James Coffman


B.A., Carleton College, 1981; Ph.D., Duke University 1990

Research Interests

I am interested in how the phenotypic characteristics of an organism come to exist developmentally, via the interplay between the genomically-encoded information, cell physiology, and the environment, and how development contributes to aging and constrains phenotypic plasticity and regenerative capacity over an organism’s lifespan. My laboratory uses zebrafish and sea urchins as model systems to address these questions, because their embryos are highly accessible to experimental manipulation at many different levels, and their genomes have been sequenced and annotated.

Selected Publications

  • Cortisol-treated zebrafish embryos develop into pro-inflammatory adults with aberrant immune gene regulation. Hartig, E.I., Zhu, S., King, B.L, and Coffman, J.A. (2016). Biology Open, 5: 1134-1141.
  • An Elk transcription factor is required for Runx-dependent survival signaling in the sea urchin embryo. Rizzo, F., Coffman, J.A., and Arnone, M.I. (2016). Dev. Biol., 416: 173-186.
  • Maintenance of somatic tissue regeneration with age in short- and long-lived species of sea urchins. Bodnar, A.G. and Coffman, J.A.(2016). Aging Cell, 15: 778-787.
  • Comparative biology of tissue repair, regeneration, and aging. Coffman, J.A., Rieger, S., Rogers, A.N., Updike, D.L, and Yin, V.P. (2016). npj Regen. Med., 1: 16003.
  • Developmental control of transcriptional and proliferative potency during the evolutionary emergence of animals. Arenas-Mena, C. and Coffman, J.A. (2015). Dev. Dyn., 244: 1193-1201.
  • Gene expression changes associated with the developmental plasticity of sea urchin larvae in response to food availability. Carrier, T.J., King, B.L., and Coffman, J.A. (2015). Biological Bulletin, 228: 171-180.
  • Oral-aboral axis specification in the sea urchin embryo IV. Hypoxia radializes embryos by preventing the initial spatialization of nodal activity. Coffman, J.A., Wessels, A., DeSchiffart, C., and Rydlizky, K. (2014). Dev. Biol. 386: 302-307.
  • On the meaning of chance in biology. Coffman, J.A. (2014). Biosemiotics 7: 377-388.
  • Developmental cis-regulatory analysis of the cyclin D gene in the sea urchin Strongylocentrotus purpuratus. McCarty, C.M., and Coffman, J.A. (2013). Biochem. Biophys. Research Comm. 440: 413-418.
  • Sea urchin akt activity is Runx-dependent and required for post-cleavage stage cell division. Robertson, A.J., Coluccio, A., Jensen, S., Rydlizky, K., and Coffman, J.A. (2013). Biology Open, 2: 472-478.
  • Global Insanity: How Homo sapiens Lost Touch with Reality while Transforming the World. Coffman, J.A. and Mikulecky, D.C. (2012). Emergent Publications (ISBN 9781938158049).
  • Nodal-mediated epigenesis requires dynamin-mediated endocytosis. Ertl, R.P., Robertson, A.J., Saunders, D., and Coffman, J.A. (2011). Dev. Dyn. 240: 704-711.
  • Oxygen, pH, and oral-aboral axis specification in the sea urchin embryo. Coluccio, A.E., LaCasse, T.J., and Coffman, J.A. (2011). Mol. Rep. & Dev. 78: 68.
  • Information as a manifestation of development. Coffman, J.A. (2011). Information 2 (1): 102-116.
  • The evolution of Runx genes. II. The C-terminal Groucho recruitment motif is present in both eumetazoans and homoscleromorphs but absent in a haplosclerid demosponge. Robertson, A.J., Larroux, C., Degnan, B.M., and Coffman, J.A. (2009). BMC Research Notes 2: 59.
  • Oral-aboral axis specification in the sea urchin embryo III. Role of mitochondrial redox signaling via H2O2. Coffman, J.A., Coluccio, A., Planchart, A., and Robertson, A.J. (2009). Dev. Biol. 330: 123-130.
  • Is Runx a linchpin for developmental signaling in metazoans? Coffman, J.A. (2009). J. Cellular Biochem. 107: 194-202.
  • Mitochondria and metazoan epigenesis. Coffman, J.A. (2009). Semin. Cell Dev. Biol. 20: 321-329.
  • Runx expression is mitogenic and mutually linked to wnt activity in blastula-stage sea urchin embryos. Robertson, A.J., Coluccio, A., Knowlton, P., Dickey-Sims, C., and Coffman, J.A. (2008). PLoS One. 3: 11.
  • Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Nam, J., Su, Y.-H., Lee, P.Y., Robertson A. J., Coffman, J. A., and Davidson, E.H. (2007). Dev. Biol. 306: 860-869.
  • Mitochondria, redox signaling, and axis specification in metazoan embryos. Coffman, J.A. and Denegre, J.M. (2007). Dev. Biol. 308: 266-280.
  • CBFbeta is a facultative Runx partner in the sea urchin embryo. Robertson, A.J., Dickey-Sims, C., Ransick, A., Rupp, D.E., McCarthy, J.J., and Coffman, J.A. (2006). BMC Biol. 4: 4.
  • The genome of the sea urchin Strongylocentrotus purpuratus. Sodergren E., Weinstock G. M., Davidson E. H., Cameron R. A., Gibbs R. A., Angerer R. C., Angerer L. M., Arnone M. I., Burgess D. R., Burke R. D., Coffman J.A., et al. (The Sea Urchin Genome Sequencing Consortium) (2006). Science. 314: 941-952.
  • The sea urchin kinome: a first look. Bradham, C.A., Beane, W.S., Arnone, M.I., Rizzo, F., Coffman, J.A., Mushegian, A., Goel, M., Morales, J., Geneviere, A-M., Lapraz, F., Robertson, A.J., Kelkar, H., Loza-Coll, M., Townley, I.R., Raisch, M., Roux, M.M., Lepage, T., Gache, C., McClay, D.R., and Foltz, K.R. (2006). Dev. Biol. 300: 180-193.
  • Protein tyrosine and ser-thr phosphatases in the sea urchin, Strongylocentrotus purpuratus: identification and potential functions. Byrum, C.A., Walton, K., Robertson, A.J., Carbonneau, S., Thomason, R., Bradham, C.A., Coffman, J.A., and McClay, D.R. (2006). Dev. Biol. 300: 194-218.
  • The genomic repertoire for cell cycle control and DNA metabolism in S. purpuratus. Fernandez-Guerra, A., Aze, A., Morales, J., Mulner-Lorillon, O., Cosson, B., Cormier, P., Bradham, C., Adams, N., Robertson, A.J., Marzluff, W.F., Coffman, J.A., and Genevière, A.M. (2006). Dev. Biol. 300: 238-251.
  • The genomic underpinnings of apoptosis in Strongylocentrotus purpuratus. Robertson, A.J., Croce, J., Carbonneau, S., Voronina, E., Miranda, E., McClay, D.R. and Coffman, J.A. (2006). Dev. Biol. 300: 321-334.
  • Developmental ascendency: from bottom-up to top-down control. Coffman, J.A. (2006). Biological Theory 1 (2):165-178.
  • Sea urchin vault structure, composition, and differential localization during development. Stewart, P.L., Makabi, M., Lang, J., Dickey-Sims, C., Robertson, A.J., Coffman, J.A., and Suprenant, K.A. (2005). BMC Dev. Biol. 5: 3.
  • Runx-dependent expression of PKC is critical for cell survival in the sea urchin embryo. Dickey-Sims, C., Robertson, A.J., Rupp, D.E., McCarthy, J.J., and Coffman, J.A. (2005). BMC Biol. 3: 18.
  • Evaluation of developmental phenotypes produced by morpholino antisense targeting of a sea urchin Runx gene. Coffman, J.A., Dickey-Sims, C., Haug, J.S., McCarthy, J.J., and Robertson, A.J. (2004). BMC Biol. 2: 6.
  • Oral-aboral axis specification in the sea urchin embryo. II. Mitochondrial distribution and redox state contribute to establishing polarity in Strongylocentrotus purpuratus. Coffman, J.A., McCarthy, J.J., Dickey-Sims, C., and Robertson, A.J. (2004). Dev. Biol. 273: 160-171.
  • Cell cycle development. Coffman, J.A. (2004). Dev. Cell 6: 321-327.
  • The evolution of Runx genes. I. A comparative study of sequences from phylogenetically diverse model organisms. Rennert, J., Coffman, J.A., Mushegian, A.R., and Robertson, A.J. (2003). BMC Evol. Biol. 3: 4.
  • Runx transcription factors and the developmental balance between cell proliferation and differentiation. Coffman, J.A. (2003). Cell Biol. Int. 27: 315-324.
  • The expression of SpRunt during sea urchin embryogenesis. Robertson, AJ., Dickey, C.E., McCarthy, J.J., and Coffman, J.A. (2002). Mech. Dev. 117: 327-330.
  • Oral-aboral axis specification in the sea urchin embryo. I. Axis entrainment by respiratory asymmetry. Coffman, J.A., and Davidson, E.H. (2001). Dev. Biol. 230: 18-28. (Cover Photo)


Manuscript reviewer for Development, Developmental Biology, Mechanisms of Development,Developmental Dynamics, Development Growth & Differentiation, Molecular Reproduction & Development, Biology Open, PNAS, PLoS Genetics, Antioxidants & Redox Signaling, Journal of Experimental Biology, BioEssays, Birth Defects Research A, Mol. & Cell. Endocrinology, Mol. Biol. & Evol., Nuc. Acids Res., Comp. Biochem. & Phys., Intl. J. Dev. Biol., Intl. J. Cancer, BMC Mol. Biol.,Acta Biotheoretica, Proc. Royal Society: Biol. Sci., Biol. Bulletin, FEBS Lett., Exp. Cell Res., Genome Biol., In Vitro Cell. & Dev. Biol. – Animal, Nature Protocols, WIREs Dev. Biol., Zool. Science, J. Cell. Biochem., and Encyclopedia of Life Sciences

Grant reviewer for the National Science Foundation (USA), Breast Cancer Campaign (UK), Association for International Cancer Research (UK), Bi-national Science Foundation (Israel-USA), Israel Science Foundation (Israel), and Biomedical Research Council (Singapore)

Community Service

  • 2001 to 2001 — Sea Urchin Genome Advisory Group
  • 2002 to 2002 — Co-organizer, Developmental Biology of the Sea Urchin XIV Conference
  • 2005 to 2006 — Coordinator, Sea Urchin Genome Annotation Consortium
  • 2005 to 2005 — NSF Developmental Systems (Animal and Evolution) Advisory Panel
  • 2005 to 2005 — NIH NCI P01 Cluster Review, Genomic Instability Special Emphasis Panel
  • 2006 to 2007 — NIH Neurogenesis and Cell Fate Study Section
  • 2007 to 2007 — NIH NICHD Initial Review Group, Developmental Biology Subcommittee
  • 2009 to 2009 — NIH ZRG1-BDA-M (95) S Review, Special Emphasis Panel
  • 2009 to 2009 — NIH NIEHS Superfund Basic Research Program (P42) Review Panel
  • 2009 to 2011 — NIH DEV-1 Study Section (Ad Hoc)
  • 2011 — Sea Urchin Genome Resource Advisory Committee

Dissertation Students

James Coffman