More Than One-to-Four via 2R: Evidence of an Independent Amphioxus Expansion and Two-Gene Ancestral Vertebrate State for MyoD-Related Myogenic Regulatory Factors (MRFs)

Deeply conserved synteny resolves early events in vertebrate evolution

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

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage

(2018) Thomas B. Barton-Owen et al.   Scientific Reports

The Ciona myogenic regulatory factor functions as a typical MRF but possesses a novel N-terminus that is essential for activity

(2018) Lindsay E. Ratcliffe et al.   DEVELOPMENTAL BIOLOGY

Amphioxus functional genomics and the origins of vertebrate gene regulation

(2018) Ferdinand Marlétaz et al.   NATURE

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

FlyBase 2.0: the next generation

(2018) Jim Thurmond et al.   NUCLEIC ACIDS RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing

(2017) Nga Thi Thuy Nguyen et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Xenbase: a genomic, epigenomic and transcriptomic model organism database

(2017) Kamran Karimi et al.   NUCLEIC ACIDS RESEARCH

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

(2017) Matija Brozovic et al.   NUCLEIC ACIDS RESEARCH

Gene regulatory networks and cell lineages that underlie the formation of skeletal muscle

(2017) Margaret Buckingham   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Function of the myogenic regulatory factors Myf5, MyoD, Myogenin and MRF4 in skeletal muscle, satellite cells and regenerative myogenesis

(2017) Peter S. Zammit   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Echinobase: an expanding resource for echinoderm genomic information

(2017) Parul Kudtarkar et al.   Database-The Journal of Biological Databases and Curation

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

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

(2016) Ingo Braasch et al.   NATURE GENETICS

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

Gene Regulatory Networks and Transcriptional Mechanisms that Control Myogenesis

(2014) Margaret Buckingham et al.   DEVELOPMENTAL CELL

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional studies of the Ciona intestinalis myogenic regulatory factor reveal conserved features of chordate myogenesis

(2013) Stephanie A. Izzi et al.   DEVELOPMENTAL BIOLOGY

Dial M(RF) for myogenesis

(2013) Natalia Moncaut et al.   FEBS Journal

Development of oral and branchial muscles in lancelet larvae ofBranchiostoma japonicum

(2013) Kinya Yasui et al.   JOURNAL OF MORPHOLOGY

Myogenesis in the sea urchin embryo: the molecular fingerprint of the myoblast precursors

(2013) Carmen Andrikou et al.   EvoDevo

A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus?

(2012) J. Paps et al.   Briefings in Functional Genomics

Evolutionary crossroads in developmental biology: amphioxus

(2011) S. Bertrand et al.   DEVELOPMENT

Phylogenetic diversification of the globin gene superfamily in chordates

(2011) Jay F. Storz et al.   IUBMB LIFE

Amphioxus FGF signaling predicts the acquisition of vertebrate morphological traits

(2011) S. Bertrand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Paralogs of Atlantic salmon myoblast determination factor genes are distinctly regulated in proliferating and differentiating myogenic cells

(2010) Neil I. Bower et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

A manual collection of Syt, Esyt, Rph3a, Rph3al, Doc2, and Dblc2 genes from 46 metazoan genomes - an open access resource for neuroscience and evolutionary biology

(2010) Molly Craxton   BMC GENOMICS

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Induced early expression of mrf4 but not myog rescues myogenesis in the myod/myf5 double-morphant zebrafish embryo

(2009) E. Schnapp et al.   JOURNAL OF CELL SCIENCE

WormBase: a comprehensive resource for nematode research

(2009) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

Evidence for stasis and not genetic piracy in developmental expression patterns of Branchiostoma lanceolatum and Branchiostoma floridae, two amphioxus species that have evolved independently over the course of 200 Myr

(2008) Ildiko Somorjai et al.   DEVELOPMENT GENES AND EVOLUTION

Global transcriptional regulation of the locus encoding the skeletal muscle determination genes Mrf4 and Myf5

(2008) J. J. Carvajal et al.   GENES & DEVELOPMENT

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

(2008) L. Z. Holland et al.   GENOME RESEARCH

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE

SpBase: the sea urchin genome database and web site

(2008) R. A. Cameron et al.   NUCLEIC ACIDS RESEARCH

Subfunctionalization of Duplicated Zebrafish pax6 Genes by cis-Regulatory Divergence

(2008) Dirk A. Kleinjan et al.   PLoS Genetics

An Update on MyoD Evolution in Teleosts and a Proposed Consensus Nomenclature to Accommodate the Tetraploidization of Different Vertebrate Genomes

(2008) Daniel J. Macqueen et al.   PLoS One