Anne J. Shiu

I am an L.E. Dickson Instructor in the Department of Mathematics at the University of Chicago.

Email address: annejls at math dot uchicago dot edu
Office: Eckhart 322
My CV.

I received a Ph.D. in 2010 from the Department of Mathematics at the University of California Berkeley. My advisors were Bernd Sturmfels and Lior Pachter. During 2010-2011, I was an NSF Postdoctoral Fellow in the Department of Mathematics at Duke University.

I was an undergraduate at the University of Chicago; view the Chicago Mathematics Alumnae Project.

Teaching:

During Spring 2012, I am teaching Basic Algebra-3 (Math 25600, section 31 - Introduction to Abstract Algebra-3).
During Winter 2012, I taught Basic Algebra-2 (Math 25500, section 33 - Introduction to Abstract Algebra-2).
During Fall 2011, I taught Basic Algebra-1 (Math 25400, section 33 - Introduction to Abstract Algebra-1).

Research interests:
My research focuses on algebraic and combinatorial approaches to problems in computational biology. My thesis developed the algebraic study of biochemical reaction networks, and in particular, toric dynamical systems. I also am interested in algebraic statistics and genomics.

Papers:

Atoms of multistationarity in chemical reaction networks, with Badal Joshi. Submitted. 2011.

Simplifying the Jacobian Criterion for precluding multistationarity in chemical reaction networks, with Badal Joshi. Accepted to SIAM J. Appl. Math. 2012.

Chemical reaction systems with toric steady states, with Mercedes Perez Millan, Alicia Dickenstein, and Carsten Conradi. Accepted to Bulletin of Mathematical Biology. 2011.

Algebraic methods for biochemical reaction network theory, Ph.D. thesis, 2010.

Siphons in chemical reaction networks, with Bernd Sturmfels. Bulletin of Mathematical Biology, 72:6, pp. 1448-1463 (2010).

The dynamics of weakly reversible population processes near facets, with David F. Anderson. SIAM J. Appl. Math. 70:6, pp. 1840-1858.

The smallest multistationary chemical reaction network. Proceedings of the Third International Conference, Algebraic Biology 2008, Castle of Hagenberg, Austria, July 31-August 2, 2008.

Toric dynamical systems, with Gheorghe Craciun, Alicia Dickenstein, and Bernd Sturmfels. Journal of Symbolic Computation 44, pp. 1551-1565 (2009).

Comparing pattern detection methods in microarray time series of the segmentation clock, with M. Dequeant, S. Ahnert, H. Edelsbrunner, T. Fink, E. Glynn, G. Hattem, A. Kudlicki, Y. Mileyko, J. Morton, A. Mushegian, L. Pachter, M. Rowicka, B. Sturmfels, and O. Pourquie. PLoS ONE 3:8, e2856 (2008).

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.

Convex rank tests and semigraphoids, with Jason Morton, Lior Pachter, Bernd Sturmfels, Oliver Wienand. SIAM J. Discrete Math. 23:3, pp. 1117-1134 (2009).

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. The third European Workshop on Probabilistic Graphical Models, Prague, Czech Republic, Sept. 12-15, 2006.

Link to my papers on the ArXiv.

Upcoming Workshops and Conferences:

Algebraic Methods in Systems and Evolutionary Biology workshop, MBI, Columbus OH, (May 7-11, 2012).
SIAM Conference on the Life Sciences, (August 7-12, 2012).
Combinatorial Commutative Algebra and Applications workshop, MSRI (December 3-7, 2012).

With Francois Boulier, Thomas Sturm, and Andreas Weber, I am organizing a Symbolic Methods for Chemical Reaction Networks seminar at Castle Dagstuhl in Germany (November 12-16, 2012).

With Alicia Dickenstein and Jeremy Gunawardena, I am organizing a workshop on Mathematical problems arising from biochemical reaction networks at AIM in Palo Alto CA (March 25-29, 2013).

Past Workshops and Conferences:
Listed here.

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

With Valerie Hower, I organized a mini-symposium at the SIAM Math for Industry conference (October 9-11, 2009 in San Francisco). The mini-symposium took place 2:15 p.m.-4:15 p.m. on Saturday, October 10.

With Trevor Potter, Betsy Stovall, and Cynthia Vinzant, I organized a monthly seminar at UC Berkeley entitled Career Talks. This series introduced math graduate students to career paths within academia and industry.
With Sonja Mapes, I organized the Duke Algebraic Geometry seminar (Spring 2011).
With Manoj Gopalkrishnan and Casian Pantea, I organized a minisymposium on biochemical reaction networks at the SIAM Conference on Applied Algebraic Geometry, NC State, Raleigh NC (Thurs.-Sun., Oct. 6-9, 2011).

Upcoming Talks:

"Chemical reaction systems with toric steady states", Algebraic Methods in Systems and Evolutionary Biology workshop, MBI, (May 7-11, 2012).
"Steady states of multisite phosphorylation systems", SIAM Conference on the Life Sciences minisymposium, (August 7-12, 2012).
TBA, Combinatorial Commutative Algebra and Applications workshop, MSRI (December 3-7, 2012).

Past Talks:
Listed here.

Previous activities:

Women and Mathematics Mentoring Program, Durham County NC.
Noetherian Ring at Duke University (organization supporting women in mathematics)

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. 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 made a human reference-based annotation of the May 2006 build of the chicken genome, under the guidance of Sourav Chatterji, using GeneMapper.
In spring 2009, I participated in a new Genome Project Lab course, in which we assembled, annotated, and analyzed a newly-sequenced genome.

I am supported by an NSF Postdoctoral Fellowship.