Jena L. Chojnowski, Ph.D.Jena L. Chojnowski, Ph. D.

Assistant Professor of Developmental and Molecular Biology
One University Boulevard
Bluffton, SC 29909
Hilton Head Gateway Campus
Office: 843-208-8266


Developmental Biology, Stem Cell Biology, and Eye Development and Maintenance.


My research consists of two main areas of interest: developmental biology and stem cell biology. My study system is vision; specifically, I study the development of eyes in different species and how a population of stem cells in the eye maintains vision over time. The gene PAX6 is very important for eye development and stem cell maintenance and loss of half of its expression results in developmental eye defects as well as dysfunctional stem cells. My lab focuses on a developmental comparative anatomy approach to understand how one organ that accomplishes one goal, to detect light and convert it into electro-chemical impulses in neurons, can be utilized in so many diverse ways. In addition, my lab focuses on the relationship between PAX6 and stem cell maintenance. Without properly functioning stem cells, our vision rapidly degenerates. Studying how stem cells develop and are maintained is important for future biomedical advances in stem cell therapy.


  • B.S. in Zoology, University of Florida (2002)
  • Ph.D. in Zoology, University of Florida (2010)
        Advisor: Dr. Edward L. Braun
  • Postdoctoral Associate in Developmental Biology, University of Georgia (2011-2013)
        Advisor: Dr. Nancy Manley
  • Postdoctoral Associate in Cell Biology, University of Georgia (2013-2015)
        Advisor: Dr. James D. Lauderdale


  • Biological Principles I & II
  • General Biology
  • Cell and Molecular Biology
  • Developmental Biology


(Undergraduate co-authors on papers and presentations are indicated by *)

[13]  Chojnowski, J.L., H. Trau, K. Masuda, and N.R. Manley. Temporal and spatial
         requirements for Hoxa3 in regulating pharyngeal region development. In press at
         Developmental Biology.

[12]  Nakayama, T., M. Fisher, K. Nakajima, A.O. Odeleye, K.B. Zimmerman, M.B. Fish, Y.
         Yaoita, J.L. Chojnowski, J.D. Lauderdale, P.A. Netland, and R.M. Grainger.
         Xenopus pax6 mutants affect eye development and other organ systems, and
         have phenotypic similarities to human aniridia patients. Developmental Biology
         (2015) doi:10.1016/j.ydbio.2015.02.012.

[11]  Chojnowski, J.L., K. Masuda, H. Trau, K. Thomas, M. Capecchi, and N.R. Manley.
         Multiple roles for Hoxa3 in regulating thymus and parathyroid differentiation and
         morphogenesis in mouse. Development (2014) 141:3697.
[10]  Yuri, T., R.T. Kimball, J. Harshman, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, K. Han,
         S.J. Hackett, C.J. Huddleston, W.S. Moore, S. Reddy, F.H. Sheldon, D.W.
         Steadman, C.C. Witt, and E.L. Braun. Parsimony and model-based analyses of
         indels in avian nuclear genes reveal congruent and incongruent phylogenetic
         signals. Biology (2013) 2:419.
 [9]   Chojnowski, J.L. and E.L. Braun. An unbiased approach to identify genes involved in
         development in a turtle with temperature-dependent sex determination. BMC
         Genomics (2012) 13:308.

 [8]   Braun, E.L., R.T. Kimball, K-L. Han, N. Iuhasz*, A. Bonilla*, J.L. Chojnowski, J.V.
         Smith*, R.C.K. Bowie, M.J. Braun, S.J. Hackett, J. Harshman, C.J. Huddleston,
         B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, C.C. Witt and T.
         Yuri. Homoplastic microinversions and the avian tree of life. BMC Evolutionary
         Biology (2011) 11:141.

 [7]  Han, K-L., E.L. Braun, R.T. Kimball, S. Reddy, R. Bowie, M. Braun, J.L. Chojnowski, S.
         Hackett, J. Harshman, C. Huddleston, B. Marks, K. Miglia, W.S. Moore, F.H.
         Sheldon, D. Steadman, C. Witt, and T. Yuri. Are transposable element insertions
         homoplasy free?: an examination using the avian tree of life. Systematic Biology
         (2011) 60:375.

 [6]  Kimball, R.T., E.L. Braun, F.K. Barker, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, S.J.
         Hackett, K-L. Han, J. Harshman, V. Heimer-Torres*, W. Holznagel, C.J.
         Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, J.V.
         Smith*, C.C. Witt, and T. Yuri . A well-tested set of primers to amplify regions
         spread across the avian genome. Molecular Phylogenetics and Evolution (2009)
[5]    Chojnowski, J.L., R.T. Kimball, E.L. Braun. Introns outperform exons in analyses of
         basal avian phylogeny using clathrin heavy chain genes. Gene (2008) 410:89.
[4]    Chojnowski, J.L. and E.L. Braun.  Turtle isochore structure is intermediate between
         amphibians and other amniotes. Integrative and Comparative Biology (2008)
[3]    Hackett, S., R.T. Kimball, S. Reddy, E.L. Braun, M. Braun, R. Bowie, J.L. Chojnowski,
         K-L. Han, J. Harshman, C. Huddleston, B. Marks, K. Miglia, W.A. Moore, F.H.
         Sheldon, D. Steadman, and C. Witt. Multi-gene phylogeny of the major lineages
         of birds. Science (2008) 320:1763.
[2]    Harshman, J. E.L. Braun, M.J. Braun, C.J. Huddleston, R.C.K. Bowie, J.L. Chojnowski,
         S. Hackett, K-L. Han, R.T. Kimball, B.D. Marks, K.J. Miglia, W.A. Moore, S.
         Reddy, F.H. Sheldon, C. Witt, and T. Yuri. Phylogenomic evidence for multiple
         losses of flight in ratite birds. PNAS (2008) 105:13462.

[1]    Chojnowski, J.L., J. Franklin*, Y. Katsu, T. Iguchi, L.J. Guillette Jr., R.T. Kimball, E.L.
         Braun.  Patterns of vertebrate isochore evolution revealed by comparison of
         expressed mammalian, avian and crocodilian genes. Journal of Molecular
         Evolution (2007) 65:259.