European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle

(2014) Songlin Chen et al.   NATURE GENETICS

Consed: a graphical editor for next-generation sequencing

(2013) David Gordon et al.   BIOINFORMATICS

Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

(2013) Anthony G Doran et al.   BMC BIOINFORMATICS

Novel sex-determining genes in fish and sex chromosome evolution

(2013) Kiyoshi Kikuchi et al.   DEVELOPMENTAL DYNAMICS

Coelacanth genomes reveal signatures for evolutionary transition from water to land

(2013) M. Nikaido et al.   GENOME RESEARCH

Phylogenetic revision of the claudin gene family

(2013) David A. Baltzegar et al.   Marine Genomics

Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species

(2013) Camille Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

(2013) Manfred Schartl et al.   NATURE GENETICS

Characterization of Gonadal Transcriptomes from Nile Tilapia (Oreochromis niloticus) Reveals Differentially Expressed Genes

(2013) Wenjing Tao et al.   PLoS One

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

(2013) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

(2012) Hiroaki Iwata et al.   NUCLEIC ACIDS RESEARCH

Gene flow at major transitional areas in sea bass (Dicentrarchus labrax) and the possible emergence of a hybrid swarm

(2012) Nolwenn Quéré et al.   Ecology and Evolution

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Predicted expansion of the claudin multigene family

(2011) Katsuhiko Mineta et al.   FEBS LETTERS

The oxytocin/vasopressin receptor family has at least five members in the gnathostome lineage, inclucing two distinct V2 subtypes

(2011) Daniel Ocampo Daza et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication

(2011) Angel Amores et al.   GENETICS

Directed sequencing and annotation of three Dicentrarchus labrax L. chromosomes by applying Sanger- and pyrosequencing technologies on pooled DNA of comparatively mapped BAC clones

(2011) Heiner Kuhl et al.   GENOMICS

A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

(2011) Sergei L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

The coupling hypothesis: why genome scans may fail to map local adaptation genes

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

(2010) M. G. Grabherr et al.   BIOINFORMATICS

The zebrafish genome encodes the largest vertebrate repertoire of functional aquaporins with dual paralogy and substrate specificities similar to mammals

(2010) Angèle Tingaud-Sequeira et al.   BMC EVOLUTIONARY BIOLOGY

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

(2010) Heiner Kuhl et al.   BMC GENOMICS

A radiation hybrid map of the European sea bass (Dicentrarchus labrax) based on 1581 markers: Synteny analysis with model fish genomes

(2010) Richard Guyon et al.   GENOMICS

A Comparative BAC Map for the Gilthead Sea Bream (Sparus aurataL.)

(2010) Heiner Kuhl et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Piscine aquaporins: an overview of recent advances

(2010) Joan Cerdà et al.   Journal of Experimental Zoology Part A-Ecological Genetics and Physiology

Genomics and the future of conservation genetics

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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

A novel prolactin-like protein (PRL-L) gene in chickens and zebrafish: Cloning and characterization of its tissue expression

(2009) Yajun Wang et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Salinity regulates claudin mRNA and protein expression in the teleost gill

(2008) Christian K. Tipsmark et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bassDicentrarchus labraxL.

(2008) D. A. Chistiakov et al.   ANIMAL GENETICS

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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