UC Berkeley Mathematical and Computational Biology

Here are some selections of papers from areas of interest. For complete listings see the faculty and student web sites.

Introductory papers: The mathematics of phylogenomics

B. Sturmfels and L. Pachter

SIAM Review, in press.; 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; 15(90001):R51-R56.

Phylogenetics: Toric ideals of phylogenetic invariants

B. Sturmfels and S. Sullivant

Journal of Computational Biology 12 (2005) 204-228.; Reconstructing trees from subtree weights

L. Pachter and D. Speyer

Applied Mathematics Letters 17 (2004), 615-621.

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.

Maximum likelihood for phylogenetics: Solving the likelihood equations

S. Hosten, A. Khetan, and B. Sturmfels

Foundations of Computational Mathematics, 2005; 5:389-407.

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-quilibrium 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.