Anne J. Shiu


I am a math graduate student.
(And so is my best 'math friend' from my University of Chicago days, Emily.)

Email address: annejls at math dot berkeley dot edu
Advisors:
Bernd Sturmfels
Lior Pachter


Toric Dynamical Systems:
My research focuses on Toric Dynamical Systems; a paper with that title is available on the arXiv here.


Workshops and Conferences:
MSRI summer graduate workshop: Mathematical aspects of computational biology (June 2006)

With Sourav Chatterji, I organized a Berkeley-Davis Mathematical Genomics Meeting (Friday, September 15, 2006 at the UC Davis Genome Center).

IMA Applications in Biology, Dynamics, and Statistics workshop (March 2007)

From genotypes to phenotypes: geometry, statistics, and biology ETH Zurich (November 30, 2007)


Talks:
"Geometry of Rank Tests" at the MSRI Arrangements and Configuration Spaces workshop.
University of Kansas Combinatorics Seminar, January 31, 2007
University of California, Davis Combinatorics Seminar, February 15, 2007

"The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies," University of Wisconsin, Madison, May 24, 1007

"Toric dynamical systems," UCB Commutative Algebra & Algebraic Geometry Seminar , September 11, 2007 (3:45 pm, Evans 939)
UCB L. Pachter ASCB/Genomics seminar, Tuesday, September 18, 2007 (2:30 pm, Evans 939)
UCB Dynamics seminar, Tuesday, October 16, 2007 (3:00 pm, Evans 959)
TU Berlin Pure and applied algebra seminar, Tuesday, December 4, 2007 (2:15 pm, MA 313)
Stanford University seminar, Tuesday, February 12, 2008 (12:30-2)

TBA, UCB Designated Emphasis in Genomics and Computational Biology Student Seminar, Monday, March 17, 1008 (5:00 pm, Campbell Annex)



Teaching:
In Spring 2008, I am the GSI for Math 239, Discrete Mathematics for the Life Sciences. The instructor is Lior Pachter. My office hours are 9:30-11 on Tuesdays in Evans 743.


Older Projects:
Under the direction of Lior Pachter and Bernd Sturmfels, two fellow students - Jason Morton and Oliver Wienand - and I undertook a project in the spring of 2006 analyzing microarray data. This took us to a meeting hosted by the Olivier Pourquié lab at the Stowers Institute in Kansas City. This inspired a paper entitled, Geometry of Rank Tests, and a follow-up paper Three Counterexamples on Semigraphoids, to appear in Combinatorics, Probability and Computing.
Jason presented our papers in September 2006 at the Probabilistic Graphical Models conference.
Our paper The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies describes the implementation of a rank test inspired by algebraic combinatorics for finding interesting gene expressions in microarray experiments.

I attended a chicken genome workshop at Cold Spring Harbor lab in New York.
I have made a human reference-based annotation of the latest (May 2006) build of the chicken genome, under the guidance of Sourav Chatterji, using GeneMapper. "> UCSC Genome Browser.

Reference-based annotation:
GeneMapper


Papers

The smallest multistationary chemical reaction network. Submitted.

Toric dynamical systems, with Gheorghe Craciun, Alicia Dickenstein, and Bernd Sturmfels. Submitted.

The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies, with Jason Morton, Lior Pachter, Bernd Sturmfels. Statistical Applications in Genetics and Molecular Biology: Vol. 6 : Iss. 1, Article 21. Available from BE Press.

Convex Rank Tests and Semigraphoids, with Jason Morton, Lior Pachter, Bernd Sturmfels, Oliver Wienand.

Three Counterexamples on Semigraphoids, with Raymond Hemmecke, Jason Morton, Bernd Sturmfels, Oliver Wienand. Combinatorics, Probability and Computing. 17:02, March 2008, pp 239-257.

Geometry of rank tests, with Jason Morton, Lior Pachter, Bernd Sturmfels, Oliver Wienand.

Link to my papers on the ArXiv.


I am supported by a Lucent Technologies Bell Labs Graduate Research Fellowship.