Here are some selections of papers from areas of interest to the lab members. For complete listings see the faculty and student web sites.
Introductory papers
L. Pachter and B. Sturmfels
SIAM Review (2007).
B. Sturmfels
Article for the Clay Mathematics Institute Annual Report (2005).
C.N. Dewey and L. Pachter
Human Molecular Genetics (2006).
Phylogenetics
R. Mihaescu and L. Pachter
Proceedings of the National Academy of Sciences (2008).
B. Sturmfels and S. Sullivant
Journal of Computational Biology (2005).
Comparative genomics
Multiple organism gene finding by collapsed Gibbs sampling
S. Chatterji and L. Pachter
Journal of Computational Biology, in press.
J. D. McAuliffe, M. I. Jordan and L. Pachter
Proceedings of the National Academy of Sciences, 2005; 102(22):7900-7905.
Parametric inference
L. Pachter and B. Sturmfels
Proceedings of the National Academy of Sciences, 2004; 101(46):16138-16143.
C.N. Dewey, P.M. Huggins, K. Woods, B. Sturmfels and L. Pachter
PLoS Computational Biology, 2006; 2(6):e73.
DNA topology
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.
M. Vazquez, S.D. Colloms, and D.W. Sumners
J Mol Biol, 2005; 346(2):493-504.
Population genetics
S.N. Evans, Y. Shvets and M. Slatkin
Theoretical Population Biology, in press.
N. Beerenwinkel, L. Pachter and B. Sturmfels
Statistica Sinica, in press.
On the origin of species