Closing the genotype-phenotype gap: Emerging technologies for evolutionary genetics in ecological model vertebrate systems

The Evolutionary Genomics of Cichlid Fishes: Explosive Speciation and Adaptation in the Postgenomic Era

(2014) Frederico Henning et al.   Annual Review of Genomics and Human Genetics

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

(2014) Edith Heard et al.   CELL

Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos

(2014) Yuyu Niu et al.   CELL

Embryonic bauplans and the developmental origins of facial diversity and constraint

(2014) N. M. Young et al.   DEVELOPMENT

Ezh2 is required for neural crest-derived cartilage and bone formation

(2014) D. Schwarz et al.   DEVELOPMENT

Coverage and efficiency in current SNP chips

(2014) Ngoc-Thuy Ha et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Efficient and Heritable Gene Targeting in Tilapia by CRISPR/Cas9

(2014) Minghui Li et al.   GENETICS

Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period

(2014) J. J. Tena et al.   GENOME RESEARCH

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

Interspecific Variation in Rx1 Expression Controls Opsin Expression and Causes Visual System Diversity in African Cichlid Fishes

(2014) Jane E. Schulte et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping

(2014) Frederico Henning et al.   MOLECULAR ECOLOGY

Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs

(2014) Javier Lopez-Rios et al.   NATURE

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

A molecular basis for classic blond hair color in Europeans

(2014) Catherine A Guenther et al.   NATURE GENETICS

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6

(2014) P. A. Cleves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes

(2014) Kathryn R. Elmer et al.   Nature Communications

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

(2013) Klara Stefflova et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair

(2013) T. O. Auer et al.   GENOME RESEARCH

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

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

(2013) Ozren Bogdanović et al.   METHODS

Genomics: Zebrafish earns its stripes

(2013) Alexander F. Schier   NATURE

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Enhancing the hunt for enhancers

(2013) Louisa Flintoft   NATURE REVIEWS GENETICS

Epistasis and quantitative traits: using model organisms to study gene–gene interactions

(2013) Trudy F. C. Mackay   NATURE REVIEWS GENETICS

Enhancers: five essential questions

(2013) Len A. Pennacchio et al.   NATURE REVIEWS GENETICS

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

Pitfalls of predicting complex traits from SNPs

(2013) Naomi R. Wray et al.   NATURE REVIEWS GENETICS

Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish

(2013) An Xiao et al.   NUCLEIC ACIDS RESEARCH

Tol2-Mediated Generation of a Transgenic Haplochromine Cichlid, Astatotilapia burtoni

(2013) Scott A. Juntti et al.   PLoS One

Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

(2013) Li-En Jao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine

(2013) I. Guerreiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ezh2 Orchestrates Topographic Migration and Connectivity of Mouse Precerebellar Neurons

(2013) T. Di Meglio et al.   SCIENCE

Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon

(2013) M. D. Shapiro et al.   SCIENCE

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

(2013) C. Attanasio et al.   SCIENCE

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Gene transfer and mutagenesis mediated by Sleeping Beauty transposon in Nile tilapia (Oreochromis niloticus)

(2013) Xiaozhen He et al.   TRANSGENIC RESEARCH

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Dynamics of DNA Methylation in Recent Human and Great Ape Evolution

(2013) Irene Hernando-Herraez et al.   PLoS Genetics

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Lost in Transgenesis

(2012) Jennifer Davis et al.   CIRCULATION RESEARCH

Advances in targeted genome editing

(2012) Pablo Perez-Pinera et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Hoxd13 Contribution to the Evolution of Vertebrate Appendages

(2012) Renata Freitas et al.   DEVELOPMENTAL CELL

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

TALENs: a widely applicable technology for targeted genome editing

(2012) J. Keith Joung et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Hundreds of conserved non-coding genomic regions are independently lost in mammals

(2012) Michael Hiller et al.   NUCLEIC ACIDS RESEARCH

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome

(2012) Xiaochun Ni et al.   PLOS BIOLOGY

Progress of genome wide association study in domestic animals

(2012) Hui Zhang et al.   Journal of Animal Science and Biotechnology

Tol2-mediated transgenesis in tilapia (Oreochromis niloticus)

(2011) Koji Fujimura et al.   AQUACULTURE

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

(2011) Felicity C. Jones et al.   CURRENT BIOLOGY

Forward and Reverse Genetic Approaches for the Analysis of Vertebrate Development in the Zebrafish

(2011) Nathan D. Lawson et al.   DEVELOPMENTAL CELL

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

(2011) G. H. Perry et al.   GENOME RESEARCH

DNA Methylation Rebalances Gene Dosage after Mammalian Gene Duplications

(2011) A. Y.-F. Chang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Transposon-Mediated Transgenesis in the Short-Lived African Killifish Nothobranchius furzeri , a Vertebrate Model for Aging

(2011) Dario Riccardo Valenzano et al.   G3-Genes Genomes Genetics

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Systematic variation improves reproducibility of animal experiments

(2010) S Helene Richter et al.   NATURE METHODS

Insulators and promoters: closer than we think

(2010) Jesse R. Raab et al.   NATURE REVIEWS GENETICS

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence

(2009) Sabina Benko et al.   NATURE GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Sexual Conflict Resolved by Invasion of a Novel Sex Determiner in Lake Malawi Cichlid Fishes

(2009) R. B. Roberts et al.   SCIENCE

Genomic analysis of cichlid fish ‘natural mutants’

(2008) Shigehiro Kuraku et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Regulatory divergence modifies limb length between mammals

(2008) C. J. Cretekos et al.   GENES & DEVELOPMENT

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

MicroRNAs and the advent of vertebrate morphological complexity

(2008) A. M. Heimberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Are we there yet? Tracking the development of new model systems

(2008) Arhat Abzhanov et al.   TRENDS IN GENETICS

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

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