Stacia Wyman

Stacia Wyman

Stacia K. Wyman

Former Visiting Assistant Professor (2004-2006)

Current Address:
Fred Hutchinson Cancer Research Center
1100 Fairview Ave N
Seattle, WA 98109
email:

phone: 206-434-8600

Classes:

Spring 2006:

Fall 2005:

CSCI 134: Digital Computation and Communication
- General information from the department web pages
- The course page
CSCI 319: Integrative Bioinformatics, Genomics, and Proteomics
- General information from the department web pages
- The course page from the bioinformatics module

Spring 2005:

CSCI 256: Algorithm Design and Analysis

Winter Study 2005:

CSCI 11: Programming Perl for the Sciences

Fall 2004:

CSCI 134: Intro to Computer Science (in Java, taught with Steve Freund)

You can find my CV here: pdf, html (abbreviated)

Research Interests:	My main research area is computational biology. I am interested in all aspects of whole genome analysis and my work has involved whole genome annotation, phylogenetic reconstruction, identifying regulatory elements, and, most recently, comparative repeat analysis.
Software:	Both packages hosted by Jeff Boore's group at the DOE Joint Genome Institute: If you are interested in organellar genome annotation and DOGMA (my annotation software), please send me email or go to DOGMA. Software for comparative repeat analysis is here.
Publications	St. John, K. and Wyman, S.K., "Algorithms for Analyzing and Clustering Repeats in Whole Genomes,'' in preparation. Holtschulte, N. and Wyman, S.K., "Comparative Repeat Analysis of Whole Genomes," in preparation. Jansen R.K., Raubeson L.A., Boore J.L., dePamphilis C.W., Chumley T.W., Haberle R.C., Wyman S.K., Alverson A.J., Peery R., Herman S.J., Fourcade H.M., Kuehl J.V., McNeal J.R., Leebens-Mack J., Cui L. (book chapter) "Methods for obtaining and analyzing whole chloroplast genome sequences.'' Methods Enzymol. 2005; ( 395):348-84. Wyman, S.K., Jansen, R.K., and Boore, J.L., "Automatic annotation of organellar genomes with DOGMA,'' Bioinformatics. 2004;20( 17):3252-5. PDF Wyman, S.K., and Boore, J.L., "Annotating animal mitochondrial tRNAs: an experimental evaluation of four methods," Proc. of European Conference on Computational Biology (ECCB 2003),Paris, France, 2003. PDF Moret, B.M.E., Wang, L., Warnow, T., and Wyman, S.K., "New approaches to phylogeny reconstruction from gene order data," 9th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB 2001), Copenhagen, in Bioinformatics 17 (2001), S165-S173; chosen as one of the 5 best papers at the conference. PDF Moret, B.M.E., Wyman, S.K., Bader, D.A., Warnow, T., and Yan, M., "A new implementation and detailed study of breakpoint analysis," Proc. 6th Pacific Symp. on Biocomputing (PSB 2001), Hawaii, World Scientific Pub. (2001), 583-594. PDF Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.S., Warnow, T., and Wyman, S.K., "An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae," in Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, D. Sankoff and J. Nadeau, eds., Kluwer Academic Publishers, Dordrecht, 2000, 99-121. PDF Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.S., Warnow, T., and Wyman, S.K., "A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data," Proc. 8th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB 2000), San Diego (2000), 104-115. PDF