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

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis

(2017) Matthew D. MacManes et al.   Scientific Reports

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

Saving the spandrels? Adaptive genomic variation in conservation and fisheries management

(2016) D. E. Pearse   JOURNAL OF FISH BIOLOGY

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

Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application

(2016) Brittany A. Garner et al.   TRENDS IN ECOLOGY & EVOLUTION

Reply to Garner et al.

(2016) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

Hypothalamic Agrp Neurons Drive Stereotypic Behaviors beyond Feeding

(2015) Marcelo O. Dietrich et al.   CELL

Parallel evolution of the summer steelhead ecotype in multiple populations from Oregon and Northern California

(2015) Martha Arciniega et al.   CONSERVATION GENETICS

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

(2015) O. A. Ali et al.   GENETICS

Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

(2015) Marine S. O. Brieuc et al.   MOLECULAR ECOLOGY

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

(2015) Nicola J. Barson et al.   NATURE

Genetic history of salmonid fishes of the genus Oncorhynchus

(2015) L. A. Zhivotovsky   RUSSIAN JOURNAL OF GENETICS

Genomics and the challenging translation into conservation practice

(2015) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss

(2015) Fredrick E Henry et al.   eLife

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Diversity in sympatric chinook salmon runs: timing, relative fat content and maturation

(2014) James W. Hearsey et al.   ENVIRONMENTAL BIOLOGY OF FISHES

Consideration of GREB1 as a potential therapeutic target for hormone-responsive or endocrine-resistant cancers

(2014) Kendra M Hodgkinson et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

Trade-offs and utility of alternative RADseq methods: Reply to Puritzet al.

(2014) Kimberly R. Andrews et al.   MOLECULAR ECOLOGY

Planning Pacific Salmon and Steelhead Reintroductions Aimed at Long-Term Viability and Recovery

(2014) Joseph H. Anderson et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

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

The biodiversity of species and their rates of extinction, distribution, and protection

(2014) S. L. Pimm et al.   SCIENCE

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

(2014) Camille Berthelot et al.   Nature Communications

Adaptive potential of a Pacific salmon challenged by climate change

(2014) Nicolas J. Muñoz et al.   Nature Climate Change

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Contemporary Population Structure in Klamath River Basin Chinook Salmon Revealed by Analysis of Microsatellite Genetic Data

(2013) Andrew P. Kinziger et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Endogenous Purification Reveals GREB1 as a Key Estrogen Receptor Regulatory Factor

(2013) Hisham Mohammed et al.   Cell Reports

The expression of estrogen receptors as well as GREB1, c-MYC, and cyclin D1, estrogen-regulated genes implicated in proliferation, is increased in peritoneal endometriosis

(2012) Chiara Pellegrini et al.   FERTILITY AND STERILITY

Association Testing for Next-Generation Sequencing Data Using Score Statistics

(2012) Line Skotte et al.   GENETIC EPIDEMIOLOGY

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

Framing the Salmonidae Family Phylogenetic Portrait: A More Complete Picture from Increased Taxon Sampling

(2012) Alexis Crête-Lafrenière et al.   PLoS One

Harnessing genomics for delineating conservation units

(2012) W. Chris Funk et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2011) H. Li   BIOINFORMATICS

Estimation of allele frequency and association mapping using next-generation sequencing data

(2011) Su Kim et al.   BMC BIOINFORMATICS

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

(2011) MICHAEL R. MILLER et al.   MOLECULAR ECOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Habitat fragmentation causes immediate and time-delayed biodiversity loss at different trophic levels

(2010) Jochen Krauss et al.   ECOLOGY LETTERS

New approaches to population stratification in genome-wide association studies

(2010) Alkes L. Price et al.   NATURE REVIEWS GENETICS

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One