Publications 2007-2008

 

Livi, C. B. and Davidson, E. H.  Regulation of spblimp1/krox1a, an alternatively transcribed isoform expressed in midgut and hindgut of the sea urchin gastrula.  Gene Exp. Patterns 7, 1-7, 2007.

Ben-Tabou de-Leon, S. and Davidson, E. H.  Gene regulation:  Gene control network in development.  Ann. Rev. Biophys. Biomol. Struct. 36, 191-212, 2007. 

Oliveri, P. and Davidson, E. H.  Built to run, not fail.  Science 315, 1510-1511, 2007. 

Nam, J., Su, Y.-H., Lee, P. Y., Robertson, A. J., Coffman, J. A. and Davidson, E. H.  cis-Regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network.  Dev. Biol. 306, 860-869, 2007.

Lee, P. Y., Nam, J. and Davidson, E. H.  Exclusive developmental functions of gatae cis-regulatory modules in the Strongylocentrotus purpuratus embryo.  Dev. Biol. 307, 434-445, 2007.

Vokes, S. A., Ji, H. K., McCuine, S., Tenzen, T., Giles, S., Zhong, S., Longabaugh, W. J. R., Davidson, E. H., Wong, W. H. and McMahon, A. P.  Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning.  Development 134, 1977-1989, 2007.

Revilla-i-Domingo, R., Oliveri, P. and Davidson, E. H.  A missing link in the sea urchin embryo gene regulatory network:  hesC and the double-negative specification of micromeres.  Proc. Natl. Acad. Sci. USA 104, 12383-12388, 2007.  PMCID:  PMC 1941478.

Istrail, S., Ben-Tabou De-Leon, S. and Davidson, E. H.  The regulatory genome and the computer.  Dev. Biol. 310, 187-195, 2007. 

Cameron, C. R. and Davidson, E. H.  A basal deuterostome genome viewed as a natural experiment.  Gene 406, 1-7, 2007.

Materna, S. C. and Davidson, E. H. Logic of gene regulatory networks.  Curr. Opin. Biotechnol. 18, 351-354, 2007.

Hinman, V. F., Nguyen, A. and Davidson, E. H. Caught in the evolutionary act: precise cis-regulatory basis of difference in organization of gene networks of sea stars and sea urchins.  Dev. Biol. 312, 584-595, 2007.

Smith, J., Theodoris, C. and Davidson, E. H.  A gene regulatory network subcircuit drives a dynamic pattern of gene expression.  Science 318, 794-797, 2007. 

Hinman, V. F. and Davidson, E. H.  Evolutionary plasticity of developmental gene regulatory network architecture.  Proc. Natl. Acad. Sci. USA 104, 19404-19409, 2007.

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, in press.

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, in press.

Davidson, E. H. and Levine, M.  Properties of developmental gene regulatory networks.  Proc. Natl. Acad. Sci. USA, in press.

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