UC Berkeley Mathematical and Computational Biology

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: The mathematics of phylogenomics

L. Pachter and B. Sturmfels

SIAM Review (2007).; Can biology lead to new theorems?

B. Sturmfels

Article for the Clay Mathematics Institute Annual Report (2005).; Evolution at the nucleotide level: the problem of multiple whole-genome alignment

C.N. Dewey and L. Pachter

Human Molecular Genetics (2006).

Phylogenetics: Combinatorics of Least Squares Trees

R. Mihaescu and L. Pachter

Proceedings of the National Academy of Sciences (2008).; Toric ideals of phylogenetic invariants

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.; Subtree power analysis finds optimal species for comparative genomics

J. D. McAuliffe, M. I. Jordan and L. Pachter

Proceedings of the National Academy of Sciences, 2005; 102(22):7900-7905.

Parametric inference: Parametric inference for biological sequence analysis

L. Pachter and B. Sturmfels

Proceedings of the National Academy of Sciences, 2004; 101(46):16138-16143.; Parametric alignment of Drosophila genomes

C.N. Dewey, P.M. Huggins, K. Woods, B. Sturmfels and L. Pachter

PLoS Computational Biology, 2006; 2(6):e73.

DNA topology: DNA knots reveal a chiral organization of DNA in phage capsids

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.; Tangle analysis of Xer recombination reveals only three solutions, all consistent with a single three-dimensional topological pathway

M. Vazquez, S.D. Colloms, and D.W. Sumners

J Mol Biol, 2005; 346(2):493-504.

Population genetics: Non-equilibrium theory of the allele frequency spectrum

S.N. Evans, Y. Shvets and M. Slatkin

Theoretical Population Biology, in press.; Epistasis and shapes of fitness landscapes

N. Beerenwinkel, L. Pachter and B. Sturmfels

Statistica Sinica, in press.