Publications 2010

Nam, J., Dong, P., Tarpine, R., istrail, S. and Davidson, E. H. Functional cis-regulatory genomics for systems biology. Proc. Natl. Acad. Sci. USA 107, 3930-3935, 2010.

Publications 2009

Davidson, E. H.  Network design principles from the sea urchin embryo.  Curr Opin.in Genetics Dev., 19, 535-540, 2009.

Davidson, E. H. and Erwin, D. H.  Evolutionary innovation and stability in animal gene networks.  J. Evol. Zool. (Mol. Dev. Evol.) 312B, in press, available online.

Erwin, D. H. and Davidson, E. H. The Evolution of hierarchical gene regulatory networks. Nature Rev. Genet. 10, 141-148, 2009.

Cameron, R. A., Samanta, M., Yuan, A., He., D. and Davidson. E. H. SpBase: the sea urchin genome database and web site. Nucl. Acids Res. 37, D750-D754, 2009.

Cameron, R. A. and Davidson, E. H.  Flexibility of transcription factor target site position in conserved cis-regulatory modules.  Dev. Biol. 336, 122-135, 2009.

Chen, J.-Y., Bottjer, D. J., Davidson, E. H., Li, G., Gao, F., Cameron, R. A., Hadfield, M.G., Xian, D.C., Tafforeau, P., Jia, Q.-J., Sugiyama, H. and Tang, R. Phase contrast synchrotron X-rya microtomography of Ediacaran (Doushantuo) metazoan microfossils: Phylogenetic diversity and evolutionary implications. Precambrian Res. 173, 191-200, 2009.

Peter, I. S. and Davidson, E. H.  The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage.  Dev. Biol., in press, available online. 2009.

Peter, I. S. and Davidson, E. H. Modularity and design principles in the sea urchin embryo gene regulatory network. FEBS Letters 583, 3948-3958, 2009.

Ben-Tabou de-Leon, S. and Davidson, E. H.  Modeling the dynamics of gene regulatory networks.  Dev. Biol. 325, 317-328, 2009.

Davidson, E. H.  Developmental biology at the systems level.  Biochim. Biophys. Acta Gene Regulatory Mech. 1789, 248-249, 2009.

Longabaugh, W. J. R., Davidson, E. H. and Bolouri, H. Visualization, documentation, analysis, and communication of large scale gene regulatory networks.  Biochim. Biophys. Acta Gene Regulatory Mech. 1789, 363-374, 2009.

Su, Y.-H., Li, E., Geiss, G. K., Longabaugh, W. J. R., Krämer, A. and Davidson, E. H.  A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo.  Dev. Biol. 329, 410-421, 2009.

Peter, I. and Davidson, E. H.  Genomic control of patterning.  Int. J. Dev. Biol. 53, 707-716, 2009.

Li, E. and Davidson, E. H.  Building developmental gene regulatory networks.  Birth Defects Res.(Part C) 87, 123-130, 2009.

Bolouri, H. and Davidson, E. H.  The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example.  Dev. Biol., in press, available online.

Ben-Tabou de-Leon, S. and Davidson, E. H.  Experimentally based sea urchin gene regulatory network and the causal explanation of developmental phenomenology.  Wiley Interdisciplinary Reviews:  Systems Biol. & Med. 1, 237-246, 2009.

Wahl, M. E., Hahn, J., Gora, K., Davidson, E. H. and Oliveri, P.  The cis-regulatory system of the tbrain gene:  Alternative use of multiple modules to promote skeletogenic expression in the sea urchin embryo.  Dev. Biol. 335,  428-441, 2009.

Smith, J. and Davidson, E. H.  Regulative recovery in the sea urchin embryo, and the stabilizing role of fail-safe gene network wiring.  Proc. Natl, Acad. Sci. USA 106, 18291-18296 2009.