Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments

High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism

(2017) Yun-Juan Bao et al.   JOURNAL OF ENVIRONMENTAL SCIENCES

Functional metagenomics of extreme environments

(2016) Salvador Mirete et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes

(2016) Daniel R. Colman et al.   Frontiers in Microbiology

Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes

(2016) Ankit Gupta et al.   Frontiers in Microbiology

Using the taxon-specific genes for the taxonomic classification of bacterial genomes

(2015) Ankit Gupta et al.   BMC GENOMICS

Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs

(2015) Sóley Ruth Gudbergsdóttir et al.   ENVIRONMENTAL MICROBIOLOGY

Isolation, characterization, and survival strategies of Thermotoga sp. strain PD524, a hyperthermophile from a hot spring in Northern Thailand

(2015) Wirojne Kanoksilapatham et al.   EXTREMOPHILES

Discovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot spring metagenomic libraries

(2015) Erica Elisa Ferrandi et al.   FEBS Journal

Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs

(2015) Peter Menzel et al.   MICROBIAL ECOLOGY

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing

(2015) Chia Sing Chan et al.   Frontiers in Microbiology

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets

(2015) Nikhil Chaudhary et al.   PLoS One

Microbial communities evolve faster in extreme environments

(2014) Sheng-Jin Li et al.   Scientific Reports

Archaeal and bacterial diversity in two hot spring microbial mats from a geothermal region in Romania

(2013) Cristian Coman et al.   EXTREMOPHILES

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

A review with recent advancements on bioremediation-based abolition of heavy metals

(2013) Nisha Gaur et al.   Environmental Science-Processes & Impacts

Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park

(2013) Kara Bowen De León et al.   Frontiers in Microbiology

Metagenomic analysis and metabolite profiling of deep–sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

(2013) Nikole E. Kimes et al.   Frontiers in Microbiology

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

(2012) David A W Soergel et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes

(2012) Diego Javier Jiménez et al.   PLoS One

Metagenomic analysis of bacterial diversity of Siloam hot water spring, Limpopo, South Africa

(2011) Memory Tekere   AFRICAN JOURNAL OF BIOTECHNOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Uncultured archaea dominate in the thermal groundwater of Uzon Caldera, Kamchatka

(2011) Andrey V. Mardanov et al.   EXTREMOPHILES

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

(2010) Wei Xie et al.   ISME Journal

A novel thermostable cellulase from Fervidobacterium nodosum

(2010) Yuguo Wang et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Complete genome sequence of Meiothermus ruber type strain (21T)

(2010) Brian J Tindall et al.   Standards in Genomic Sciences

Characterization of a Polycyclic Aromatic Hydrocarbon Degradation Gene Cluster in a Phenanthrene-Degrading Acidovorax Strain

(2009) D. R. Singleton et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies

(2009) Yong Wang et al.   PLoS One

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

(2008) Ana Oliveira et al.   BMC Systems Biology

Remote sensing and geochemistry for detecting hydrocarbon microseepages

(2007) S. D. Khan et al.   GEOLOGICAL SOCIETY OF AMERICA BULLETIN