Here are some selections of papers from
areas of interest. For complete listings see the faculty and student
web sites.
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Introductory papers
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B. Sturmfels and L. Pachter
SIAM Review, in press.
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B. Sturmfels
Article for the Clay Mathematics Institute Annual Report, 2005.
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C.N. Dewey and L. Pachter
Human Molecular Genetics, 2006; 15(90001):R51-R56.
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Phylogenetics
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B. Sturmfels and S. Sullivant
Journal of Computational Biology
12 (2005) 204-228.
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L. Pachter and D. Speyer
Applied Mathematics Letters 17 (2004), 615-621.
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Comparative genomics
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Multiple organism gene finding by collapsed Gibbs sampling
S. Chatterji and L. Pachter
Journal of Computational Biology, in press.
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J. D. McAuliffe, M. I. Jordan and L. Pachter
Proceedings of the National Academy of Sciences, 2005; 102(22):7900-7905.
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Maximum likelihood for phylogenetics
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S. Hosten, A. Khetan, and B. Sturmfels
Foundations of Computational Mathematics, 2005; 5:389-407.
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Parametric inference
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L. Pachter and B. Sturmfels
Proceedings of the National Academy of Sciences, 2004; 101(46):16138-16143.
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C.N. Dewey, P.M. Huggins, K. Woods, B. Sturmfels and L. Pachter
PLoS Computational Biology, 2006; 2(6):e73.
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DNA topology
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J. Arsuaga, M. Vazquez, P. McGuirk, S. Trigueros, D.W. Sumners, and J. Roca
Proceedings of the National Academy of Sciences, 2005; 102(26):9165-9169.
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M. Vazquez, S.D. Colloms, and D.W. Sumners
J Mol Biol, 2005; 346(2):493-504.
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Population genetics
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S.N. Evans, Y. Shvets and M. Slatkin
Theoretical Population Biology, in press.
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N. Beerenwinkel, L. Pachter and B. Sturmfels
Statistica Sinica, in press.