Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy

Small RNA regulators in bacteria: powerful tools for metabolic engineering and synthetic biology

(2014) Zhen Kang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Systems metabolic engineering design: Fatty acid production as an emerging case study

(2014) Ting Wei Tee et al.   BIOTECHNOLOGY AND BIOENGINEERING

Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7

(2014) Kerry K Cooper et al.   BMC GENOMICS

Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age

(2014) Jan P. Meier-Kolthoff et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

opm: an R package for analysing OmniLog(R) phenotype microarray data

(2013) L. A. I. Vaas et al.   BIOINFORMATICS

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

Production of advanced biofuels in engineered E. coli

(2013) Miao Wen et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Alignment-Free Genome Tree Inference by Learning Group-Specific Distance Metrics

(2013) Kaustubh R. Patil et al.   Genome Biology and Evolution

Exploitation of the health-promoting and sensory properties of organic pomegranate (Punica granatum L.) juice through lactic acid fermentation

(2013) Pasquale Filannino et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria

(2013) K. P. Williams et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The discriminatory power of ribotyping as automatable technique for differentiation of bacteria

(2013) Peter Schumann et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema

(2013) Birte Abt et al.   Standards in Genomic Sciences

Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects

(2013) Markus Göker et al.   Standards in Genomic Sciences

Escherichia coli in Europe: An Overview

(2013) Nerino Allocati et al.   International Journal of Environmental Research and Public Health

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

(2012) Rolf S Kaas et al.   BMC GENOMICS

Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics

(2012) Lea A. I. Vaas et al.   PLoS One

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation

(2012) Konstantinos Mavromatis et al.   PLoS One

The ClermontEscherichia coliphylo-typing method revisited: improvement of specificity and detection of new phylo-groups

(2012) Olivier Clermont et al.   Environmental Microbiology Reports

Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta

(2012) Birte Abt et al.   Standards in Genomic Sciences

Shigella Strains Are Not Clones of Escherichia coli but Sister Species in the Genus Escherichia

(2012) Guanghong Zuo et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The DNA Bank Network: The Start from a German Initiative

(2011) Birgit Gemeinholzer et al.   BIOPRESERVATION AND BIOBANKING

Characterization of the cryptic Escherichia lineages: rapid identification and prevalence

(2011) Olivier Clermont et al.   ENVIRONMENTAL MICROBIOLOGY

Hydrotalea sandarakina sp. nov., isolated from a hot spring runoff, and emended descriptions of the genus Hydrotalea and the species Hydrotalea flava

(2011) L. Albuquerque et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

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

Novel Insights into the Diversity of Catabolic Metabolism from Ten Haloarchaeal Genomes

(2011) Iain Anderson et al.   PLoS One

Codivergence of Mycoviruses with Their Hosts

(2011) Markus Göker et al.   PLoS One

Complete genome sequence of Isosphaera pallida type strain (IS1BT)

(2011) Markus Göker et al.   Standards in Genomic Sciences

The Genomic Standards Consortium

(2011) Dawn Field et al.   PLOS BIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

En route to a genome-based classification of Archaea and Bacteria?

(2010) H.-P. Klenk et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

(2010) Alexander F. Auch et al.   Standards in Genomic Sciences

Antimicrobial Resistance-Conferring Plasmids with Similarity to Virulence Plasmids from Avian Pathogenic Escherichia coli Strains in Salmonella enterica Serovar Kentucky Isolates from Poultry

(2009) W. F. Fricke et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification in Agrobacterium tumefaciens of the d-galacturonic acid dehydrogenase gene

(2009) Harry Boer et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

Notes on the characterization of prokaryote strains for taxonomic purposes

(2009) B. J. Tindall et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora

(2009) Markus Göker et al.   PLoS One

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes

(2009) Konstantinos Mavromatis et al.   Standards in Genomic Sciences

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH