Anne J. Shiu



I am a fourth year math graduate student at the University of California Berkeley. My CV.

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



Mini-symposium on mathematical biology in industry:
With Valerie Hower, I am organizing a mini-symposium at the SIAM Math for Industry conference (October 9-11, 2009 in San Francisco).


Computational Biology in the Math Department at Berkeley:
Find out more about our new Laboratory for Mathematical and Computational Biology.

I am part of the Designated Emphasis for Computational and Genomic Biology.

Toric Dynamical Systems:
My research focuses on Toric Dynamical Systems, and more generally, on algebraic and combinatorial approaches for (bio)chemical reaction network theory.


Papers:

Siphons in chemical reaction networks, with Bernd Sturmfels. Submitted. Available from the ArXiv here.

Persistence of deterministic population processes and the Global Attractor Conjecture, with David F. Anderson. Submitted. Available from the ArXiv here.

The smallest multistationary chemical reaction network. Third International Conference, AB 2008, Castle of Hagenberg, Austria, July 31-August 2, 2008 Proceedings. Available from here.

Toric dynamical systems, with Gheorghe Craciun, Alicia Dickenstein, and Bernd Sturmfels. Accepted to Special Issue of the Journal of Symbolic Computation: Work Inspired by Karin Gatermann, "Computer Algebra in Chemistry, Biology and Other Branches of Science". Available here.

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. To appear in SIAM J. on Discrete Math.

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.


Upcoming Workshops and Conferences:

Transition Workshop (Algebraic Methods in Systems Biology and Statistics), SAMSI, (June 18-20, 2009).

Tropical Geometry semester, MSRI, (Fall 2009).

Mini-symposium at the SIAM Math for Industry conference (October 9-11, 2009 in San Francisco).

Mathematical Developments Arising from Biology workshop, MBI, (November 8-10, 2009).

Joint Meetings, San Francisco, CA, (January 13-16, 2010).

Past Workshops and Conferences:
Listed here.


Events organized:

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

With Gheorghe Craciun and Manoj Gopalkrishnan, I organized a Special Session on the Mathematics of Biochemical Reaction Networks, which took place at the 2009 AMS Spring Southeastern Section Meeting in Raleigh, NC, April 4-5, 2009 (Saturday - Sunday).

Discrete Math Seminar:
With Raman Sanyal, I organized the Berkeley Discrete Math Seminar during Spring 2009.


Career Talks:
With Betsy Stovall and Cynthia Vinzant, I organize a new monthly seminar entitled Career Talks. This series is one of the activities put on by Unbounded Representation, a new math graduate group focused on issues of diversity in mathematics.

Noetherian Ring:
Find out more about our group here.

Upcoming Talks:

"TBA", Transition Workshop (Algebraic Methods in Systems Biology and Statistics), SAMSI (Friday, June 19, 2009) 3:00.

"TBA", Institute Henri Poincare, Paris (Thursday, July 2, 2009) 10:30.

Past Talks:
Listed here.


Teaching:
In Spring 2008, I was the GSI for Math 239, Discrete Mathematics for the Life Sciences. The instructor was Lior Pachter.

LaTex tips: Visit this page.


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.

Reference-based annotation:
GeneMapper




I am supported by a Lucent Technologies Bell Labs Graduate Research Fellowship and a UC Berkeley Chancellor's Fellowship.


(This is a photo with my best 'math friend' from my University of Chicago days, Emily.
View M. Duchin's Chicago Mathematics Alumnae Project here.)