De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages

The Divergent Genomes of Teleosts

(2018) Vydianathan Ravi et al.   Annual Review of Animal Biosciences

Genetic parameters and quantitative trait loci analysis associated with body size and timing at metamorphosis into glass eels in captive-bred Japanese eels (Anguilla japonica)

(2018) Kazuharu Nomura et al.   PLoS One

Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy

(2018) Paul D. Blischak et al.   Annual Review of Ecology Evolution and Systematics

Abundance of specific mRNA transcripts impacts hatching success in European eel, Anguilla anguilla L

(2016) Christoffer Rozenfeld et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Three nuclear and two membrane estrogen receptors in basal teleosts, Anguilla sp.: Identification, evolutionary history and differential expression regulation

(2016) Anne-Gaëlle Lafont et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Changes in ovarian gene expression profiles and plasma hormone levels in maturing European eel ( Anguilla anguilla ); Biomarkers for broodstock selection

(2016) Erik Burgerhout et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Phylogenomic analysis reveals ancient segmental duplications in the human genome

(2016) Madiha Hafeez et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

(2016) Ingo Braasch et al.   NATURE GENETICS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

(2016) Chao Bian et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Whole genome duplications in plants: an overview fromArabidopsis

(2015) Juan Carlos del Pozo et al.   JOURNAL OF EXPERIMENTAL BOTANY

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

(2015) Jun Inoue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Duplicated Leptin Receptors in Two Species of Eel Bring New Insights into the Evolution of the Leptin System in Vertebrates

(2015) Marina Morini et al.   PLoS One

Demonstration of the Coexistence of Duplicated LH Receptors in Teleosts, and Their Origin in Ancestral Actinopterygians

(2015) Gersende Maugars et al.   PLoS One

The polyploidy revolution then...and now: Stebbins revisited

(2014) D. E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Whole-genome duplication in teleost fishes and its evolutionary consequences

(2014) Stella M. K. Glasauer et al.   MOLECULAR GENETICS AND GENOMICS

Telomere-centric genome repatterning determines recurring chromosome number reductions during the evolution of eukaryotes

(2014) Xiyin Wang et al.   NEW PHYTOLOGIST

The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei

(2014) Eric B. Rondeau et al.   PLoS One

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

(2014) Frédéric J. J. Chain et al.   PLoS Genetics

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

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

(2013) Manfred Schartl et al.   NATURE GENETICS

Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications

(2013) Samuel Peña-Llopis 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

The Pituitary Gland of the European Eel Reveals Massive Expression of Genes Involved in the Melanocortin System

(2013) Eirill Ager-Wick et al.   PLoS One

Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates

(2013) Cristian Cañestro et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Primitive Duplicate Hox Clusters in the European Eel's Genome

(2012) Christiaan V. Henkel et al.   PLoS One

Multiple Kisspeptin Receptors in Early Osteichthyans Provide New Insights into the Evolution of This Receptor Family

(2012) Jérémy Pasquier et al.   PLoS One

Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)

(2012) M. Chester et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polyploidy in fungi: evolution after whole-genome duplication

(2012) W. Albertin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Integration of the Genetic Map and Genome Assembly of Fugu Facilitates Insights into Distinct Features of Genome Evolution in Teleosts and Mammals

(2011) Wataru Kai et al.   Genome Biology and Evolution

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

Mechanisms of Chromosome Number Evolution in Yeast

(2011) Jonathan L. Gordon et al.   PLoS Genetics

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

(2010) Heng Li et al.   BIOINFORMATICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Evolutionary consequences of autopolyploidy

(2010) Christian Parisod et al.   NEW PHYTOLOGIST

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

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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

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

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

Two Distinct Dopamine D2 Receptor Genes in the European Eel: Molecular Characterization, Tissue-Specific Transcription, and Regulation by Sex Steroids

(2008) Catherine Pasqualini et al.   ENDOCRINOLOGY