Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages

Isolation of a New Infectious Pancreatic Necrosis Virus (IPNV) Variant from a Fish Farm in Scotland

(2021) Jessica Benkaroun et al.   Viruses-Basel

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

State-of-the-Art Vaccine Research for Aquaculture Use: The Case of Three Economically Relevant Fish Species

(2021) Andrea Miccoli et al.   Vaccines

Effect of vaccines against pancreas disease in farmed Atlantic salmon

(2021) Magnus Vikan Røsæg et al.   JOURNAL OF FISH DISEASES

Emergence of Salmonid Alphavirus Genotype 2 in Norway—Molecular Characterization of Viral Strains Circulating in Norway and Scotland

(2021) Monika J. Hjortaas et al.   Viruses-Basel

Challenges and Solutions to Viral Diseases of Finfish in Marine Aquaculture

(2021) Kizito K. Mugimba et al.   Pathogens

Identification of a New Infectious Pancreatic Necrosis Virus (IPNV) Variant in Atlantic Salmon (Salmo salar L.) that can Cause High Mortality Even in Genetically Resistant Fish

(2021) Borghild Hillestad et al.   Frontiers in Genetics

Genome-wide target enriched viral sequencing reveals extensive ‘hidden’ salmonid alphavirus diversity in farmed and wild fish populations

(2020) Michael D. Gallagher et al.   AQUACULTURE

Harnessing genomics to fast-track genetic improvement in aquaculture

(2020) Ross D. Houston et al.   NATURE REVIEWS GENETICS

Genome Sequencing of SAV3 Reveals Repeated Seeding Events of Viral Strains in Norwegian Aquaculture

(2020) Michael D. Gallagher et al.   Frontiers in Microbiology

Genomics and epidemiological surveillance

(2020) Stephanie W. Lo et al.   NATURE REVIEWS MICROBIOLOGY

Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7)

(2020) AJ Tighe et al.   DISEASES OF AQUATIC ORGANISMS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

(2018) R. D. Houston et al.   ANIMAL GENETICS

Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades

(2018) Kristina Ulrich et al.   JOURNAL OF GENERAL VIROLOGY

Nanopore sequencing for rapid diagnostics of salmonid RNA viruses

(2018) Michael D. Gallagher et al.   Scientific Reports

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

(2017) N. R. Faria et al.   NATURE

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Towards a genomics-informed, real-time, global pathogen surveillance system

(2017) Jennifer L. Gardy et al.   NATURE REVIEWS GENETICS

New Paradigms to Help Solve the Global Aquaculture Disease Crisis

(2017) Grant D. Stentiford et al.   PLoS Pathogens

The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens

(2017) Sion C. Bayliss et al.   Frontiers in Microbiology

The epidemiology of pancreas disease in salmonid aquaculture: a summary of the current state of knowledge

(2016) M D Jansen et al.   JOURNAL OF FISH DISEASES

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

(2016) Jana Trifinopoulos et al.   NUCLEIC ACIDS RESEARCH

Feeding 9 billion by 2050 – Putting fish back on the menu

(2015) Christophe Béné et al.   Food Security

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

Supersize me: how whole-genome sequencing and big data are transforming epidemiology

(2014) Rowland R. Kao et al.   TRENDS IN MICROBIOLOGY

Identification of a wild reservoir of salmonid alphavirus in common dab Limanda limanda, with emphasis on virus culture and sequencing

(2014) DW Bruno et al.   Aquaculture Environment Interactions

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Multiple introductions of salmonid alphavirus from a wild reservoir have caused independent and self-sustainable epizootics in aquaculture

(2013) M. Karlsen et al.   JOURNAL OF GENERAL VIROLOGY

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

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

The first detections of subtype 2-related salmonid alphavirus (SAV2) in Atlantic salmon,Salmo salarL., in Norway

(2012) M J Hjortaas et al.   JOURNAL OF FISH DISEASES

Viruses of Fish: An Overview of Significant Pathogens

(2011) Mark Crane et al.   Viruses-Basel

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Phylogenetic analyses and molecular epidemiology of European salmonid alphaviruses (SAV) based on partial E2 and nsP3 gene nucleotide sequences

(2008) E Fringuelli et al.   JOURNAL OF FISH DISEASES