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Activation of pmar1 controls specification of micromeres in the sea urchin embryo. , Oliveri P , Davidson EH , McClay DR ., Dev Biol. June 1, 2003; 258 (1): 32-43.
Spdeadringer, a sea urchin embryo gene required separately in skeletogenic and oral ectoderm gene regulatory networks. , Amore G, Yavrouian RG, Peterson KJ, Ransick A, McClay DR , Davidson EH ., Dev Biol. September 1, 2003; 261 (1): 55-81.
Developmental gene regulatory network architecture across 500 million years of echinoderm evolution. , Hinman VF , Nguyen AT, Cameron RA , Davidson EH ., Proc Natl Acad Sci U S A. November 11, 2003; 100 (23): 13356-61.
Gene regulatory network analysis in sea urchin embryos. , Oliveri P , Davidson EH ., Methods Cell Biol. January 1, 2004; 74 775-94.
An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network. , Yuh CH, Dorman ER, Howard ML, Davidson EH ., Dev Biol. May 15, 2004; 269 (2): 536-51.
A genetic regulatory network for Xenopus mesendoderm formation. , Loose M, Patient R., Dev Biol. July 15, 2004; 271 (2): 467-78.
SpHnf6, a transcription factor that executes multiple functions in sea urchin embryogenesis. , Otim O, Amore G, Minokawa T , McClay DR , Davidson EH ., Dev Biol. September 15, 2004; 273 (2): 226-43.
R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres. , Revilla-i-Domingo R, Minokawa T , Davidson EH ., Dev Biol. October 15, 2004; 274 (2): 438-51.
A systems biology approach to developmental toxicology. , Cummings A, Kavlock R., Reprod Toxicol. January 1, 2005; 19 (3): 281-90.
LvGroucho and nuclear beta- catenin functionally compete for Tcf binding to influence activation of the endomesoderm gene regulatory network in the sea urchin embryo. , Range RC , Venuti JM, McClay DR ., Dev Biol. March 1, 2005; 279 (1): 252-67.
Endomesoderm specification in Caenorhabditis elegans and other nematodes. , Maduro MF., Bioessays. October 1, 2006; 28 (10): 1010-22.
The Snail repressor is required for PMC ingression in the sea urchin embryo. , Wu SY, McClay DR ., Development. March 1, 2007; 134 (6): 1061-70.
Gene regulatory networks and developmental plasticity in the early sea urchin embryo: alternative deployment of the skeletogenic gene regulatory network. , Ettensohn CA , Kitazawa C, Cheers MS, Leonard JD, Sharma T., Development. September 1, 2007; 134 (17): 3077-87.
A gene regulatory network subcircuit drives a dynamic pattern of gene expression. , Smith J, Theodoris C, Davidson EH ., Science. November 2, 2007; 318 (5851): 794-7.
Evolutionary plasticity of developmental gene regulatory network architecture. , Hinman VF , Davidson EH ., Proc Natl Acad Sci U S A. December 4, 2007; 104 (49): 19404-9.
Caught in the evolutionary act: precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins. , Hinman VF , Nguyen A, Davidson EH ., Dev Biol. December 15, 2007; 312 (2): 584-95.
A protocol for unraveling gene regulatory networks. , Materna SC, Oliveri P ., Nat Protoc. January 1, 2008; 3 (12): 1876-87.
Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution. , Gao F, Davidson EH ., Proc Natl Acad Sci U S A. April 22, 2008; 105 (16): 6091-6.
Global regulatory logic for specification of an embryonic cell lineage. , Oliveri P , Tu Q, Davidson EH ., Proc Natl Acad Sci U S A. April 22, 2008; 105 (16): 5955-62.
Twist is an essential regulator of the skeletogenic gene regulatory network in the sea urchin embryo. , Wu SY, Yang YP, McClay DR ., Dev Biol. July 15, 2008; 319 (2): 406-15.
Lessons from a gene regulatory network: echinoderm skeletogenesis provides insights into evolution, plasticity and morphogenesis. , Ettensohn CA ., Development. January 1, 2009; 136 (1): 11-21.
Genomic control of patterning. , Peter IS , Davidson EH ., Int J Dev Biol. January 1, 2009; 53 (5-6): 707-16.
Gene regulatory network interactions in sea urchin endomesoderm induction. , Sethi AJ, Angerer RC , Angerer LM ., PLoS Biol. February 3, 2009; 7 (2): e1000029.
Evolution of gene regulatory network architectures: examples of subcircuit conservation and plasticity between classes of echinoderms. , Hinman VF , Yankura KA, McCauley BS., Biochim Biophys Acta. April 1, 2009; 1789 (4): 326-32.
Gene regulatory networks for ectoderm specification in sea urchin embryos. , Su YH ., Biochim Biophys Acta. April 1, 2009; 1789 (4): 261-7.
A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. , Su YH , Li E, Geiss GK, Longabaugh WJ, Krämer A, Davidson EH ., Dev Biol. May 15, 2009; 329 (2): 410-21.
Building developmental gene regulatory networks. , Li E, Davidson EH ., Birth Defects Res C Embryo Today. June 1, 2009; 87 (2): 123-30.
Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. , Kühn C, Wierling C, Kühn A, Klipp E, Panopoulou G, Lehrach H, Poustka AJ., BMC Syst Biol. August 23, 2009; 3 83.
Modularity and design principles in the sea urchin embryo gene regulatory network. , Peter IS , Davidson EH ., FEBS Lett. December 17, 2009; 583 (24): 3948-58.
Practical computational methods for regulatory genomics: a cisGRN-Lexicon and cisGRN-browser for gene regulatory networks. , Istrail S, Tarpine R, Schutter K, Aguiar D., Methods Mol Biol. January 1, 2010; 674 369-99.
Functional cis-regulatory genomics for systems biology. , Nam J , Dong P, Tarpine R, Istrail S, Davidson EH ., Proc Natl Acad Sci U S A. February 23, 2010; 107 (8): 3930-5.
Activation of the skeletogenic gene regulatory network in the early sea urchin embryo. , Sharma T, Ettensohn CA ., Development. April 1, 2010; 137 (7): 1149-57.
The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example. , Bolouri H, Davidson EH ., Dev Biol. April 15, 2010; 340 (2): 170-8.
The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage. , Peter IS , Davidson EH ., Dev Biol. April 15, 2010; 340 (2): 188-99.
A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos. , McCauley BS, Weideman EP, Hinman VF ., Dev Biol. April 15, 2010; 340 (2): 200-8.
Cis-regulatory analysis of the sea urchin pigment cell gene polyketide synthase. , Calestani C , Rogers DJ., Dev Biol. April 15, 2010; 340 (2): 249-55.
Information processing at the foxa node of the sea urchin endomesoderm specification network. , de-Leon SB , Davidson EH ., Proc Natl Acad Sci U S A. June 1, 2010; 107 (22): 10103-8.
Conserved early expression patterns of micromere specification genes in two echinoid species belonging to the orders clypeasteroida and echinoida. , Yamazaki A, Furuzawa Y, Yamaguchi M., Dev Dyn. December 1, 2010; 239 (12): 3391-403.
Ancestral regulatory circuits governing ectoderm patterning downstream of Nodal and BMP2/4 revealed by gene regulatory network analysis in an echinoderm. , Saudemont A, Haillot E, Mekpoh F, Bessodes N, Quirin M, Lapraz F, Duboc V, Röttinger E, Range R , Oisel A, Besnardeau L, Wincker P, Lepage T ., PLoS Genet. December 23, 2010; 6 (12): e1001259.
The dynamic gene expression patterns of transcription factors constituting the sea urchin aboral ectoderm gene regulatory network. , Chen JH, Luo YJ, Su YH ., Dev Dyn. January 1, 2011; 240 (1): 250-60.
The control of foxN2/3 expression in sea urchin embryos and its function in the skeletogenic gene regulatory network. , Rho HK, McClay DR ., Development. March 1, 2011; 138 (5): 937-45.
Regulative deployment of the skeletogenic gene regulatory network during sea urchin development. , Sharma T, Ettensohn CA ., Development. June 1, 2011; 138 (12): 2581-90.
Wnt6 activates endoderm in the sea urchin gene regulatory network. , Croce J , Range R , Wu SY, Miranda E, Lhomond G, Peng JC, Lepage T , McClay DR ., Development. August 1, 2011; 138 (15): 3297-306.
Precise cis-regulatory control of spatial and temporal expression of the alx-1 gene in the skeletogenic lineage of s. purpuratus. , Damle S, Davidson EH ., Dev Biol. September 15, 2011; 357 (2): 505-17.
Synthetic in vivo validation of gene network circuitry. , Damle SS, Davidson EH ., Proc Natl Acad Sci U S A. January 31, 2012; 109 (5): 1548-53.
The genomic regulatory control of skeletal morphogenesis in the sea urchin. , Rafiq K, Cheers MS, Ettensohn CA ., Development. February 1, 2012; 139 (3): 579-90.
Cis-regulatory logic driving glial cells missing: self-sustaining circuitry in later embryogenesis. , Ransick A, Davidson EH ., Dev Biol. April 15, 2012; 364 (2): 259-67.
Early developmental gene regulation in Strongylocentrotus purpuratus embryos in response to elevated CO₂ seawater conditions. , Hammond LM, Hofmann GE., J Exp Biol. July 15, 2012; 215 (Pt 14): 2445-54.
Predictive computation of genomic logic processing functions in embryonic development. , Peter IS , Faure E, Davidson EH ., Proc Natl Acad Sci U S A. October 9, 2012; 109 (41): 16434-42.
Networking development by Boolean logic. , Tu S, Pederson T, Weng Z., Nucleus. January 1, 2013; 4 (2): 89-91.