Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax)

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

jvenn: an interactive Venn diagram viewer

(2014) Philippe Bardou et al.   BMC BIOINFORMATICS

Systematic Variation in the Pattern of Gene Paralog Retention between the Teleost Superorders Ostariophysi and Acanthopterygii

(2014) Daniel Garcia de la serrana et al.   Genome Biology and Evolution

MicroRNA in Teleost Fish

(2014) T. T. Bizuayehu et al.   Genome Biology and Evolution

The Atlantic Bonito (Sarda sarda, Bloch 1793) Transcriptome and Detection of Differential Expression during Larvae Development

(2014) Elena Sarropoulou et al.   PLoS One

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

(2014) Mbaye Tine et al.   Nature Communications

RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks

(2013) Jun Kitano et al.   BMC GENOMICS

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

Transcriptome of Atlantic Cod (Gadus morhua L.) Early Embryos from Farmed and Wild Broodstocks

(2013) Carlos Frederico Ceccon Lanes et al.   MARINE BIOTECHNOLOGY

The miR-30 MicroRNA Family Targets smoothened to Regulate Hedgehog Signalling in Zebrafish Early Muscle Development

(2013) Ami Ketley et al.   PLoS One

Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire

(2013) Michaël Bekaert et al.   PLoS One

Orthopedia Transcription Factor otpa and otpb Paralogous Genes Function during Dopaminergic and Neuroendocrine Cell Specification in Larval Zebrafish

(2013) António M. Fernandes et al.   PLoS One

Fantastically plastic: fish larvae equipped for a new world

(2013) Karin Pittman et al.   Reviews in Aquaculture

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

microRNA expression signature in skeletal muscle of Nile tilapia

(2012) Biao Yan et al.   AQUACULTURE

Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression

(2012) Guan-Zheng Luo et al.   BMC GENOMICS

Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote

(2012) Shikai Liu et al.   BMC GENOMICS

Fast skeletal muscle transcriptome of the Gilthead sea bream (Sparus aurata) determined by next generation sequencing

(2012) Daniel Garcia de la serrana et al.   BMC GENOMICS

Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development

(2012) Teshome T Bizuayehu et al.   BMC GENOMICS

Dietary vegetable oils do not alter the intestine transcriptome of gilthead sea bream (Sparus aurata), but modulate the transcriptomic response to infection with Enteromyxum leei

(2012) Josep A Calduch-Giner et al.   BMC GENOMICS

MicroRNAs regulate and provide robustness to the myogenic transcriptional network

(2012) Jeffrey Gagan et al.   CURRENT OPINION IN PHARMACOLOGY

Comparison of Next-Generation Sequencing Systems

(2012) Lin Liu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

miR-203b: a novel regulator of MyoD expression in tilapia skeletal muscle

(2012) B. Yan et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Characterization of European Sea Bass Transcripts by RNA SEQ After Oral Vaccine Against V. anguillarum

(2012) E. Sarropoulou et al.   MARINE BIOTECHNOLOGY

MicroRNA and cancer

(2012) Martin D. Jansson et al.   Molecular Oncology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identification and Profiling of MicroRNAs from Skeletal Muscle of the Common Carp

(2012) Xuechun Yan et al.   PLoS One

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

The zebrafish transcriptome during early development

(2011) Liselotte Vesterlund et al.   BMC DEVELOPMENTAL BIOLOGY

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Embryonic development of the sea bass Dicentrarchus labrax

(2011) Patricia Cucchi et al.   HELGOLAND MARINE RESEARCH

Functional Divergences of GAPDH Isoforms During Early Development in Two Perciform Fish Species

(2011) Elena Sarropoulou et al.   MARINE BIOTECHNOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer

(2011) Jun Hong Xia et al.   PLoS One

Identification and Differential Expression of MicroRNAs during Metamorphosis of the Japanese Flounder (Paralichthys olivaceus)

(2011) Yuanshuai Fu et al.   PLoS One

Jamb and Jamc Are Essential for Vertebrate Myocyte Fusion

(2011) Gareth T. Powell et al.   PLOS BIOLOGY

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Duplicate dmbx1 genes regulate progenitor cell cycle and differentiation during zebrafish midbrain and retinal development

(2010) Loksum Wong et al.   BMC DEVELOPMENTAL BIOLOGY

Discovery and characterization of medaka miRNA genes by next generation sequencing platform

(2010) Sung-Chou Li 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

Advancing RNA-Seq analysis

(2010) Brian J Haas et al.   NATURE BIOTECHNOLOGY

Exploring microRNA functions in zebrafish

(2010) Anders Fjose et al.   New Biotechnology

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Parallel DNA pyrosequencing unveils new zebrafish microRNAs

(2009) Ana R Soares et al.   BMC GENOMICS

Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates

(2009) K. S. Kassahn et al.   GENOME RESEARCH

A MicroRNA Repertoire for Functional Genome Research in Rainbow Trout (Oncorhynchus mykiss)

(2009) Mohamed Salem et al.   MARINE BIOTECHNOLOGY

Evolution of a multifunctional gene: The warm temperature acclimation protein Wap65 in the European seabass Dicentrarchus labrax

(2009) Elena Sarropoulou et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Cloning and characterization of microRNAs from rainbow trout (Oncorhynchus mykiss): Their expression during early embryonic development

(2008) Raghuveer K Ramachandra et al.   BMC DEVELOPMENTAL BIOLOGY

Gene expression and functional analysis of zebrafish larval fin fold regeneration

(2008) Nozomi Yoshinari et al.   DEVELOPMENTAL BIOLOGY

The microRNA-30 Family Is Required for Vertebrate Hepatobiliary Development

(2008) Nicholas J. Hand et al.   GASTROENTEROLOGY

Linking the Genomes of Nonmodel Teleosts Through Comparative Genomics

(2008) E. Sarropoulou et al.   MARINE BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS