Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Competing tradeoffs between increasing marine mammal predation and fisheries harvest of Chinook salmon

(2017) Brandon E. Chasco et al.   Scientific Reports

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The invasion of an Atlantic Ocean river basin in Patagonia by Chinook salmon: new insights from SNPs

(2015) Javier E. Ciancio et al.   BIOLOGICAL INVASIONS

Effects of Crossovers Between Homeologs on Inheritance and Population Genomics in Polyploid-Derived Salmonid Fishes

(2015) F. W. Allendorf et al.   JOURNAL OF HEREDITY

Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

(2015) Benjamin C. Hecht et al.   MOLECULAR ECOLOGY

An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

(2015) G. J. McKinney et al.   Molecular Ecology Resources

The molecular basis for centromere identity and function

(2015) Kara L. McKinley et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Response of chinook salmon to climate change

(2015) Nathan J. Mantua et al.   Nature Climate Change

Genome-Wide Association Study (GWAS) for Growth Rate and Age at Sexual Maturation in Atlantic Salmon (Salmo salar)

(2015) Alejandro P. Gutierrez et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

(2014) D. J. Macqueen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

Dramatic improvement in genome assembly achieved using doubled-haploid genomes

(2014) Hong Zhang et al.   Scientific Reports

A Dense Linkage Map for Chinook salmon ( Oncorhynchus tshawytscha ) Reveals Variable Chromosomal Divergence After an Ancestral Whole Genome Duplication Event

(2014) Marine S. O. Brieuc et al.   G3-Genes Genomes Genetics

Recent advances of genome mapping and marker-assisted selection in aquaculture

(2013) Gen Hua Yue   FISH AND FISHERIES

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Genomic toolboxes for conservation biologists

(2011) Francesco Angeloni et al.   Evolutionary Applications

Pacific salmon abundance trends and climate change

(2011) J. R. Irvine et al.   ICES JOURNAL OF MARINE SCIENCE

SyMAP v3.4: a turnkey synteny system with application to plant genomes

(2011) Carol Soderlund et al.   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS