| Research Interests |
My main research area is the role of miRNAs in cancer.
My past work has involed whole genome annotation, phylogenetic reconstruction from gene order data, identifying regulatory elements,
and most recently, comparative repeat analysis.
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| Education |
2004 Ph.D. in Computer Sciences, University of Texas at Austin
1992 M.S. in Computer Science, University of Wisconsin-Madison
1990 B.A. in Computer Science, cum laude, with honors in Computer Science, Smith College
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| Honors |
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International Society for Computational Biology Travel Fellowship, 2003
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NSF Integrative Graduate Education and Research Training Fellowship, 2001-2003
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George H. Mitchell Award for Excellence in Graduate Research, 2001
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David Bruton Graduate Fellowship, 2000
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Best Paper Award, Hawaii Int'l Conference for the System Sciences, 1992
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First-year Graduate Student Summer Research Fellowship, 1991
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General Electric Graduate Fellowship, 1990-1991
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Elected to Sigma Xi, 1990
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Elected to Phi Beta Kappa, 1990
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First Group Scholar, Smith College, 1987-1990
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| Software |
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DOGMA:
Dual Organellar Genome Annotator
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Tool
for Comparative Repeat Analysis of Small Genomes
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| Publications |
- Wyman, S.K. and St. John, K.,
"Algorithms for Analyzing and Clustering Repeats in Whole Genomes,''
in preparation.
- Wyman, S.K. and Holtschulte, N.,
"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
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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
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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
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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
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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
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Istvanick, W., Kryder, A., Lewandowski, G., Meidanis, J., Rang, A.,
Wyman, S.K., "Dynamic Methods for Fragment Assembly in Large-scale
Genome Sequencing Projects," Proc. Hawaii International Conference
for the System Sciences, 1992.
PDF
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| Presentations |
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"Comparative Chloroplast Genomics of Seed Plants: Annotation and Analysis of Genomic Sequences," Wyman, S.K., Haberle, R., Chumley, T., Boore, J.L., Jansen, R.K., IMA RECOMB Satellite Workshop on Comparative Genomics, University of Minneapolis, Minneapolis, MN, 2003 (poster).
- "An experimental evaluation of four methods for identifying animal mitochondrial tRNAs," Wyman, S.K., Boore, J.L., Evolution, Chico State University, Chico, CA 2003.
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"Comparative chloroplast genomics; Integrating computational methods, phylogeny, and molecular evolution,"
Jansen, R.K., Raubeson, L.A., Haberle, R.C., Wyman, S.K., Chumley, T., Moret, B.M.E., Boore, J.L., Fourcade, M., Wang, L.S., Warnow, T.,
Plant and Animal Genomics Conference, San Diego, CA, 2003.
- "Inferring phylogenetic relationships using gene order data:
a case study of photosynthetic organelles and chloroplast genomes,"
Raubeson, L.A., Moret, B.M.E., Tang, J., Warnow, T., Wyman, S.K.,
Evolution, Chico State University, Chico, CA, 2003.
- "Structure and evolution of two highly rearranged chloroplast genomes in the Campanulaceae", Haberle, R.,
Boore, J.L., Fourcade, M.H., Jansen, R.K., Wyman, S.K., Evolution, Chico State University, Chico, CA, 2003.
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"AMICA: A new annotation program for animal mitochondrial and
chloroplast genomes,"
Wyman, S.K., Haberle, R.C., Raubeson, L.A., Fourcade, M.,
Boore, J.L., Jansen, R.K.,
Keck/GCC Bioinformatics Consortium 2002 Bioinformatics Symposium, Rice University,
Houston, TX, 2002 (poster).
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"Evolutionary implications of the complete sequence of the Trachelium caeruleum
(Campanulaceae) chloroplast genome,"
Haberle, R.C., Wyman, S.K., Eddie, W.M., Boore, J.L., Jansen, R.K.,
Botany 2002, Botanical Society of America, Madison , WI, 2002.
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"High-performance algorithm engineering for gene-order phylogenies,"
Bader, D.A., Moret, B.M.E., Warnow, T., Wyman, S.K., and Yan, M.,
DIMACS Workshop on Whole Genome Comparison, Rutgers U., 2001.
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