Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris

Geometric control of ciliated band regulatory states in the sea urchin embryo

(2015) J. C. Barsi et al.   DEVELOPMENT

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

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

A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA

(2015) Natasha M O'Brown et al.   eLife

A dynamic regulatory network explains ParaHox gene control of gut patterning in the sea urchin

(2014) R. Annunziata et al.   DEVELOPMENT

Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins

(2014) K. Rafiq et al.   DEVELOPMENT

Transcriptomic Analysis of the Highly Derived Radial Body Plan of a Sea Urchin

(2014) Jennifer A. Wygoda et al.   Genome Biology and Evolution

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

Short-range Wnt5 signaling initiates specification of sea urchin posterior ectoderm

(2013) D. C. McIntyre et al.   DEVELOPMENT

Notch and Nodal control forkhead factor expression in the specification of multipotent progenitors in sea urchin

(2013) S. C. Materna et al.   DEVELOPMENT

New regulatory circuit controlling spatial and temporal gene expression in the sea urchin embryo oral ectoderm GRN

(2013) Enhu Li et al.   DEVELOPMENTAL BIOLOGY

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

(2013) Leif Väremo et al.   NUCLEIC ACIDS RESEARCH

Cryptic Variation in Morphological Evolution: HSP90 as a Capacitor for Loss of Eyes in Cavefish

(2013) N. Rohner et al.   SCIENCE

The Impact of Gene Expression Variation on the Robustness and Evolvability of a Developmental Gene Regulatory Network

(2013) David A. Garfield et al.   PLOS BIOLOGY

Integration of Canonical and Noncanonical Wnt Signaling Pathways Patterns the Neuroectoderm Along the Anterior–Posterior Axis of Sea Urchin Embryos

(2013) Ryan C. Range et al.   PLOS BIOLOGY

Gene regulatory control in the sea urchin aboral ectoderm: Spatial initiation, signaling inputs, and cell fate lockdown

(2012) Smadar Ben-Tabou de-Leon et al.   DEVELOPMENTAL BIOLOGY

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

(2012) Michal Levin et al.   DEVELOPMENTAL CELL

Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis

(2012) Q. Tu et al.   GENOME RESEARCH

Sequential Signaling Crosstalk Regulates Endomesoderm Segregation in Sea Urchin Embryos

(2012) A. J. Sethi et al.   SCIENCE

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

Opposing Nodal and BMP Signals Regulate Left–Right Asymmetry in the Sea Urchin Larva

(2012) Yi-Jyun Luo et al.   PLOS BIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Regulative deployment of the skeletogenic gene regulatory network during sea urchin development

(2011) T. Sharma et al.   DEVELOPMENT

The control of foxN2/3 expression in sea urchin embryos and its function in the skeletogenic gene regulatory network

(2011) H. K. Rho et al.   DEVELOPMENT

The genomic regulatory control of skeletal morphogenesis in the sea urchin

(2011) K. Rafiq et al.   DEVELOPMENT

Wnt6 activates endoderm in the sea urchin gene regulatory network

(2011) J. Croce et al.   DEVELOPMENT

Evolutionary crossroads in developmental biology: sea urchins

(2011) D. R. McClay   DEVELOPMENT

Mapping Gene Expression in Two Xenopus Species: Evolutionary Constraints and Developmental Flexibility

(2011) Itai Yanai et al.   DEVELOPMENTAL CELL

A gene regulatory network controlling the embryonic specification of endoderm

(2011) Isabelle S. Peter et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Co-option and dissociation in larval origins and evolution: the sea urchin larval gut

(2010) Alan C. Love et al.   EVOLUTION & DEVELOPMENT

Multi-trait evolution in a cave fish, Astyanax mexicanus

(2010) Meredith Protas et al.   EVOLUTION & DEVELOPMENT

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species

(2010) D. Xie et al.   GENOME RESEARCH

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

Conserved developmental transcriptomes in evolutionarily divergent species

(2010) Anup Parikh et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The sea urchin animal pole domain is a Six3-dependent neurogenic patterning center

(2009) Z. Wei et al.   DEVELOPMENT

A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo

(2009) Yi-Hsien Su et al.   DEVELOPMENTAL BIOLOGY

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

The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage

(2009) Isabelle S. Peter et al.   DEVELOPMENTAL BIOLOGY

Fluorescent in situ hybridization reveals multiple expression domains for SpBrn1/2/4 and identifies a unique ectodermal cell type that co-expresses the ParaHox gene SpLox

(2009) A.G. Cole et al.   GENE EXPRESSION PATTERNS

Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved

(2009) I. Yanai et al.   GENOME RESEARCH

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

(2009) Y. F. Chan et al.   SCIENCE

Gene Regulatory Network Interactions in Sea Urchin Endomesoderm Induction

(2009) Aditya J Sethi et al.   PLOS BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species

(2008) Sangyun Jeong et al.   CELL

Morphogenetic mechanisms of coelom formation in the direct-developing sea urchin Heliocidaris erythrogramma

(2008) Margaret S. Smith et al.   DEVELOPMENT GENES AND EVOLUTION

Nodal expression and heterochrony in the evolution of dorsal-ventral and left-right axes formation in the direct-developing sea urchinHeliocidaris erythrogramma

(2008) Margaret S. Smith et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

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