Publications 2009-2008

Davidson, E. H.  Network design principles from the sea urchin embryo.  Curr Opin.in Genetics Dev., in press, available online. 2009

Davidson, E. H. and Erwin, D. H.  Evolutionary innovation and stability in animal gene networks.  J. Evol. Zool., in press. 2009

Cameron, R. A. and Davidson, E. H.  Flexibility of transcription factor target site position in conserved cis-regulatory modules.  Dev. Biol., in press, available online. 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, in press.

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, 18291-18296 2009.

Publications 2008

Laubichler, M. D. and Davidson, E. H.  Boveri's long experiment:  Sea urchin merogones and the establishment of the role of nuclear chromosomes in development.  Dev. Biol. 314, 1-11, 2008.

Geiss, G. K., Bumgarner, R. E., Birditt, B., Dahl, T., Dowidar, N., Dunaway, D. L., Fell, H. P., Ferree, S., George, R. D., Grogan, T., James, J. J., Maysuria, M., Mitton, J. D., Oliveri, P., Osborn, J. L., Peng, T., Ratcliffe, A. L., Webster, P. J., Davidson, E. H. and Hood, L.  Direct multiplexed measurement of gene expression with color-coded probe pairs.  Nature Biotechnol. 26, 317-325, 2008. 

Smith, J., Kraemer, E., Liu, H., Theodoris, C. and Davidson, E. H.  A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo.  Dev. Biol. 313, 863-875, 2008.

Oliveri, P., Tu, Q. and Davidson, E. H.  Global regulatory logic for specification of an embryonic cell lineage.  Proc. Natl. Acad. Sci. USA 105, 5955-5962, 2008.

Gao, F. and Davidson, E. H.  Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution.  Proc. Natl. Acad. Sci. USA 105, 6091-6096, 2008.

Smith, J. and Davidson, E. H.  A new method, using cis-regulatory control, for blocking embryonic gene expression.  Dev. Biol. 318, 360-365, 2008.

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.

Smith, J. and Davidson, E. H.  Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo.  Proc. Natl. Acad. Sci. USA, 105, 20089-20094, 2008.

Davidson, E. H. and Levine, M.  Properties of developmental gene regulatory networks.  Proc. Natl. Acad. Sci. USA, 105, 20063-20066, 2008.

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.