Metagenomics as a tool for the investigation of uncultured microorganisms

Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”

(2014) Brian P. Hedlund et al.   EXTREMOPHILES

Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics

(2014) Christian Rinke et al.   Nature Protocols

Adding genomic 'foliage' to the tree of life

(2014) Alan Walker   NATURE REVIEWS MICROBIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Dissecting genomic diversity, one cell at a time

(2013) Paul C Blainey et al.   NATURE METHODS

Pyrosequencing Reveals High-Temperature Cellulolytic Microbial Consortia in Great Boiling Spring after In Situ Lignocellulose Enrichment

(2013) Joseph P. Peacock et al.   PLoS One

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

The impact of genomics on research in diversity and evolution of archaea

(2012) A. V. Mardanov et al.   BIOCHEMISTRY-MOSCOW

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies

(2012) J. Droge et al.   BRIEFINGS IN BIOINFORMATICS

Classification of metagenomic sequences: methods and challenges

(2012) S. S. Mande et al.   BRIEFINGS IN BIOINFORMATICS

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

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

(2012) Toshiaki Namiki 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

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Phylogeny and evolution of the Archaea: one hundred genomes later

(2011) Celine Brochier-Armanet et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2011) Andrey V. Mardanov et al.   EXTREMOPHILES

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

(2011) Priya Narasingarao et al.   ISME Journal

Saliva microbiomes distinguish caries-active from healthy human populations

(2011) Fang Yang et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Genovo: De Novo Assembly for Metagenomes

(2011) Jonathan Laserson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Molecular analysis of microbial diversity in the Zavarzin Spring, Uzon Caldera, Kamchatka

(2011) V. M. Gumerov et al.   MICROBIOLOGY

New Abundant Microbial Groups in Aquatic Hypersaline Environments

(2011) Rohit Ghai et al.   Scientific Reports

TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

(2011) Hernan A. Lorenzi et al.   Standards in Genomic Sciences

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

(2010) Zhili He et al.   ISME Journal

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

Enigmatic, ultrasmall, uncultivated Archaea

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

Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group

(2009) Anke Meyerdierks et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka

(2009) Laila Johanne Reigstad et al.   ISME Journal

Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment

(2009) Shoko Iwai et al.   ISME Journal

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

(2009) Jennifer M. Brulc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS

(2008) S. Behrens et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

A korarchaeal genome reveals insights into the evolution of the Archaea

(2008) J. G. Elkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE