGY

Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in E. coli

(2010) Xuewen Chen et al.   METABOLIC ENGINEERING

Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme

(2010) Rafael F. Say et al.   NATURE

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

(2010) Takuro Nunoura et al.   NUCLEIC ACIDS RESEARCH

Probing carbon flux patterns through soil microbial metabolic networks using parallel position-specific tracer labeling

(2010) Paul Dijkstra et al.   SOIL BIOLOGY & BIOCHEMISTRY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

New insights into short-chain prenyltransferases: structural features, evolutionary history and potential for selective inhibition

(2009) Sophie Vandermoten et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin

(2009) Kyle C. Costa et al.   EXTREMOPHILES

13C-based metabolic flux analysis

(2009) Nicola Zamboni et al.   Nature Protocols

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol

(2008) José R. de la Torre et al.   ENVIRONMENTAL MICROBIOLOGY

Metabolic Network Fluxes in Heterotrophic Arabidopsis Cells: Stability of the Flux Distribution under Different Oxygenation Conditions

(2008) T. C.R. Williams et al.   PLANT PHYSIOLOGY