Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon

Utility of pooled sequencing for association mapping in nonmodel organisms

(2018) Steven J. Micheletti et al.   Molecular Ecology Resources

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

(2018) Kris A. Christensen et al.   PLoS One

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome

(2017) Morten T. Limborg et al.   MOLECULAR ECOLOGY

Congruent population structure across paralogous and nonparalogous loci in Salish Sea chum salmon (Oncorhynchus keta )

(2017) R. K. Waples et al.   MOLECULAR ECOLOGY

Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach

(2017) María Inés Fariello et al.   MOLECULAR ECOLOGY

Fructose-driven glycolysis supports anoxia resistance in the naked mole-rat

(2017) Thomas J. Park et al.   SCIENCE

The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation

(2017) Daniel J. Prince et al.   Science Advances

The paradox of “premature migration” by adult anadromous salmonid fishes: patterns and hypotheses

(2016) Thomas P. Quinn et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

(2016) Jon E. Hess et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Salmon, Science, and Reciprocity on the Northwest Coast

(2016) D. Bruce Johnsen   ECOLOGY AND SOCIETY

Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers

(2016) John Gilbey et al.   PLoS One

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

Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

(2015) Nicola J. Barson et al.   NATURE

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

(2015) Sangeet Lamichhaney et al.   NATURE GENETICS

Abnormal Activation of RhoA/ROCK-I Signaling in Junctional Zone Smooth Muscle Cells of Patients With Adenomyosis

(2015) S. Wang et al.   Reproductive Sciences

Whole-body endothermy in a mesopelagic fish, the opah, Lampris guttatus

(2015) N. C. Wegner et al.   SCIENCE

The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males

(2015) Fernando Ayllon et al.   PLoS Genetics

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Monitoring Stock-Specific Abundance, Run Timing, and Straying of Chinook Salmon in the Columbia River Using Genetic Stock Identification (GSI)

(2014) Jon E. Hess et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

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

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Earlier Migration Timing, Decreasing Phenotypic Variation, and Biocomplexity in Multiple Salmonid Species

(2013) Ryan P. Kovach et al.   PLoS One

Endogenous Purification Reveals GREB1 as a Key Estrogen Receptor Regulatory Factor

(2013) Hisham Mohammed et al.   Cell Reports

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Extent and scale of local adaptation in salmonid fishes: review and meta-analysis

(2011) D J Fraser et al.   HEREDITY

Population diversity and the portfolio effect in an exploited species

(2010) Daniel E. Schindler et al.   NATURE