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Tyrone Ryba

Assistant Professor of Bioinformatics

B.A., New College of Florida
Ph.D., Florida State University

Professor Ryba is a computational biologist with interests in epigenetic regulation and applying computational methods to study the biology of human disease. His research examines relationships between genome structure and function, with a focus on large-scale domain regulation and misregulation in respiratory disorders and pediatric leukemia. He enjoys teaching the theory and practice of deriving information from biological data, and participating in related ISPs, tutorials, and collaborative projects.

Recent courses
Principles of Bioinformatics
Applied Bioinformatics Laboratory
Topics in Epigenetics

Selected Publications
Ryba, T., Battaglia, D., Chang, B.H., Shirley, J.W., Buckley, Q., Pope, B.D., Devidas, M., Druker, B.J., and Gilbert, D.M. (2012) Abnormal developmental control of replication timing domains in pediatric acute lymphoblastic leukemia. Genome Research 22(10): 1833-1844.

Takebayashi, S.-I., Dileep, V., Ryba, T., Dennis, J., and Gilbert, D.M. (2012) Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding. Proc Natl Acad Sci USA. 109(31): 12574-12579.

Mouse ENCODE Consortium. (2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 13(8): 418.

Ryba, T., Hiratani, I., Sasaki, T., Battaglia, D., Kulik, M., Zhang, J., Dalton, S., and Gilbert, D.M. (2011) Replication timing: a fingerprint for cell identity and pluripotency. PLoS Comp. Biol. 7(10): e1002225.

Ryba, T., Battaglia, D., Pope, B.D., Hiratani, I., and Gilbert, D.M. (2011) Genome-Scale Analysis of Replication Timing: from Bench to Bioinformatics. Nature Protocols 6(6): 870-895.

Ryba, T., Hiratani, I., Lu, J., Itoh, M., Kulik, M., Zhang, J., Schulz, T.C., Robins, A.J., Dalton, S., and Gilbert, D.M. (2010) Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Research 20(6): 761-770.

Hiratani, I., Ryba, T., Itoh, M., Rathjen, J., Kulik, M., Papp, B., Plath, K., Dalton, S., Rathjen, P.D., and Gilbert, D.M. (2010) Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Research 20(2): 155-169.

Hiratani, I., Ryba, T., Itoh, M., Yokochi, T., Schwaiger, M., Chang, C.-W., Lyou, Y., Townes, T.M., Schübeler, D., and Gilbert, D.M. (2008) Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation. PLoS Biology 6(10): e245.

Contact Information
New College of Florida

Division of Natural Sciences
5800 Bay Shore Road
Sarasota, FL 34243-2109


Office of the Provost
New College of Florida
5800 Bay Shore Road
Sarasota, Florida  34243

Phone: (941) 487-4200
Fax: (941) 487-4201