Anne J. Shiu
I am an Assistant Professor in the Department of Mathematics
at Texas A&M University.
I received a Ph.D. in 2010 in Mathematics with designated emphasis in genomic and computational biology from 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. During 2011-2014, I was an NSF Postdoc and L.E. Dickson Instructor in the Department of Mathematics at the University of Chicago.
- Email address: annejls at math dot tamu dot edu
- Office: Blocker 601 E
- My CV.
I was an undergraduate at the University of Chicago; view the Chicago Mathematics Alumnae Project.
Research Experience for Undergraduates 2017:
The Department of Mathematics at Texas A&M hosted an eight-week Research Experience for Undergraduates (REU) from May 30 to July 21, 2017. I will mentor
the program on Algebraic Methods in Computational Biology. Details and how to apply are here.
Results and photos from our 2015 REU and
In Spring 2017, I will teach Modern Algebra II (Math 416, stacked sections 200 and 500; Tues/Thurs 11:10 AM to 12:25 PM in Blocker 605-AX).
In Fall 2016, I am teaching Discrete Mathematics (Math 302, section 501; Tues/Thurs 12:45 PM to 2:00 PM).
In Spring 2016, I taught Introduction to Mathematical Biology (Math 469, section 500).
During Fall 2015, I taught Modern Algebra I (Math 415, section 502).
During Fall 2015, I co-taught with Jay Walton a graduate seminar course on Mathematical Biology (Math 669).
During Spring 2015, I taught Calculus I for Biological Sciences (Math 147, sections 501-502-503).
During Fall 2014, I taught Calculus I for Biological Sciences (Math 147, sections 510-511-512).
Algebraic, geometric, and combinatorial approaches to mathematical biology; biochemical dynamical systems; neural coding; algebraic statistics; genomics.
Link to my papers on the ArXiv.
Gröbner bases of neural ideals, with Rebecca Garcia, Luis Garcia Puente, Ryan Kruse, Jessica Liu, Dane Miyata, Ethan Petersen, and Kaitlyn Phillipson. Submitted.
An all-encompassing global convergence result for processive multisite phosphorylation systems, with Mitchell Eithun. Submitted.
Which small reaction networks are multistationary?, with Badal Joshi. Accepted to SIAM Journal on Applied Dynamical Systems.
Obstructions to convexity in neural codes, with Caitlin Lienkaemper and Zev Woodstock. Advances in Applied Mathematics, vol. 85, pp. 31--59 (2017).
What makes a neural code convex?, with Carina Curto, Elizabeth Gross,
Jack Jeffries, Katherine Morrison, Mohamed Omar, Zvi Rosen, and Nora Youngs. Submitted to SIAM Journal on Applied Algebra and
Analyzing multistationarity in chemical reaction networks using the determinant optimization method, with Bryan Félix and Zev Woodstock. Applied Mathematics and Computation. Volumes 287–288, pp. 60-73 (2016).
- Sign conditions for injectivity of generalized polynomial maps with applications to chemical reaction networks and real algebraic geometry, with Stefan Muller, Elisenda Feliu, Georg Regensburger, Carsten Conradi, and Alicia Dickenstein. Foundations of Computational Mathematics, 16:1, pp. 69-97 (2016).
- A survey of methods for deciding whether a reaction network is multistationary, with Badal Joshi. Mathematical Modelling of Natural Phenomena, special issue on "Chemical dynamics", 10:5, pp. 47-67 (2015).
- A global convergence result for processive multisite phosphorylation systems, with Carsten Conradi. Bulletin of Mathematical Biology 77:1, pp. 126-155 (2015).
- A geometric approach to the global attractor conjecture, with Manoj Gopalkrishnan and Ezra Miller. SIAM J. Appl. Dyn. Syst., 13:2, pp. 758-797 (2014).
- A projection argument for differential inclusions, with applications to persistence of mass-action kinetics, with Manoj Gopalkrishnan and Ezra Miller. SIGMA 9 (2013), 025, 25 pages.
- Atoms of multistationarity in chemical reaction networks, with Badal Joshi. Journal of Mathematical Chemistry, 51:1, pp. 153-178 (2013).
- Simplifying the Jacobian Criterion for precluding multistationarity in chemical reaction networks, with Badal Joshi. SIAM J. Appl. Math., 72:3, pp. 857-876 (2012).
- Chemical reaction systems with
toric steady states, with Mercedes Perez Millan,
Alicia Dickenstein, and Carsten Conradi. Bulletin
of Mathematical Biology, 74:5, pp. 1027-1065 (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 (2010).
- The smallest multistationary chemical reaction network. Proceedings of the Third International Conference, Algebraic Biology 2008, Castle of Hagenberg, Austria, July 31-August 2, 2008. Lect. Notes Comput. Sc. 5147, pp. 172-184 (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 (2007).
- 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, pp 239-257 (2008).
- 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.
Upcoming Workshops and Conferences:
Past Workshops and Conferences:
Events I am organizing:
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).
- With Francois Boulier, Thomas Sturm, and Andreas Weber,
I organized a Symbolic Methods for Chemical Reaction Networks seminar at
Castle Dagstuhl in Germany (November 12-16, 2012). The Dagstuhl report of this seminar is available here.
- With Alicia Dickenstein and Jeremy Gunawardena, I organized a workshop on Mathematical problems arising from biochemical reaction networks at AIM in Palo Alto CA (March 25-29, 2013). Computer algebra tutorial file available here.
- With Gilles Gnacadja, I organized a minisymposium on Algebraic Aspects of Biochemical Reaction Networks at the SIAM Conference on Applied Algebraic Geometry 2013 at Colorado State University (August 1-4, 2013).
- I was one of the organizers of the 2015 Texas Algebraic Geometry Symposium, Texas A&M University (April 10-12, 2015).
With Alicia Dickenstein, I organized a minisymposium on Algebraic structures arising in systems biology at the SIAM Conference on Applied Algebraic Geometry (AG15), Daejeon, South Korea, (August 3-7, 2015).
- I was one of the organizers of the Mini-TAGS workshop at Texas A&M (Saturdays, September 26, 2015 and October 24, 2015)
With Paulo Lima-Filho and Jay Walton, I organized an IAMCS workshop on Contemporary Mathematical Challenges in the Life Sciences (May 16-18, 2016). See also this article.
Prior and current support:
- NSF Postdoctoral Fellowship 2010-2013 (DMS-1004380)
- NSF grant: "Biochemical reaction systems: multistationarity, persistence, and identifiability" 2013-2017 (DMS-1312473, transferred to DMS-1513364)