The bowfin genome illuminates the developmental evolution of ray-finned fishes

Giant lungfish genome elucidates the conquest of land by vertebrates

(2021) Axel Meyer et al.   NATURE

Dissection of the Fgf8 regulatory landscape by in vivo CRISPR-editing reveals extensive intra- and inter-enhancer redundancy

(2021) A. Hörnblad et al.   Nature Communications

Coevolution of enamel, ganoin, enameloid, and their matrix SCPP genes in osteichthyans

(2021) Kazuhiko Kawasaki et al.   iScience

African lungfish genome sheds light on the vertebrate water-to-land transition

(2021) Kun Wang et al.   CELL

Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes

(2021) Xupeng Bi et al.   CELL

RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data

(2021) Romain Feron et al.   Molecular Ecology Resources

Toll-like Receptors and the Control of Immunity

(2020) Katherine A. Fitzgerald et al.   CELL

Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis

(2020) Blanca Pijuan-Sala et al.   NATURE CELL BIOLOGY

The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

(2020) Kang Du et al.   Nature Ecology & Evolution

Deeply conserved synteny resolves early events in vertebrate evolution

(2020) Oleg Simakov et al.   Nature Ecology & Evolution

pyGenomeTracks: reproducible plots for multivariate genomic data sets

(2020) Lucille Lopez-Delisle et al.   BIOINFORMATICS

Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis

(2020) Yingshu Li et al.   GENOME RESEARCH

Changes in Nkx2.1, Sox2, Bmp4 , and Bmp16 expression underlying the lung‐to‐gas bladder evolutionary transition in ray‐finned fishes

(2020) Emily C. Funk et al.   EVOLUTION & DEVELOPMENT

Dorsoventral inversion of the air‐filled organ (lungs, gas bladder) in vertebrates: RNAsequencing of laser capture microdissected embryonic tissue

(2020) Emily Funk et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Immunoglobulin T genes in Actinopterygii

(2020) Serafin Mirete-Bachiller et al.   FISH & SHELLFISH IMMUNOLOGY

The American Paddlefish Genome Provides Novel Insights into Chromosomal Evolution and Bone Mineralization in Early Vertebrates

(2020) Peilin Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fgf-signaling is compartmentalized within the mesenchyme and controls proliferation during salamander limb development

(2019) Sruthi Purushothaman et al.   eLife

Global Rate Variation in Bony Vertebrates

(2018) Naoko Takezaki   Genome Biology and Evolution

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

(2018) Lily C. Hughes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

The Divergent Genomes of Teleosts

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

Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates

(2018) Yuichiro Hara et al.   Nature Ecology & Evolution

Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development

(2018) Xuefei Yuan et al.   Nature Communications

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element

(2017) Peng Huang et al.   GENES & DEVELOPMENT

Spotted Gar and the Evolution of Innate Immune Receptors

(2017) Dustin J. Wcisel et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

SCPP Genes and Their Relatives in Gar: Rapid Expansion of Mineralization Genes in Osteichthyans

(2017) Kazuhiko Kawasaki et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

“Holostei versus Halecostomi” Problem: Insight from Cytogenetics of Ancient Nonteleost Actinopterygian Fish, Bowfin Amia calva

(2017) Zuzana Majtánová et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure

(2017) Sergey V. Ulianov et al.   Epigenetics & Chromatin

Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database

(2016) Jeremy Pasquier et al.   BMC GENOMICS

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

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

(2016) Ingo Braasch et al.   NATURE GENETICS

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

Regulatory evolution ofTbx5and the origin of paired appendages

(2016) Noritaka Adachi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Little evidence for enhanced phenotypic evolution in early teleosts relative to their living fossil sister group

(2016) John T. Clarke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cis -regulatory programs in the development and evolution of vertebrate paired appendages

(2016) Andrew R. Gehrke et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Molecular developmental mechanism in polypterid fish provides insight into the origin of vertebrate lungs

(2016) Norifumi Tatsumi et al.   Scientific Reports

HoxD expression in the fin-fold compartment of basal gnathostomes and implications for paired appendage evolution

(2016) Frank J. Tulenko et al.   Scientific Reports

Collagen duplicate genes of bone and cartilage participate during regeneration of zebrafish fin skeleton

(2015) I. Duran et al.   GENE EXPRESSION PATTERNS

New genomic and fossil data illuminate the origin of enamel

(2015) Qingming Qu et al.   NATURE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Lauren C. Sallan   BIOLOGICAL REVIEWS

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

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

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Uncovering Enhancer Functions Using the α-Globin Locus

(2014) Douglas Vernimmen   PLoS Genetics

Spatial-temporal targeting of lung-specific mesenchyme by a Tbx4 enhancer

(2013) Wenming Zhang et al.   BMC BIOLOGY

An Integrated Holo-Enhancer Unit Defines Tissue and Gene Specificity of the Fgf8 Regulatory Landscape

(2013) Mirna Marinić et al.   DEVELOPMENTAL CELL

Innate immunity of finfish: Primordial conservation and function of viral RNA sensors in teleosts

(2013) Takashi Aoki et al.   FISH & SHELLFISH IMMUNOLOGY

Coelacanth genomes reveal signatures for evolutionary transition from water to land

(2013) M. Nikaido et al.   GENOME RESEARCH

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

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

The Astonishing Diversity of Ig Classes and B Cell Repertoires in Teleost Fish

(2013) Simon Fillatreau et al.   Frontiers in Immunology

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Twist2 contributes to termination of limb bud outgrowth and patterning through direct regulation of Grem1

(2012) Christine Wade et al.   DEVELOPMENTAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

The MHC, disease and selection

(2011) John Trowsdale   IMMUNOLOGY LETTERS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

(2011) Jarrod A. Chapman et al.   PLoS One

The Divergent Development of the Apical Ectodermal Ridge in the Marsupial Monodelphis domestica

(2010) Carolyn K. Doroba et al.   Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development

(2010) Amir A Abbasi et al.   BMC DEVELOPMENTAL BIOLOGY

Different Phylogenomic Approaches to Resolve the Evolutionary Relationships among Model Fish Species

(2010) E. Negrisolo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Loss of fish actinotrichia proteins and the fin-to-limb transition

(2010) Jing Zhang et al.   NATURE

The apical ectodermal ridge in the pectoral fin of the Australian Lungfish (Neoceratodus forsteri): keeping the fin to limb transition in the fold

(2009) Verity S. Hodgkinson et al.   ACTA ZOOLOGICA

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

Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split

(2009) Anna Z Komisarczuk et al.   DEVELOPMENTAL BIOLOGY

Origin and evolution of the integumentary skeleton in non-tetrapod vertebrates

(2009) Jean-Yves Sire et al.   JOURNAL OF ANATOMY

Shared developmental mechanisms pattern the vertebrate gill arch and paired fin skeletons

(2009) J. A. Gillis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Dual hindlimb control elements in the Tbx4 gene and region-specific control of bone size in vertebrate limbs

(2008) D. B. Menke et al.   DEVELOPMENT

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

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

Noncanonical role of Hox14 revealed by its expression patterns in lamprey and shark

(2008) S. Kuraku et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA