Smith Recent Publications

 

seaurchin resized

 

Tulin, S.*, Aguiar, D.*,Istrail, S.and Smith, J. A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems. Accepted for publication in EvoDevo Journal.

Helm, R. R., Siebert, S., Tulin, S., Smith, J., Dunn, C. Characterization of differential transcript abundance through time during Nematostella vectensis development.  BMC Genomics.14(1):266, 2013. http://www.ncbi.nlm.nih.gov/pubmed/23601508

Materna, S., Swartz, S. and Smith, J. Notch and Nodal control forkhead factor expression in the specification of multipotent progenitors in sea urchin. Development. 140(8):1796-806, 2013. http://www.ncbi.nlm.nih.gov/pubmed/23533178

Fischer, A. H. L. and Smith, J. Evo-devo in the era of gene regulatory networks. Integrative and Comparative Biology. Integrative and Comparative Biology, volume 52, number 6, pp. 842–849 doi:10.1093/icb/ics112, 2012. http://www.ncbi.nlm.nih.gov/pubmed/22927135

Evo-Devo GRN:

Tulin, S.*, Aguiar, D.*, Istrail, S. and Smith, J. A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems. Accepted for publication in EvoDevo Journal.

Helm, R. R., Siebert, S., Tulin, S., Smith, J., Dunn, C. Characterization of differential transcript abundance through time during Nematostella vectensis development.  BMC Genomics.14(1):266, 2013. http://www.ncbi.nlm.nih.gov/pubmed/23601508

Fischer, A. H. L. and Smith, J. Evo-devo in the era of gene regulatory networks. Integrative and Comparative Biology. Integrative and Comparative Biology, volume 52, number 6, pp. 842–849 doi:10.1093/icb/ics112, 2012. http://www.ncbi.nlm.nih.gov/pubmed/22927135

Smith, J., Morgan, J. R., Zottoli, S. J., Smith, P. J., Buxbaum, J. D., and Bloom, O. E. Regeneration in the era of functional genomics and gene network analysis. The Biological Bulletin, 221(1), 18-34, 2011. http://www.ncbi.nlm.nih.gov/pubmed/21876108

Sea Urchin Gene Networks:

Materna, S., Swartz, S. and Smith, J. Notch and Nodal control forkhead factor expression in the specification of multipotent progenitors in sea urchin. Development. 140(8):1796-806, 2013. http://www.ncbi.nlm.nih.gov/pubmed/23533178

Smith, J. and Davidson, E. Regulative recovery in the sea urchin embryo, and thestabilizing role of fail-safe gene network wiring. PNAS 106, 18291-18296, 2009. http://www.ncbi.nlm.nih.gov/pubmed/19822764

Smith, J. and Davidson, E. Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo. PNAS 105, 20089-20094, 2008. http://www.ncbi.nlm.nih.gov/pubmed/19104065

Smith, J. A protocol describing the principles of cis-regulatory analysis in the sea urchin. Nature Protocols 3, 710-718, 2008. http://www.ncbi.nlm.nih.gov/pubmed/18388954

Smith, J. and Davidson, E.  A new method for blocking embryonic gene expression using cis-regulatory control. Dev Biol. 318, 360-365, 2008. http://www.ncbi.nlm.nih.gov/pubmed/18423438

Smith, J., Kraemer, E., Liu, H.-D., Theodoris, C., and Davidson, E. A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo. Dev Biol. 313, 863-875, 2008. http://www.ncbi.nlm.nih.gov/pubmed/18061160

Smith, J., Theodoris, C., and Davidson, E. A gene regulatory network subcircuit drives a dynamic pattern of gene expression. Science 318, 794-797, 2007. http://www.ncbi.nlm.nih.gov/pubmed/17975065

Sea Urchin Genome Sequencing Consortium. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314, 941-952, 2006. http://www.ncbi.nlm.nih.gov/pubmed/17095691

Noble, M., Smith, J., Power, J., Mayer-Pröschel, M.  Redox state as a central modulator of precursor cell function. Ann N Y Acad Sci. 991, 251-271, 2003. http://www.ncbi.nlm.nih.gov/pubmed/12846992

Power, J., Mayer-Pröschel, M., Smith, J., Noble, M. Oligodendrocyte precursor cells from different brain regions express divergent properties consistent with the differing time courses of myelination in these regions. Dev Biol. 245, 362-375, 2002. http://www.ncbi.nlm.nih.gov/pubmed/11977987

Smith, J., Ladi, E., Mayer-Pröschel, M.,  and Noble, M.  Redox state is a central modulator of the balance between self-renewal and differentiation in a dividing glial precursor cell.  PNAS  97, 10032-10037, 2000. http://www.ncbi.nlm.nih.gov/pubmed/10944195