Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

(2013) M. T. G. Holden et al.   GENOME RESEARCH

Evolution of infectious salmon anaemia virus (ISA virus)

(2012) Heidrun Plarre et al.   ARCHIVES OF VIROLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

(2012) Kathryn E Holt et al.   NATURE GENETICS

Disease interaction and pathogens exchange between wild and farmed fish populations with special reference to Norway

(2011) L.-H. Johansen et al.   AQUACULTURE

Epidemiology of Renibacterium salmoninarum in Scotland and the potential for compartmentalised management of salmon and trout farming areas

(2011) Alexander G. Murray et al.   AQUACULTURE

A new strategy for better genome assembly from very short reads

(2011) Yan Ji et al.   BMC BIOINFORMATICS

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford et al.   NATURE GENETICS

Modelling management strategies for a disease including undetected sub-clinical infection: Bacterial kidney disease in Scottish salmon and trout farms

(2011) Alexander G. Murray et al.   Epidemics

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

An investigation into the prevalence of Renibacterium salmoninarum in farmed rainbow trout, Oncorhynchus mykiss (Walbaum), and wild fish populations in selected river catchments in England and Wales between 1998 and 2000

(2010) E Chambers et al.   JOURNAL OF FISH DISEASES

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Yersinia ruckeri biotype 2 isolates from mainland Europe and the UK likely represent different clonal groups

(2009) RW Wheeler et al.   DISEASES OF AQUATIC ORGANISMS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Renibacterium salmoninarum p57 antigenic variation is restricted in geographic distribution and correlated with genomic markers

(2008) GD Wiens et al.   DISEASES OF AQUATIC ORGANISMS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

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

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

Genome Sequence of the Fish Pathogen Renibacterium salmoninarum Suggests Reductive Evolution away from an Environmental Arthrobacter Ancestor

(2008) G. D. Wiens et al.   JOURNAL OF BACTERIOLOGY