De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Comparative performance of transcriptome assembly methods for non-model organisms

(2016) Xin Huang et al.   BMC GENOMICS

Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

(2016) A. L. De Oliveira et al.   BMC GENOMICS

Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database

(2016) Jeremy Pasquier et al.   BMC GENOMICS

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

(2016) Kathryn R. Elmer   HYDROBIOLOGIA

Sequencing and characterization of a multi-organ Arctic charr transcriptome: A toolbox for investigating polymorphism and seasonal life in a high Arctic fish

(2016) Elodie Magnanou et al.   Marine Genomics

De Novo assembly and annotation of the freshwater crayfish Astacus astacus transcriptome

(2016) Kathrin Theissinger et al.   Marine Genomics

Multi-tissue transcriptome profiles for coho salmon ( Oncorhynchus kisutch ), a species undergoing rediploidization following whole-genome duplication

(2016) Jin-Hyoung Kim et al.   Marine Genomics

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

(2015) Erik A. Visser et al.   BMC GENOMICS

Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes

(2015) Nina F. Ockendon et al.   Molecular Ecology Resources

Transcriptomic Responses of Atlantic Salmon (Salmo salar) to Environmental Enrichment during Juvenile Rearing

(2015) Melissa L. Evans et al.   PLoS One

Comparisons of De Novo Transcriptome Assemblers in Diploid and Polyploid Species Using Peanut (Arachis spp.) RNA-Seq Data

(2015) Ratan Chopra et al.   PLoS One

De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes

(2015) Inanc Birol et al.   PLoS One

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

(2014) Ross D Houston et al.   BMC GENOMICS

RNA-seq Reveals Transcriptomic Shock Involving Transposable Elements Reactivation in Hybrids of Young Lake Whitefish Species

(2014) Anne-Marie Dion-Côté et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication

(2013) Kris A Christensen et al.   BMC BIOINFORMATICS

Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon

(2013) Matthew A Lemay et al.   BMC GENOMICS

Effects of sustained swimming on the red and white muscle transcriptome of rainbow trout (Oncorhynchus mykiss) fed a carbohydrate-rich diet

(2013) Leonardo J. Magnoni et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish

(2013) Helen M. Gunter et al.   MOLECULAR ECOLOGY

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Validation of Reference Genes for Expression Studies during Craniofacial Development in Arctic Charr

(2013) Ehsan Pashay Ahi et al.   PLoS One

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

(2012) Ana Riesgo et al.   Frontiers in Zoology

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns

(2011) Sigbjørn Lien et al.   BMC GENOMICS

Comparative Transcriptomics of Eastern African Cichlid Fishes Shows Signs of Positive Selection and a Large Contribution of Untranslated Regions to Genetic Diversity

(2011) Laura Baldo et al.   Genome Biology and Evolution

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

(2011) D J Fraser et al.   HEREDITY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

(2011) A. Di Genova et al.   Database-The Journal of Biological Databases and Curation

Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka)

(2011) Scott A Pavey et al.   BMC ECOLOGY

Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome

(2010) Jong S Leong et al.   BMC GENOMICS

The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing

(2010) JULIE JEUKENS et al.   MOLECULAR ECOLOGY

Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonusspp. Salmonidae)

(2010) SÉBASTIEN RENAUT et al.   MOLECULAR ECOLOGY

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

(2010) K. R. ELMER et al.   MOLECULAR ECOLOGY

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

On the origin of species: insights from the ecological genomics of lake whitefish

(2010) L. Bernatchez et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

(2008) Ben F Koop et al.   BMC GENOMICS

Extensive analysis of EST sequences reveals that all cichlid species in Lake Victoria share almost identical transcript sets

(2008) Naoki Kobayashi et al.   GENE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS