Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation

Effects of short-term hyper- and hypo-osmotic exposure on the osmoregulatory strategy of unfed North Pacific spiny dogfish ( Squalus suckleyi )

(2016) Courtney A. Deck et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Morphological and molecular investigations of the holocephalan elephant fish nephron: the existence of a countercurrent-like configuration and two separate diluting segments in the distal tubule

(2015) Keigo Kakumura et al.   CELL AND TISSUE RESEARCH

Physiological and molecular responses of the spiny dogfish shark (Squalus acanthias) to high environmental ammonia: scavenging for nitrogen

(2015) C. M. Nawata et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Evolution of urea transporters in vertebrates: adaptation to urea's multiple roles and metabolic sources

(2015) C. M. R. LeMoine et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Morphological and functional characteristics of the kidney of cartilaginous fishes: with special reference to urea reabsorption

(2014) Susumu Hyodo et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function

(2014) John F Mulley et al.   BMC GENOMICS

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

Transcriptome Profiling Reveals Higher Vertebrate Orthologous of Intra-Cytoplasmic Pattern Recognition Receptors in Grey Bamboo Shark

(2014) Tirumurugaan Krishnaswamy Gopalan et al.   PLoS One

The Lineage-Specific Evolution of Aquaporin Gene Clusters Facilitated Tetrapod Terrestrial Adaptation

(2014) Roderick Nigel Finn et al.   PLoS One

Characterization of the heart transcriptome of the white shark (Carcharodon carcharias)

(2013) Vincent P Richards et al.   BMC GENOMICS

Transcriptome responses in the rectal gland of fed and fasted spiny dogfish shark (Squalus acanthias) determined by suppression subtractive hybridization

(2013) Courtney A. Deck et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

B cell receptor accessory molecule CD79α: Characterisation and expression analysis in a cartilaginous fish, the spiny dogfish (Squalus acanthias)

(2013) Ronggai Li et al.   FISH & SHELLFISH IMMUNOLOGY

Urea-based osmoregulation in the developing embryo of oviparous cartilaginous fish (Callorhinchus milii): contribution of the extraembryonic yolk sac during the early developmental period

(2013) W. Takagi et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

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

A perfusion study of the handling of urea and urea analogues by the gills of the dogfish shark (Squalus acanthias)

(2013) Chris M. Wood et al.   PeerJ

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Cell and molecular biology of the spiny dogfish Squalus acanthias and little skate Leucoraja erinacea: insights from in vitro cultured cells

(2012) D. W. Barnes   JOURNAL OF FISH BIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Hepatic and extrahepatic distribution of ornithine urea cycle enzymes in holocephalan elephant fish (Callorhinchus milii)

(2011) Wataru Takagi et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

A Natural Deletion of the HoxC Cluster in Elasmobranch Fishes

(2011) B. L. King et al.   SCIENCE

Analysis and functional annotation of expressed sequence tags from in vitro cell lines of elasmobranchs: Spiny dogfish shark (Squalus acanthias) and little skate (Leucoraja erinacea)

(2010) Angela Parton et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

A brief history of fish osmoregulation: the central role of the Mt. Desert Island Biological Laboratory

(2010) David H. Evans   Frontiers in Physiology

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

The influence of feeding and fasting on plasma metabolites in the dogfish shark (Squalus acanthias)

(2009) Chris M. Wood et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Multiple urea transporter proteins in the kidney of holocephalan elephant fish (Callorhinchus milii)

(2009) Keigo Kakumura et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Rhesus Glycoprotein P2 (Rhp2) Is a Novel Member of the Rh Family of Ammonia Transporters Highly Expressed in Shark Kidney

(2009) Tsutomu Nakada et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A new paradigm for ammonia excretion in aquatic animals: role of Rhesus (Rh) glycoproteins

(2009) P. A. Wright et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Texas Red transport across rat and dogfish shark (Squalus acanthias) choroid plexus

(2008) Valeska Reichel et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Molecular detection and immunological localization of gill Na+/H+ exchanger in the dogfish (Squalus acanthias)

(2007) James B. Claiborne et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY