Published in Sci STKE on November 14, 2006
Establishment of medial fates along the proximodistal axis of the Drosophila leg through direct activation of dachshund by Distalless. Dev Cell (2011) 0.97
An iterative genetic and dynamical modelling approach identifies novel features of the gene regulatory network underlying melanocyte development. PLoS Genet (2011) 0.88
Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species. Mamm Genome (2007) 0.84
Logics and properties of a genetic regulatory program that drives embryonic muscle development in an echinoderm. Elife (2015) 0.82
SpGataE, a Strongylocentrotus purpuratus ortholog of mammalian Gata4/5/6: protein expression, interaction with putative target gene spec2a, and identification of friend of Gata factor SpFog1. Dev Genes Evol (2007) 0.79
A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions. Nucleic Acids Res (2012) 0.78
A basal deuterostome genome viewed as a natural experiment. Gene (2007) 0.78
Comparative analysis of distinct non-coding characteristics potentially contributing to the divergence of human tissue-specific genes. Genetica (2008) 0.77
The sea urchin genome as a window on function. Biol Bull (2008) 0.77
Robustness and Accuracy in Sea Urchin Developmental Gene Regulatory Networks. Front Genet (2016) 0.75
Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol (2008) 15.90
The genome of the sea urchin Strongylocentrotus purpuratus. Science (2006) 6.41
Gene regulatory networks for development. Proc Natl Acad Sci U S A (2005) 4.45
Global regulatory logic for specification of an embryonic cell lineage. Proc Natl Acad Sci U S A (2008) 3.27
Transcriptional regulatory cascades in development: initial rates, not steady state, determine network kinetics. Proc Natl Acad Sci U S A (2003) 2.70
The evolution of hierarchical gene regulatory networks. Nat Rev Genet (2009) 2.62
Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development (2007) 2.60
Modeling transcriptional regulatory networks. Bioessays (2002) 2.50
Developmental gene regulatory network architecture across 500 million years of echinoderm evolution. Proc Natl Acad Sci U S A (2003) 2.30
Small bilaterian fossils from 40 to 55 million years before the cambrian. Science (2004) 2.25
Logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci U S A (2005) 2.24
The last common bilaterian ancestor. Development (2002) 2.19
Predictive computation of genomic logic processing functions in embryonic development. Proc Natl Acad Sci U S A (2012) 2.11
Computational representation of developmental genetic regulatory networks. Dev Biol (2005) 2.11
A regulatory gene network that directs micromere specification in the sea urchin embryo. Dev Biol (2002) 2.09
A gene regulatory network subcircuit drives a dynamic pattern of gene expression. Science (2007) 2.04
A missing link in the sea urchin embryo gene regulatory network: hesC and the double-negative specification of micromeres. Proc Natl Acad Sci U S A (2007) 2.00
cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification. Dev Biol (2006) 1.96
New computational approaches for analysis of cis-regulatory networks. Dev Biol (2002) 1.85
A gene regulatory network controlling the embryonic specification of endoderm. Nature (2011) 1.81
Evolution of gene regulatory networks controlling body plan development. Cell (2011) 1.80
Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus. Dev Biol (2006) 1.77
Visualization, documentation, analysis, and communication of large-scale gene regulatory networks. Biochim Biophys Acta (2008) 1.77
Sea urchin Forkhead gene family: phylogeny and embryonic expression. Dev Biol (2006) 1.76
Activation of pmar1 controls specification of micromeres in the sea urchin embryo. Dev Biol (2003) 1.72
cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network. Dev Biol (2005) 1.63
Evolutionary plasticity of developmental gene regulatory network architecture. Proc Natl Acad Sci U S A (2007) 1.62
Gene regulatory network controlling embryonic specification in the sea urchin. Curr Opin Genet Dev (2004) 1.62
The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development. Dev Biol (2006) 1.62
High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development. Gene Expr Patterns (2010) 1.61
Phosphatized polar lobe-forming embryos from the Precambrian of southwest China. Science (2006) 1.61
Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development. Dev Biol (2006) 1.60
The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage. Dev Biol (2009) 1.59
Repression of mesodermal fate by foxa, a key endoderm regulator of the sea urchin embryo. Development (2006) 1.58
Gene regulation: gene control network in development. Annu Rev Biophys Biomol Struct (2007) 1.56
Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev Biol (2002) 1.55
R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres. Dev Biol (2004) 1.55
cis-Regulatory control circuits in development. Dev Biol (2004) 1.54
Development. Built to run, not fail. Science (2007) 1.50
New early zygotic regulators expressed in endomesoderm of sea urchin embryos discovered by differential array hybridization. Dev Biol (2002) 1.50
Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Dev Biol (2007) 1.48
Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo. Proc Natl Acad Sci U S A (2008) 1.46
Isolation of pigment cell specific genes in the sea urchin embryo by differential macroarray screening. Development (2003) 1.43
Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution. Proc Natl Acad Sci U S A (2008) 1.43
A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. Dev Biol (2009) 1.42
The transcriptome of the sea urchin embryo. Science (2006) 1.42
Expression patterns of four different regulatory genes that function during sea urchin development. Gene Expr Patterns (2004) 1.41
Modularity and design principles in the sea urchin embryo gene regulatory network. FEBS Lett (2009) 1.39
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res (2012) 1.37
Modeling the dynamics of transcriptional gene regulatory networks for animal development. Dev Biol (2008) 1.37
Unusual gene order and organization of the sea urchin hox cluster. J Exp Zool B Mol Dev Evol (2006) 1.34
Paleogenomics of echinoderms. Science (2006) 1.32
An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network. Dev Biol (2004) 1.24
The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example. Dev Biol (2009) 1.21
Information processing at the foxa node of the sea urchin endomesoderm specification network. Proc Natl Acad Sci U S A (2010) 1.21
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison. BMC Bioinformatics (2005) 1.21
High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution. Dev Biol (2006) 1.20
Precambrian animal life: probable developmental and adult cnidarian forms from Southwest China. Dev Biol (2002) 1.17
Exclusive developmental functions of gatae cis-regulatory modules in the Strongylocentrorus purpuratus embryo. Dev Biol (2007) 1.17
cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo. Dev Biol (2006) 1.14
SpHnf6, a transcription factor that executes multiple functions in sea urchin embryogenesis. Dev Biol (2004) 1.13
Expression and function of blimp1/krox, an alternatively transcribed regulatory gene of the sea urchin endomesoderm network. Dev Biol (2006) 1.12
Caught in the evolutionary act: precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins. Dev Biol (2007) 1.11
Functional cis-regulatory genomics for systems biology. Proc Natl Acad Sci U S A (2010) 1.09
Transphyletic conservation of developmental regulatory state in animal evolution. Proc Natl Acad Sci U S A (2011) 1.09
Expression and function of a starfish Otx ortholog, AmOtx: a conserved role for Otx proteins in endoderm development that predates divergence of the eleutherozoa. Mech Dev (2003) 1.07
Gene regulatory control in the sea urchin aboral ectoderm: spatial initiation, signaling inputs, and cell fate lockdown. Dev Biol (2012) 1.05
Boveri's long experiment: sea urchin merogones and the establishment of the role of nuclear chromosomes in development. Dev Biol (2007) 1.05
brachyury Target genes in the early sea urchin embryo isolated by differential macroarray screening. Dev Biol (2002) 1.04
Expression of Spgatae, the Strongylocentrotus purpuratus ortholog of vertebrate GATA4/5/6 factors. Gene Expr Patterns (2004) 1.04
Modeling DNA sequence-based cis-regulatory gene networks. Dev Biol (2002) 1.03
Building developmental gene regulatory networks. Birth Defects Res C Embryo Today (2009) 1.02
The cis-regulatory system of the tbrain gene: Alternative use of multiple modules to promote skeletogenic expression in the sea urchin embryo. Dev Biol (2009) 1.02
Direct and indirect control of oral ectoderm regulatory gene expression by Nodal signaling in the sea urchin embryo. Dev Biol (2012) 1.00
Diversification of oral and aboral mesodermal regulatory states in pregastrular sea urchin embryos. Dev Biol (2012) 1.00
Spdeadringer, a sea urchin embryo gene required separately in skeletogenic and oral ectoderm gene regulatory networks. Dev Biol (2003) 0.98
A comprehensive analysis of Delta signaling in pre-gastrular sea urchin embryos. Dev Biol (2012) 0.98
The regulatory genome and the computer. Dev Biol (2007) 0.98
Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo. Proc Natl Acad Sci U S A (2014) 0.97
Cis-regulatory logic driving glial cells missing: self-sustaining circuitry in later embryogenesis. Dev Biol (2012) 0.96
Genomic control of patterning. Int J Dev Biol (2009) 0.95
Hindgut specification and cell-adhesion functions of Sphox11/13b in the endoderm of the sea urchin embryo. Dev Growth Differ (2006) 0.95
An evolutionary constraint: strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules. Proc Natl Acad Sci U S A (2005) 0.95
Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring. Proc Natl Acad Sci U S A (2009) 0.94
Synthetic in vivo validation of gene network circuitry. Proc Natl Acad Sci U S A (2012) 0.94
New regulatory circuit controlling spatial and temporal gene expression in the sea urchin embryo oral ectoderm GRN. Dev Biol (2013) 0.94
Brn1/2/4, the predicted midgut regulator of the endo16 gene of the sea urchin embryo. Dev Biol (2005) 0.93
cis-Regulatory activity of randomly chosen genomic fragments from the sea urchin. Gene Expr Patterns (2004) 0.92
Developmental gene network analysis. Int J Dev Biol (2003) 0.92
Precise cis-regulatory control of spatial and temporal expression of the alx-1 gene in the skeletogenic lineage of s. purpuratus. Dev Biol (2011) 0.91
Confocal quantification of cis-regulatory reporter gene expression in living sea urchin. Dev Biol (2006) 0.90
Expression of AmKrox, a starfish ortholog of a sea urchin transcription factor essential for endomesodermal specification. Gene Expr Patterns (2003) 0.90
Expression of a gene encoding a Gata transcription factor during embryogenesis of the starfish Asterina miniata. Gene Expr Patterns (2003) 0.89
A new method, using cis-regulatory control, for blocking embryonic gene expression. Dev Biol (2008) 0.89
Developmental biology at the systems level. Biochim Biophys Acta (2008) 0.88
Logic of gene regulatory networks. Curr Opin Biotechnol (2007) 0.88
Regulation of spblimp1/krox1a, an alternatively transcribed isoform expressed in midgut and hindgut of the sea urchin gastrula. Gene Expr Patterns (2006) 0.86
Gene regulatory network analysis in sea urchin embryos. Methods Cell Biol (2004) 0.86
Flexibility of transcription factor target site position in conserved cis-regulatory modules. Dev Biol (2009) 0.86
Experimentally based sea urchin gene regulatory network and the causal explanation of developmental phenomenology. Wiley Interdiscip Rev Syst Biol Med (2010) 0.85