Advances in genomics of bony fish

Zebrafish embryos as an alternative model for screening of drug-induced organ toxicity

(2013) S. Scholz   ARCHIVES OF TOXICOLOGY

Exploring the zebrafish embryo as an alternative model for the evaluation of liver toxicity by histopathology and expression profiling

(2013) Marja Driessen et al.   ARCHIVES OF TOXICOLOGY

Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts

(2013) Josep A Calduch-Giner et al.   BMC GENOMICS

Reprogramming the Maternal Zebrafish Genome after Fertilization to Match the Paternal Methylation Pattern

(2013) Magdalena E. Potok et al.   CELL

Sperm, but Not Oocyte, DNA Methylome Is Inherited by Zebrafish Early Embryos

(2013) Lan Jiang et al.   CELL

A Bilirubin-Inducible Fluorescent Protein from Eel Muscle

(2013) Akiko Kumagai et al.   CELL

Novel sex-determining genes in fish and sex chromosome evolution

(2013) Kiyoshi Kikuchi et al.   DEVELOPMENTAL DYNAMICS

A large-scale zebrafish gene knockout resource for the genome-wide study of gene function

(2013) G. K. Varshney et al.   GENOME RESEARCH

Coelacanth genomes reveal signatures for evolutionary transition from water to land

(2013) M. Nikaido et al.   GENOME RESEARCH

Rapid metabolic screening of early zebrafish embryogenesis based on direct infusion-nanoESI-FTMS

(2013) Robert-Jan Raterink et al.   Metabolomics

Perspectives for identification of mutations in the zebrafish: Making use of next-generation sequencing technologies for forward genetic approaches

(2013) Katrin Henke et al.   METHODS

The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos

(2013) Ozren Bogdanović et al.   METHODS

Robotic injection of zebrafish embryos for high-throughput screening in disease models

(2013) Herman P. Spaink et al.   METHODS

Genomics: Zebrafish earns its stripes

(2013) Alexander F. Schier   NATURE

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

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

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

(2013) Jeramiah J Smith et al.   NATURE GENETICS

Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish

(2013) Arjan P. Palstra et al.   PLoS One

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

(2013) Alex R. Hastie et al.   PLoS One

Deep mRNA Sequencing Analysis to Capture the Transcriptome Landscape of Zebrafish Embryos and Larvae

(2013) Hongxing Yang et al.   PLoS One

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

(2013) Y. Nakamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of an alternative in vitro test battery for detecting reproductive toxicants

(2013) A.H. Piersma et al.   REPRODUCTIVE TOXICOLOGY

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

New Insights into the Pathogenesis of Tuberculosis Revealed by Mycobacterium marinum: The Zebrafish Model from the Systems Biology Perspective

(2012) Wanyan Deng et al.   CRITICAL REVIEWS IN EUKARYOTIC GENE EXPRESSION

Cancer and Inflammation: An Aspirin a Day Keeps the Cancer at Bay

(2012) Marina Mione et al.   CURRENT BIOLOGY

An Immune-Related Gene Evolved into the Master Sex-Determining Gene in Rainbow Trout, Oncorhynchus mykiss

(2012) Ayaka Yano et al.   CURRENT BIOLOGY

First draft genome sequence of the Japanese eel, Anguilla japonica

(2012) Christiaan V. Henkel et al.   GENE

Horizontal Transfers of Tc1 Elements between Teleost Fishes and Their Vertebrate Parasites, Lampreys

(2012) Shigehiro Kuraku et al.   Genome Biology and Evolution

Hooked! Modeling human disease in zebrafish

(2012) Cristina Santoriello et al.   JOURNAL OF CLINICAL INVESTIGATION

PROTEOMICS in aquaculture: Applications and trends

(2012) Pedro M. Rodrigues et al.   Journal of Proteomics

Changes in Liver Proteome Expression of Senegalese Sole (Solea senegalensis) in Response to Repeated Handling Stress

(2012) Odete D. Cordeiro et al.   MARINE BIOTECHNOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Primitive Duplicate Hox Clusters in the European Eel's Genome

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

Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics

(2012) Peifeng Ji et al.   PLoS One

Genome-Wide SNP Discovery from Transcriptome of Four Common Carp Strains

(2012) Jian Xu et al.   PLoS One

Expanding the zebrafish embryo proteome using multiple fractionation approaches and tandem mass spectrometry

(2012) Christopher Lößner et al.   PROTEOMICS

Comparison of the Exomes of Common Carp (Cyprinus carpio) and Zebrafish (Danio rerio)

(2012) Christiaan V. Henkel et al.   Zebrafish

Zebrafish-As an integrative model for twenty-first century toxicity testing

(2011) Nisha S. Sipes et al.   BIRTH DEFECTS RESEARCH PART C-EMBRYO TODAY-REVIEWS

Developmental energetics of zebrafish, Danio rerio

(2011) S. Augustine et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Sex Determination: Switch and Suppress

(2011) Amaury Herpin et al.   CURRENT BIOLOGY

Molecular profiling of marine fauna: Integration of omics with environmental assessment of the world's oceans

(2011) Nik Veldhoen et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Reproducible1H NMR-Based Metabolomic Responses in Fish Exposed to Different Sewage Effluents in Two Separate Studies

(2011) Linda M. Samuelsson et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Vertebrate sex determination: questioning the hierarchy

(2011) Amaury Herpin et al.   FEBS Journal

Quantitative proteomics in teleost fish: Insights and challenges for neuroendocrine and neurotoxicology research

(2011) Christopher J. Martyniuk 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

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

Genomics of adaptation and speciation in cichlid fishes: recent advances and analyses in African and Neotropical lineages

(2011) S. Fan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Establishing Zebrafish as a Novel Exercise Model: Swimming Economy, Swimming-Enhanced Growth and Muscle Growth Marker Gene Expression

(2011) Arjan P. Palstra et al.   PLoS One

A Full Lifecycle Bioenergetic Model for Bluefin Tuna

(2011) Marko Jusup et al.   PLoS One

The zebrafish embryo model in toxicology and teratology, September 2–3, 2010, Karlsruhe, Germany

(2011) Wibke Busch et al.   REPRODUCTIVE TOXICOLOGY

Zebrafish embryos as an alternative to animal experiments—A commentary on the definition of the onset of protected life stages in animal welfare regulations

(2011) Uwe Strähle et al.   REPRODUCTIVE TOXICOLOGY

A Natural Deletion of the HoxC Cluster in Elasmobranch Fishes

(2011) B. L. King et al.   SCIENCE

Cave-Dwelling Fish Provide Clues to the Circadian Cycle

(2011) Robin Mejia   PLOS BIOLOGY

High-pressure adaptation of muscle proteins from deep-sea fishes, Coryphaenoides yaquinae and C. armatus

(2010) Takami Morita   Annals of the New York Academy of Sciences

The Art of Medaka Genetics and Genomics: What Makes Them So Unique?

(2010) Hiroyuki Takeda et al.   Annual Review of Genetics

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

The National BioResource Project Medaka (NBRP Medaka): An Integrated Bioresource for Biological and Biomedical Sciences

(2010) Takao SASADO et al.   EXPERIMENTAL ANIMALS

Incorporating Zebrafish Omics into Chemical Biology and Toxicology

(2010) Hendrian Sukardi et al.   Zebrafish

The zebrafish:scalable in vivo modeling for systems biology

(2010) Rahul C. Deo et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

A novel application of metabolomics in vertebrate development

(2009) Shunsuke Hayashi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Single-Molecule Microscopy Reveals Membrane Microdomain Organization of Cells in a Living Vertebrate

(2009) Marcel J.M. Schaaf et al.   BIOPHYSICAL JOURNAL

Molecular mechanisms of sex determination and evolution of the Y-chromosome: Insights from the medakafish (Oryzias latipes)

(2009) Amaury Herpin et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Metabolic Fingerprinting Reveals Developmental Regulation of Metabolites during Early Zebrafish Embryogenesis

(2009) Cyrus Papan et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Fish proteome analysis: Model organisms and non-sequenced species

(2009) Ignasi Forné et al.   PROTEOMICS

Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels

(2009) Ian Sudbery et al.   GENOME BIOLOGY

High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research

(2009) Kathrin Reichwald et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Autonomous onset of the circadian clock in the zebrafish embryo

(2008) Marcus P S Dekens et al.   EMBO JOURNAL

Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids

(2008) Yong-Hwee E Loh et al.   GENOME BIOLOGY