Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins

Animal Evolution: Are Phyla Real?

(2016) Andreas Hejnol et al.   CURRENT BIOLOGY

Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms

(2016) Eric M. Erkenbrack et al.   DEVELOPMENT GENES AND EVOLUTION

The mid-developmental transition and the evolution of animal body plans

(2016) Michal Levin et al.   NATURE

Divergence of ectodermal and mesodermal gene regulatory network linkages in early development of sea urchins

(2016) Eric M. Erkenbrack   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks

(2016) David Viktor Dylus et al.   EvoDevo

Juvenile skeletogenesis in anciently diverged sea urchin clades

(2015) Feng Gao et al.   DEVELOPMENTAL BIOLOGY

Expession patterns of mesenchyme specification genes in two distantly related echinoids, Glyptocidaris crenularis and Echinocardium cordatum

(2015) Atsuko Yamazaki et al.   GENE EXPRESSION PATTERNS

Embracing the comparative approach: how robust phylogenies and broader developmental sampling impacts the understanding of nervous system evolution

(2015) A. Hejnol et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses

(2015) Eric M. Erkenbrack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution

(2015) Melanie J. Hopkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics

(2015) Tsvia Gildor et al.   PLoS Genetics

Reorganization of sea urchin gene regulatory networks at least 268 million years ago as revealed by oldest fossil cidaroid echinoid

(2015) Jeffrey R. Thompson et al.   Scientific Reports

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Larval mesenchyme cell specification in the primitive echinoid occurs independently of the double-negative gate

(2014) A. Yamazaki et al.   DEVELOPMENT

strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence

(2014) Mark A. Bell et al.   PALAEONTOLOGY

Phylogenomic analysis of echinoderm class relationships supports Asterozoa

(2014) M. J. Telford et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenetic Analysis of Gene Expression

(2013) C. W. Dunn et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Probabilistic error correction for RNA sequencing

(2013) Hai-Son Le et al.   NUCLEIC ACIDS RESEARCH

Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms

(2012) Brenna S McCauley et al.   EvoDevo

Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

Evolutionary crossroads in developmental biology: sea urchins

(2011) D. R. McClay   DEVELOPMENT

The phylogeny and classification of post-Palaeozoic echinoids

(2011) Andreas Kroh et al.   JOURNAL OF SYSTEMATIC PALAEONTOLOGY

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

(2011) M. d. Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Best Practices for Justifying Fossil Calibrations

(2011) James F. Parham et al.   SYSTEMATIC BIOLOGY

Activation of the skeletogenic gene regulatory network in the early sea urchin embryo

(2010) T. Sharma et al.   DEVELOPMENT

Conserved early expression patterns of micromere specification genes in two echinoid species belonging to the orders clypeasteroida and echinoida

(2010) Atsuko Yamazaki et al.   DEVELOPMENTAL DYNAMICS

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos

(2009) Brenna S. McCauley et al.   DEVELOPMENTAL BIOLOGY

Genomic control of patterning

(2009) Isabelle S. Peter et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Structure–function correlation of micro1 for micromere specification in sea urchin embryos

(2009) Atsuko Yamazaki et al.   MECHANISMS OF DEVELOPMENT

Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring

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

Lessons from a gene regulatory network: echinoderm skeletogenesis provides insights into evolution, plasticity and morphogenesis

(2008) C. A. Ettensohn   DEVELOPMENT

Global regulatory logic for specification of an embryonic cell lineage

(2008) P. Oliveri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA