The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes

Similar Ratios of Introns to Intergenic Sequence across Animal Genomes

(2017) Warren R. Francis et al.   Genome Biology and Evolution

Dynamics of genome size evolution in birds and mammals

(2017) Aurélie Kapusta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes

(2017) Prosanta Chakrabarty et al.   SYSTEMATIC BIOLOGY

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

(2017) Martin Malmstrøm et al.   Scientific Data

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

(2017) Dahiana Arcila et al.   Nature Ecology & Evolution

The Sinocyclocheilus cavefish genome provides insights into cave adaptation

(2016) Junxing Yang et al.   BMC BIOLOGY

Resolving Cypriniformes relationships using an anchored enrichment approach

(2016) Carla C. Stout et al.   BMC EVOLUTIONARY BIOLOGY

Phenotypic Novelty in EvoDevo: The Distinction Between Continuous and Discontinuous Variation and Its Importance in Evolutionary Theory

(2016) Tim Peterson et al.   Evolutionary Biology

Digits and fin rays share common developmental histories

(2016) Tetsuya Nakamura et al.   NATURE

Evolution of the immune system influences speciation rates in teleost fishes

(2016) Martin Malmstrøm et al.   NATURE GENETICS

Rphylopars: fast multivariate phylogenetic comparative methods for missing data and within-species variation

(2016) Eric W. Goolsby et al.   Methods in Ecology and Evolution

The contribution of transposable elements to size variations between four teleost genomes

(2016) Bo Gao et al.   Mobile DNA

Paedomorphosis as an Evolutionary Driving Force: Insights from Deep-Sea Brittle Stars

(2016) Sabine Stöhr et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

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

The significance of Hox gene collinearity

(2015) Stephen J. Gaunt   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Danionella dracula, an escape from the cypriniformBauplanvia developmental truncation?

(2015) Ralf Britz et al.   JOURNAL OF MORPHOLOGY

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

Advancing biology through a deeper understanding of zebrafish ecology and evolution

(2015) David M Parichy   eLife

Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing

(2015) Melissa C. Keinath et al.   Scientific Reports

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

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

Phylogeny of Zebrafish, a “Model Species,” within Danio, a “Model Genus”

(2014) Braedan M. McCluskey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Thyroid hormone-dependent adult pigment cell lineage and pattern in zebrafish

(2014) S. K. McMenamin et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Miniatures, morphology and molecules:Paedocyprisand its phylogenetic position (Teleostei, Cypriniformes)

(2014) Ralf Britz et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

(2014) Joanna L. Kelley et al.   Nature Communications

Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution

(2014) Larissa B. Patterson et al.   Nature Communications

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Evolution of Hox gene clusters in deuterostomes

(2013) Juan Pascual-Anaya et al.   BMC DEVELOPMENTAL BIOLOGY

The regulation of Hox gene expression during animal development

(2013) Moisés Mallo et al.   DEVELOPMENT

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

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

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

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

(2013) Kerstin Howe et al.   NATURE

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

(2012) Benoît Chénais et al.   GENE

The Evolution of Intron Size in Amniotes: A Role for Powered Flight?

(2012) Qu Zhang et al.   Genome Biology and Evolution

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Primitive Duplicate Hox Clusters in the European Eel's Genome

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

Chromosome Evolution and Genome Miniaturization in Minifish

(2012) Shaojun Liu et al.   PLoS One

Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons

(2012) Francesco Vezzi et al.   PLoS One

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Comparative Analysis of Teleost Genome Sequences Reveals an Ancient Intron Size Expansion in the Zebrafish Lineage

(2011) Stephen P. Moss et al.   Genome Biology and Evolution

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

(2011) Cheng Sun et al.   Genome Biology and Evolution

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

The role of developmental plasticity in evolutionary innovation

(2011) A. P. Moczek et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

The world’s smallest vertebrate species of the genus Paedocypris: A new family of freshwater fishes and the sister group to the world’s most diverse clade of freshwater fishes (Teleostei: Cypriniformes)

(2010) Richard L. Mayden et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae)

(2010) Kevin L. Tang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Spectacular morphological novelty in a miniature cyprinid fish, Danionella dracula n. sp.

(2009) R. Britz et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Molecular phylogenetic interrelationships of the south Asian cyprinid generaDanio, DevarioandMicrorasbora(Teleostei, Cyprinidae, Danioninae)

(2009) Fang Fang et al.   ZOOLOGICA SCRIPTA

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

Osteology ofPaedocypris, a miniature and highly developmentally truncated fish (Teleostei: Ostariophysi: Cyprinidae)

(2008) R. Britz et al.   JOURNAL OF MORPHOLOGY

Genome Size Reduction in the Chicken Has Involved Massive Loss of Ancestral Protein-Coding Genes

(2008) A. L. Hughes et al.   MOLECULAR BIOLOGY AND EVOLUTION