Prokaryotic taxonomy and nomenclature in the age of big sequence data
The classification of life forms into a hierarchical system (taxonomy) and the application of
names to this hierarchy (nomenclature) is at a turning point in microbiology. The …
names to this hierarchy (nomenclature) is at a turning point in microbiology. The …
Reconstruction of biochemical networks in microorganisms
Abstract Systems analysis of metabolic and growth functions in microbial organisms is
rapidly develo** and maturing. Such studies are enabled by reconstruction, at the …
rapidly develo** and maturing. Such studies are enabled by reconstruction, at the …
[HTML][HTML] RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
Abstract The RAST (Rapid Annotation using Subsystem Technology) annotation engine was
built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard …
built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard …
Integrative analysis of environmental sequences using MEGAN4
A major challenge in the analysis of environmental sequences is data integration. The
question is how to analyze different types of data in a unified approach, addressing both the …
question is how to analyze different types of data in a unified approach, addressing both the …
Ecology drives a global network of gene exchange connecting the human microbiome
Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental
lineages, is known to be important in bacterial evolution,. In particular, HGT provides rapid …
lineages, is known to be important in bacterial evolution,. In particular, HGT provides rapid …
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
From the standpoints of both basic research and biotechnology, there is considerable
interest in reaching a clearer understanding of the diversity of biological mechanisms …
interest in reaching a clearer understanding of the diversity of biological mechanisms …
Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils
The complete genomes of three strains from the phylum Acidobacteria were compared.
Phylogenetic analysis placed them as a unique phylum. They share genomic traits with …
Phylogenetic analysis placed them as a unique phylum. They share genomic traits with …
CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
C Bland, TL Ramsey, F Sabree, M Lowe, K Brown… - BMC …, 2007 - Springer
Abstract Background Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are
a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are …
a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are …
Targeted isolation and cultivation of uncultivated bacteria by reverse genomics
KL Cross, JH Campbell, M Balachandran… - Nature …, 2019 - nature.com
Most microorganisms from all taxonomic levels are uncultured. Single-cell genomes and
metagenomes continue to increase the known diversity of Bacteria and Archaea; however …
metagenomes continue to increase the known diversity of Bacteria and Archaea; however …
IMG ER: a system for microbial genome annotation expert review and curation
Motivation: A rapidly increasing number of microbial genomes are sequenced by
organizations worldwide and are eventually included into various public genome data …
organizations worldwide and are eventually included into various public genome data …