James A. Coffman, Ph.D.

Other Research Activities

In addition to his experimental research, Dr. Coffman is interested in theoretical approaches to the problem of biological development and evolution from the perspective of complex systems, and he has published numerous papers and one book on that subject. He also directs the Maine IDeA Network of Biomedical Research Excellence (INBRE) in Comparative Functional Genomics, a statewide collaborative network of 14 academic and research institutions, led by the MDI Biological Laboratory and funded by the National Institute of General Medical Sciences of the NIH. The overarching goal of the Maine INBRE is to strengthen biomedical research and research infrastructure in the state of Maine, by providing biomedical research resources, funding, mentorship and training to undergraduates, post-graduates, and faculty.

News Articles

• 2022 MDI Biological Laboratory Publications Blog · January 13, 2023
• Breaking Through: Creating a Center of Biomedical Research Excellence Publication · Fall 2022
• MDI researchers win NIH grants Mount Desert Islander · April 17, 2022
• MDI Biological Laboratory Researchers Win R21 Grants From the National Institutes of Health Press Release · April 1, 2022
• The Maine INBRE in its 22nd Year – Looking Back and Ahead Blog · April 1, 2022
• Courses Already in Full Swing for 2022 Blog · April 1, 2022
• Novel research clarifies new key player in the body’s response to stress Press Release · January 28, 2022
• MDI Biological Laboratory awarded grant to advance cloud computing in Maine Bangor Daily News · December 15, 2021
• MDI Biological Laboratory researching ‘stress gene’ Fox 22 WFVX Bangor · September 29, 2020
• MDI Biological Laboratory Scientists Decipher Role of a Stress Response Gene Press Release · September 9, 2020

Publications

• Glucocorticoid-mediated developmental programming of vertebrate stress responsivity. Gans, I.M. and Coffman, J.A. (2021). Frontiers in Physiology, 12: 812195.
• Glucocorticoid-responsive transcription factor Krüppel-like factor 9 regulates fkbp5 and metabolism. Gans I.M., Grendler J., Babich R., Jayasundara N., Coffman J.A. (2021). Frontiers in Cell and Developmental Biology 9. 
• Chronic cortisol exposure in early development leads to neuroendocrine dysregulation in adulthood. Hartig E.I., Zhu S., King B.L., Coffman J.A. (2020). BMC Research Notes 13(1).
• Klf9 is a key feedforward regulator of the transcriptomic response to glucocorticoid receptor activity. Gans I, Hartig EI, Zhu S, Tilden AR, Hutchins LN, Maki NJ, Graber JH, Coffman J.A. (2020). Scientific Reports 10(1).
• Chronic stress, physiological adaptation, and developmental programming of the neuroendocrine stress system. Coffman, J.A. (2020). Future Neurology 15 (1).
• Redox regulation of development and regeneration. Coffman J.A, Su YH. (2019). Current Opinion in Genetics & Development 57.
• Why functional genomics is the central concern of biology and the hard problem of abiogenesis. Coffman, J.A. (2019). Proceedings in Complexity.
• Regenerative potential across species: an eco-evo-devo perspective. Coffman, J.A. (2019). Epigenetics and Regeneration.
• Simple and fast quantification of DNA damage by real-time PCR, and its application to nuclear and mitochondrial DNA from multiple tissues of aging zebrafish. Zhu S., Coffman J.A. (2017). BMC Research Notes 10(1).
• Cortisol-treated zebrafish embryos develop into pro-inflammatory adults with aberrant immune gene regulation. Hartig E.I., Zhu S., King B.L., Coffman J.A. (2016) Biology Open 5(8).
• An Elk transcription factor is required for Runx-dependent survival signaling in the sea urchin embryo. Rizzo F, Coffman J.A, Arnone MI. (2016) Developmental Biology 416 (1).
• Comparative biology of tissue repair, regeneration, and aging. Coffman, J.A., Rieger, S., Rogers, A.N., Updike, D.L, and Yin, V.P. (2016). Regenerative Medicine 1.
• Maintenance of somatic tissue regeneration with age in short- and long-lived species of sea urchins. Bodnar A.G., Coffman J.A. (2016). Aging Cell 15 (4).
• Developmental control of transcriptional and proliferative potency during the evolutionary emergence of animals. Arenas-Mena C., Coffman J.A. (2015). Developmental Dynamics 244 (10).
• Gene Expression Changes Associated With the Developmental Plasticity of Sea Urchin Larvae in Response to Food Availability. Carrier T.J., King B.L., Coffman J.A. (2015). The Biological Bulletin 228 (3).
• Global Insanity redux. Coffman, J.A. and Mikulecky, D.C. (2015). Cosmos & History, 11 (1): 1-14.
• On the meaning of chance in biology. Coffman, J.A. (2014). Biosemiotics 7 (3).
• 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., Rydlizky K. (2014). Developmental Biology 386 (2).
• Developmental cis-regulatory analysis of the cyclin D gene in the sea urchin Strongylocentrotus purpuratus. McCarty C.M., Coffman J.A. (2013). Biochemical and Biophysical Research Communications 440(3).
• Sea urchin akt activity is Runx-dependent and required for post-cleavage stage cell division. Robertson A.J., Coluccio A., Jensen S., Rydlizky K., Coffman J.A. (2013). Biology Open 2 (5).
• Global Insanity: How Homo sapiens Lost Touch with Reality while Transforming the World. Coffman, J.A. and Mikulecky, D.C. (2012). Emergent Publications.
• Nodal-mediated epigenesis requires dynamin-mediated endocytosis. Ertl R.P., Robertson A.J., Saunders D., Coffman J.A. (2011). Developmental Dynamics 240 (3).
• Oxygen, pH, and oral-aboral axis specification in the sea urchin embryo. Coluccio A.E., LaCasse T.J., Coffman J.A. (2011). Molecular Reproduction and Development 78 (2).
• Mitochondria and metazoan epigenesis. Coffman J.A. (2009). Seminars in Cell and Developmental Biology 20 (3).
• Mitochondrial patterns and function in animal development. Coffman J.A. (2009). Seminars in Cell and Developmental Biology 20 (3).
• Information as a manifestation of development. Coffman, J.A. (2011). Information 2 (1). (In the Special Issue “What is Information?”)
• On causality in non-linear complex systems: the developmentalist perspective. Coffman, J.A. (2011). In: Philosophy of Complex Systems (Cliff Hooker, ed.): pp. 287-309. North Holland/Elsevier, Oxford, UK (ISBN 9780444520760).
• 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., 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., Robertson A.J. (2009). Developmental Biology 330 (1).
• Is Runx a linchpin for developmental signaling in metazoans? Coffman J.A. (2009). Journal of Cellular Biochemistry 107 (2).
• 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., Coffman J.A. (2008). PLoS One. 3 (11).
• Mitochondria, redox signaling and axis specification in metazoan embryos. Coffman J.A., Denegre J.M. (2007). Developmental Biology 308 (2).
• 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., Davidson E.H. (2007). Developmental Biology 306 (2).
• 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., Genevière A.M. (2006). Developmental Biology 300 (1).
• The sea urchin kinome: a first look. Bradham C.A., Foltz K.R., Beane W.S., Arnone M.I., Rizzo F., Coffman J.A., Mushegian A., Goel M., Morales J., Genevière A.M., Lapraz F., Robertson A.J., Kelkar H., Loza-Coll M., Townley I.K., Raisch M., Roux M.M., Lepage T., Gache C., McClay D.R., Manning G. (2006). Developmental Biology 300 (1).
• The genomic underpinnings of apoptosis in Strongylocentrotus purpuratus. Robertson A.J., Croce J., Carbonneau S., Voronina E., Miranda E., McClay D.R., Coffman J.A. (2006). Developmental Biology 300 (1).
• The genome of the sea urchin Strongylocentrotus purpuratus. Sea Urchin Genome Sequencing Consortium, 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., Dean M., Elphick M.R., Ettensohn C.A., Foltz K.R., Hamdoun A., Hynes R.O., Klein W.H., Marzluff W., McClay D.R., Morris R.L., Mushegian A., Rast J.P., Smith L.C., Thorndyke M.C., Vacquier V.D., Wessel G.M., Wray G., Zhang L., Elsik C.G., Ermolaeva O., Hlavina W., Hofmann G., Kitts P., Landrum M.J., Mackey A.J., Maglott D., Panopoulou G., Poustka A.J., Pruitt K., Sapojnikov V., Song X., Souvorov A., Solovyev V., Wei Z., Whittaker C.A., Worley K., Durbin K.J., Shen Y., Fedrigo O., Garfield D., Haygood R., Primus A., Satija R., Severson T., Gonzalez-Garay M.L., Jackson A.R., Milosavljevic A., Tong M., Killian C.E., Livingston B.T., Wilt F.H., Adams N., Bellé R., Carbonneau S., Cheung R., Cormier P., Cosson B., Croce J., Fernandez-Guerra A., Genevière A.M., Goel M., Kelkar H., Morales J., Mulner-Lorillon O., Robertson A.J., Goldstone J.V., Cole B., Epel D., Gold B., Hahn M.E., Howard-Ashby M., Scally M., Stegeman J.J., Allgood E.L., Cool J., Judkins K.M., McCafferty S.S., Musante A.M., Obar R.A., Rawson A.P., Rossetti B.J., Gibbons I.R., Hoffman M.P., Leone A., Istrail S., Materna S.C., Samanta M.P., Stolc V., Tongprasit W., Tu Q., Bergeron K.F., Brandhorst B.P., Whittle J., Berney K., Bottjer D.J., Calestani C., Peterson K., Chow E., Yuan Q.A., Elhaik E., Graur D., Reese J.T., Bosdet I., Heesun S., Marra M.A., Schein J., Anderson M.K., Brockton V., Buckley K.M., Cohen A.H., Fugmann S.D., Hibino T., Loza-Coll M., Majeske A.J., Messier C., Nair S.V., Pancer Z., Terwilliger D.P., Agca C., Arboleda E., Chen N., Churcher A.M., Hallböök F., Humphrey G.W., Idris M.M., Kiyama T., Liang S., Mellott D., Mu X., Murray G., Olinski R.P., Raible F., Rowe M., Taylor J.S., Tessmar-Raible K., Wang D., Wilson K.H., Yaguchi S., Gaasterland T., Galindo B.E., Gunaratne H.J., Juliano C., Kinukawa M., Moy G.W., Neill A.T., Nomura M., Raisch M., Reade A., Roux M.M., Song J.L., Su Y.H., Townley I.K., Voronina E., Wong J.L., Amore G., Branno M., Brown E.R., Cavalieri V., Duboc V., Duloquin L., Flytzanis C., Gache C., Lapraz F., Lepage T., Locascio A., Martinez P., Matassi G., Matranga V., Range R., Rizzo F., Röttinger E., Beane W., Bradham C., Byrum C., Glenn T., Hussain S., Manning G., Miranda E., Thomason R., Walton K., Wikramanayke A., Wu S.Y., Xu R., Brown C.T., Chen L., Gray R.F., Lee P.Y., Nam J., Oliveri P., Smith J., Muzny D., Bell S., Chacko J., Cree A., Curry S., Davis C., Dinh H., Dugan-Rocha S., Fowler J., Gill R., Hamilton C., Hernandez J., Hines S., Hume J., Jackson L., Jolivet A., Kovar C., Lee S., Lewis L., Miner G., Morgan M., Nazareth L.V., Okwuonu G., Parker D., Pu L.L., Thorn R., Wright R. (2006). Science 314 (5801).
• 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., Coffman J.A. (2006). BMC Biology 4 (4).
• Developmental ascendency: from bottom-up to top-down control. Coffman, J.A. (2006). Biological Theory 1 (2):165-178.
• 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., Coffman J.A. (2005). BMC Biology 3 (18).
• On reductionism, organicism, somatic mutations and cancer. Coffman J.A. (2005). Bioessays 4.
• 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., Suprenant K.A. (2005). BMC Developmental Biology 5.
• Identification of sequence-specific DNA binding proteins. Coffman J.A., Yuh C.H. (2004). Methods in Cell Biology 74.
• 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., Robertson A.J. (2004). Developmental Biology 273 (1).
• 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., Robertson A.J. (2004). BMC Biology 2.
• Cell cycle development. Coffman J.A. (2004). Developmental Cell 6 (3).
• The sea urchin stem-loop-binding protein: a maternally expressed protein that probably functions in expression of multiple classes of histone mRNA. Robertson A.J., Howard J.T., Dominski Z., Schnackenberg B.J., Sumerel J.L., McCarthy J.J., Coffman J.A., Marzluff W.F. (2004). Nucleic Acids Research 32 (2).
• Runx transcription factors and the developmental balance between cell proliferation and differentiation. Coffman J.A. (2003). Cell Biology International 27 (4).
• The evolution of Runx genes I. A comparative study of sequences from phylogenetically diverse model organisms. Rennert J., Coffman J.A., Mushegian A.R., Robertson A.J. (2003). BMC Evolutionary Biology 3.
• The expression of SpRunt during sea urchin embryogenesis. Robertson A.J., Dickey C.E., McCarthy J.J., Coffman J.A. (2002). Mechanisms of Development 117(1-2).

More Publications

Education

• Ph.D., Duke University, Zoology, 1990
• B.A., Carleton College, Biology, 1981