MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

(2017) Sean P. Jungbluth et al.   PeerJ

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests

(2017) Luis E. Castañeda et al.   PeerJ

Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea

(2016) Maliheh Mehrshad et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond

(2016) Satoshi Hiraoka et al.   MICROBES AND ENVIRONMENTS

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

A robust approach for identifying differentially abundant features in metagenomic samples

(2015) Michael B. Sohn et al.   BIOINFORMATICS

A protein trisulfide couples dissimilatory sulfate reduction to energy conservation

(2015) A. A. Santos et al.   SCIENCE

The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon “Geoglobus ahangari” strain 234T

(2015) Michael P. Manzella et al.   Standards in Genomic Sciences

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Metabolic pathways for the whole community

(2014) Niels W Hanson et al.   BMC GENOMICS

GRASP: Guided Reference-based Assembly of Short Peptides

(2014) Cuncong Zhong et al.   NUCLEIC ACIDS RESEARCH

Genomic Standards Consortium Projects

(2014) Dawn Field et al.   Standards in Genomic Sciences

Comparative Genomic Analysis of Phylogenetically Closely Related Hydrogenobaculum sp. Isolates from Yellowstone National Park

(2013) Christine Romano et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogenomic clustering for selecting non-redundant genomes for comparative genomics

(2013) G. Moreno-Hagelsieb et al.   BIOINFORMATICS

Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont

(2013) Satoshi Nakagawa et al.   ISME Journal

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

(2013) Sangita Ganesh et al.   ISME Journal

Genomes from Metagenomics

(2013) I. Sharon et al.   SCIENCE

Functional assignment of metagenomic data: challenges and applications

(2012) T. Prakash et al.   BRIEFINGS IN BIOINFORMATICS

Acidithiobacillus caldus Sulfur Oxidation Model Based on Transcriptome Analysis between the Wild Type and Sulfur Oxygenase Reductase Defective Mutant

(2012) Linxu Chen et al.   PLoS One

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

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

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Metagenomic mining for microbiologists

(2011) Tom O Delmont et al.   ISME Journal

Draft Genome of the Psychrotolerant Acidophile Acidithiobacillus ferrivorans SS3

(2011) M. Liljeqvist et al.   JOURNAL OF BACTERIOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Desulfosporosinus acidiphilus sp. nov.: a moderately acidophilic sulfate-reducing bacterium isolated from acid mining drainage sediments

(2010) Didier Alazard et al.   EXTREMOPHILES

Linking bacterial identities and ecosystem processes: can ‘omic’ analyses be more than the sum of their parts?

(2010) Sergio E. Morales et al.   FEMS MICROBIOLOGY ECOLOGY

Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara

(2010) Achim Quaiser et al.   ISME Journal

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

(2010) Wei Xie et al.   ISME Journal

Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes

(2008) Alexander Loy et al.   ENVIRONMENTAL MICROBIOLOGY

The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment

(2008) L. D. Alcaraz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA