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

A comprehensive analysis of teleost MHC class I sequences

(2015) Unni Grimholt et al.   BMC EVOLUTIONARY BIOLOGY

A Platform for Rapid Exploration of Aging and Diseases in a Naturally Short-Lived Vertebrate

(2015) Itamar Harel et al.   CELL

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications

(2015) Jeramiah J. Smith et al.   GENOME RESEARCH

miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants

(2015) T. Desvignes et al.   TRENDS IN GENETICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Major issues in the origins of ray-finned fish (Actinopterygii) biodiversity

(2014) Lauren C. Sallan   BIOLOGICAL REVIEWS

Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats

(2014) Adam M Reitzel et al.   BMC EVOLUTIONARY BIOLOGY

Connectivity of vertebrate genomes: Paired-related homeobox (Prrx) genes in spotted gar, basal teleosts, and tetrapods

(2014) Ingo Braasch et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

Transgenic fish systems and their application in ecotoxicology

(2014) Okhyun Lee et al.   CRITICAL REVIEWS IN TOXICOLOGY

The POU-er of gene nomenclature

(2014) S. R. Frankenberg et al.   DEVELOPMENT

The MHC class I genes of zebrafish

(2014) Hayley Dirscherl et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

The genome ofCallorhinchusand the fossil record: a new perspective on SCPP gene evolution in gnathostomes

(2014) Bettina Ryll et al.   EVOLUTION & DEVELOPMENT

Getting more for your marrow: Boosting hematopoietic stem cell numbers with PGE2

(2014) Elliott J. Hagedorn et al.   EXPERIMENTAL CELL RESEARCH

Expanding the annotation of zebrafish microRNAs based on small RNA sequencing

(2014) Thomas Desvignes et al.   GENE

A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo

(2014) Ingo Braasch et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

The Circadian Clock of Teleost Fish: A Comparative Analysis Reveals Distinct Fates for Duplicated Genes

(2014) Jessica Toloza-Villalobos et al.   JOURNAL OF MOLECULAR EVOLUTION

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

Deep conservation of wrist and digit enhancers in fish

(2014) Andrew R. Gehrke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immunity and Immunopathology in the Tuberculous Granuloma

(2014) Antonio J. Pagán et al.   Cold Spring Harbor Perspectives in Medicine

Comprehensive analysis of MHC class II genes in teleost fish genomes reveals dispensability of the peptide-loading DM system in a large part of vertebrates

(2013) Johannes M Dijkstra et al.   BMC EVOLUTIONARY BIOLOGY

The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications

(2013) David Lagman et al.   BMC EVOLUTIONARY BIOLOGY

Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos

(2013) Nannan Chang et al.   CELL RESEARCH

Coelacanth genomes reveal signatures for evolutionary transition from water to land

(2013) M. Nikaido et al.   GENOME RESEARCH

Characterization of the Z lineage Major histocompatability complex class I genes in zebrafish

(2013) Hayley Dirscherl et al.   IMMUNOGENETICS

SCPP genes in the coelacanth: Tissue mineralization genes shared by sarcopterygians

(2013) Kazuhiko Kawasaki et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

A systematic genome-wide analysis of zebrafish protein-coding gene function

(2013) Ross N. W. Kettleborough et al.   NATURE

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

Efficient genome editing in zebrafish using a CRISPR-Cas system

(2013) Woong Y Hwang et al.   NATURE BIOTECHNOLOGY

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

(2013) Jeramiah J Smith et al.   NATURE GENETICS

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

(2013) Brant C. Faircloth et al.   PLoS One

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

Retinoid signaling in control of progenitor cell differentiation during mouse development

(2013) Gregg Duester   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

The origin of the tetrapod limb: from expeditions to enhancers

(2013) Igor Schneider et al.   TRENDS IN GENETICS

Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

(2013) Daniel L. Rabosky et al.   Nature Communications

Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

(2013) Soizik Berlivet et al.   PLoS Genetics

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

(2013) H Bradley Shaffer et al.   GENOME BIOLOGY

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference

(2012) Karen D. Crow et al.   Genome Biology and Evolution

Genomicus: five genome browsers for comparative genomics in eukaryota

(2012) Alexandra Louis et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

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

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

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

Opsin gene duplication and divergence in ray-finned fish

(2011) Diana J. Rennison et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

(2010) M. Muffato et al.   BIOINFORMATICS

The dynamic TCRδ: TCRδ chains in the amphibian Xenopus tropicalis utilize antibody-like V genes

(2010) Zuly E. Parra et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Evolution of MicroRNAs and the Diversification of Species

(2010) Yong-Hwee E. Loh et al.   Genome Biology and Evolution

Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence

(2010) E. Berezikov et al.   GENOME RESEARCH

Parallel Retention of Pdx2 Genes in Cartilaginous Fish and Coelacanths

(2010) J. F. Mulley et al.   MOLECULAR BIOLOGY AND EVOLUTION

IgT, a primitive immunoglobulin class specialized in mucosal immunity

(2010) Yong-An Zhang et al.   NATURE IMMUNOLOGY

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The SCPP gene repertoire in bony vertebrates and graded differences in mineralized tissues

(2009) Kazuhiko Kawasaki   DEVELOPMENT GENES AND EVOLUTION

The deep evolution of metazoan microRNAs

(2009) Benjamin M. Wheeler et al.   EVOLUTION & DEVELOPMENT

Automated identification of conserved synteny after whole-genome duplication

(2009) J. M. Catchen et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The oldest articulated osteichthyan reveals mosaic gnathostome characters

(2009) Min Zhu et al.   NATURE

Origin and evolution of the adaptive immune system: genetic events and selective pressures

(2009) Martin F. Flajnik et al.   NATURE REVIEWS GENETICS

Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes

(2009) Cristian Cañestro et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Rapidly evolving fish genomes and teleost diversity

(2008) Vydianathan Ravi et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Form, function and phylogenetics of NITRs in bony fish

(2008) Jeffrey A. Yoder   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

A Bony Fish Immunological Receptor of the NITR Multigene Family Mediates Allogeneic Recognition

(2008) John P. Cannon et al.   IMMUNITY

Comparative Analysis of Period Genes in Teleost Fish Genomes

(2008) Han Wang   JOURNAL OF MOLECULAR EVOLUTION

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

(2008) Andrew Grimson et al.   NATURE

Evolutionary mutant models for human disease

(2008) R. Craig Albertson et al.   TRENDS IN GENETICS