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.
Directed Reading Program
With Kari Eifler
and Eric Tovar,
I am starting a
Directed Reading Program,
which will begin in Fall 2018. Here is the poster.
Research Experience for Undergraduates:
The Department of Mathematics at Texas A&M hosts an eight-week Research Experience for Undergraduates (REU) from
May 29 to July 20, 2018.
Details and how to apply are posted here.
Results and photos from our
2015 REU and
2017 REU, in which I mentored
the program on Algebraic Methods in Computational Biology.
Algebraic, geometric, and combinatorial approaches to mathematical biology; biochemical dynamical systems; neural coding; algebraic statistics; genomics.
Link to my papers on the ArXiv.
Neural codes, decidability, and a new local obstruction to convexity
with Aaron Chen and Florian Frick. Submitted.
Nondegenerate multistationarity in small reaction networks, with Timo de Wolff. Submitted.
Identifiability of linear compartment models: the singular locus, with Elizabeth Gross and Nicolette Meshkat. Submitted.
Dynamics of post-translational modification systems: recent progress and future directions, with Carsten Conradi. Invited Perspective. Biophysical Journal, vol. 114, issue 3, pp. 507-515 (2018).
Gröbner bases of neural ideals, with Rebecca Garcia, Luis Garcia Puente, Ryan Kruse, Jessica Liu, Dane Miyata, Ethan Petersen, and Kaitlyn Phillipson. Accepted to International Journal of Algebra and Computation (2018).
An all-encompassing global convergence result for processive multisite phosphorylation systems, with Mitchell Eithun. Mathematical Biosciences, vol. 291, pp. 1-9 (2017).
Which small reaction networks are multistationary?, with Badal Joshi. SIAM Journal on Applied Dynamical Systems, vol. 16, pp. 802-833 (2017).
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. SIAM Journal on Applied Algebra and Geometry, 1:1, pp. 222-238 (2017).
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.
Papers by undergraduate students under my mentorship:
Upcoming Workshops and Conferences:
- Texas Algebraic Geometry Symposium, Texas A&M University (Apr. 6-8, 2018)
Kinetic and related models with applications in the natural sciences conference, University of Wisconsin (April 29 to May 2, 2018)
Directed Reading Program workshop, MIT (May 26-27, 2018)
- NSF/CBMS Regional Conference on “Applications of Polynomial Systems”, TCU (June 4-8, 2018).
- ECMTB 2018, Lisbon (July 23-27, 2018).
- SIAM Life Sciences conference, Minneapolis (August 6-9, 2018).
Nonlinear algebra in applications workshop, ICERM, (Nov. 12-16, 2018)
- AIM SQUARE, San Jose CA, (Mar. 4-8, 2019)
Past Workshops and Conferences:
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). Photo.
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.
- With David F. Anderson, Matthew Johnston, Casian Pantea, and Lea Popovic, I organized a
workshop on "Mathematical Analysis of Biological Interaction Networks" at Banff International Research Station (Jun. 5 to Jun. 9, 2017). Photo.
- With Carsten Conradi and Gheorghe Craciun, I organized
a minisymposium on
Algebraic Methods for Analyzing Biological Interaction Networks
at the SIAM Conference on Applied Algebraic Geometry 2017 at Georgia Tech (Aug. 2-3, 2017).
- I was one of the organizers of the 2018
Texas Algebraic Geometry Symposium, Texas A&M University (Apr. 6-8, 2018). Conference poster courtesy of David Kerr.
"Bistability and oscillations in mass-action kinetics systems arising in biology", Kinetic and related models with applications in the natural sciences conference, University of Wisconsin (May 1, 2018)
"Which neural codes are convex?", Applied algebra and topology seminar, University of Oxford (May 18, 2018 at 12:00)
- "Harnessing steady-state parametrizations arising from reaction networks",
Nonlinear algebra seminar, Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany (July 18, 2018)
- "Multisite phosphorylation systems: bistability, oscillations, and a rational
parametrization of steady states", minisymposium on "Dynamics and Oscillations of Reaction Networks" at the European Conference on Mathematical and Theoretical Biology (ECMTB 2018), Lisbon, Portugal (July 23 to 27, 2018)
- "Absolute concentration robustness: an algebraic perspective",
minisymposium on "Mathematical analysis of Biological Interaction Networks" at
the SIAM Life Sciences conference, Minneapolis (August 6-9, 2018).
Nonlinear algebra in applications workshop, ICERM, (Nov. 12-16, 2018)
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)
- Simons Foundation Collaboration Grant for Mathematicians 2017-2018 (#521874)
- NSF CAREER 2018-2023 (DMS-1752672)