Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain

Enterobacter bugandensis sp. nov., isolated from neonatal blood

(2016) Swapnil Doijad et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Identification and analysis of integrons and cassette arrays in bacterial genomes

(2016) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis

(2016) Sebastien Breurec et al.   Scientific Reports

Identification of protein secretion systems in bacterial genomes

(2016) Sophie S. Abby et al.   Scientific Reports

Elizabethkingia anophelis bacteremia is associated with clinically significant infections and high mortality

(2016) Susanna K. P. Lau et al.   Scientific Reports

Elizabethkingia anophelis: Molecular Manipulation and Interactions with Mosquito Hosts

(2015) Shicheng Chen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Complete Genome Sequence and Transcriptomic Analysis of the Novel PathogenElizabethkingia anophelisin Response to Oxidative Stress

(2015) Yingying Li et al.   Genome Biology and Evolution

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance inKlebsiella pneumoniae, an urgent threat to public health

(2015) Kathryn E. Holt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Comparative Genomic Analysis of Malaria Mosquito Vector-Associated Novel Pathogen Elizabethkingia anophelis

(2014) Jeanette Teo et al.   Genome Biology and Evolution

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights from the Genome Annotation of Elizabethkingia anophelis from the Malaria Vector Anopheles gambiae

(2014) Phanidhar Kukutla et al.   PLoS One

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads

(2013) Alexis Criscuolo et al.   GENOMICS

Elizabethkingia meningoseptica : An emerging pathogen causing meningitis in a hospitalized adult trauma patient

(2013) P Mathur et al.   Indian Journal of Medical Microbiology

DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov.

(2013) B. Holmes et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Bad design, bad practices, bad bugs: frustrations in controlling an outbreak of Elizabethkingia meningoseptica in intensive care units

(2013) M.N.D. Balm et al.   JOURNAL OF HOSPITAL INFECTION

First case of Elizabethkingia anophelis meningitis in the Central African Republic

(2013) Thierry Frank et al.   LANCET

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona

(2013) Zhemin Zhou et al.   PLoS Genetics

Rare Elizabethkingia meningosepticum meningitis case in an immunocompetent adult

(2013) Salim S Hayek et al.   Emerging Microbes & Infections

Carbapenem Resistance in Elizabethkingia meningoseptica Is Mediated by Metallo-β-Lactamase BlaB

(2012) Lisandro J. González et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Two SusD-Like Proteins Encoded within a Polysaccharide Utilization Locus of an Uncultured Ruminant Bacteroidetes Phylotype Bind Strongly to Cellulose

(2012) A. K. Mackenzie et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

(2012) Yongchao Liu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Evolution of Conjugation and Type IV Secretion Systems

(2012) Julien Guglielmini et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Clinical features, antimicrobial susceptibilities, and outcomes of Elizabethkingia meningoseptica (Chryseobacterium meningosepticum) bacteremia at a medical center in Taiwan, 1999–2006

(2011) M.-S. Hsu et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Kick-Starting the Ratchet: The Fate of Mutators in an Asexual Population

(2011) R. J. Soderberg et al.   GENETICS

Bacterial hypermutation in cystic fibrosis, not only for antibiotic resistance

(2010) A. Oliver et al.   CLINICAL MICROBIOLOGY AND INFECTION

Oxygen as a friend and enemy: How to combat the mutational potential of 8-oxo-guanine

(2010) Barbara van Loon et al.   DNA REPAIR

Elizabethkingia anophelis sp. nov., isolated from the midgut of the mosquito Anopheles gambiae

(2010) P. Kampfer et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses

(2010) C. Firth et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses

(2009) S. Duffy et al.   JOURNAL OF GENERAL VIROLOGY

Homology-dependent interactions determine the order of strand exchange by IntDOT recombinase

(2009) Jennifer Laprise et al.   NUCLEIC ACIDS RESEARCH

Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence

(2008) C. Ramsden et al.   MOLECULAR BIOLOGY AND EVOLUTION