HR job title
- Professor
- Contact Info
- ORCiD
- 0000-0002-5358-3049
Shiu, Anne Professor
Positions
- Professor, The Texas A&M University System
I have research interests in algebraic, geometric, and combinatorial approaches to mathematical biology; biochemical
dynamical systems; neural coding; algebraic statistics; and genomics.
dynamical systems; neural coding; algebraic statistics; and genomics.
- Overview
- Publications
- Research
- Teaching
- Works By Students
- Background
- Contact
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Overview
Publications
selected publications
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academic article
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Joshi, B., Kaihnsa, N., Nguyen, T. D., & Shiu, A.
(2023).
Prevalence of Multistationarity and Absolute Concentration Robustness in Reaction Networks. SIAM Journal on Applied Mathematics.
83(6), 2260-2283.
-
de Perez, A. R., Matusevich, L. F., & Shiu, A.
(2023).
Wheels: A new criterion for non-convexity of neural codes. Advances in Applied Mathematics.
150, 102567-102567.
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Bortner, C., Gross, E., Meshkat, N., Shiu, A., & Sullivant, S.
(2023).
Identifiability of linear compartmental tree models and a general formula for input-output equations. 146, 102490-102490.
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Chan, P., Johnston, K., Lent, J., De Perez, A. R., & Shiu, A.
(2023).
NONDEGENERATE NEURAL CODES AND OBSTRUCTIONS TO CLOSED-CONVEXITY. SIAM Journal on Discrete Mathematics.
37(1), 114-145.
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Gerberding, S., Obatake, N., & Shiu, A.
(2022).
Identifiability of linear compartmental models: the effect of moving inputs, outputs, and leaks. Linear and Multilinear Algebra.
70(14), 2782-2803.
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Meshkat, N., Shiu, A., & Torres, A.
(2022).
Absolute Concentration Robustness in Networks with Low-Dimensional Stoichiometric Subspace. Vietnam Journal of Mathematics.
50(3), 623-651.
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Gambacini, B., Jeffs, R. A., Macdonald, S., & Shiu, A.
(2022).
Non-Monotonicity of Closed Convexity in Neural Codes. Vietnam Journal of Mathematics.
50(2), 359-373.
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Gross, E., Meshkat, N., & Shiu, A.
(2022).
Identifiability of linear compartmental models: The singular locus. 133, 102268-102268.
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Conradi, C., Obatake, N., Shiu, A., & Tang, X.
(2021).
Dynamics of ERK regulation in the processive limit. 82(4), 32.
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Obatake, N., Shiu, A., & Sofia, D.
(2020).
Mixed volume of small reaction networks. 13(5), 845-860.
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Gross, E., Harrington, H., Meshkat, N., & Shiu, A.
(2020).
Joining and decomposing reaction networks. 80(6), 1683-1731.
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de Perez, A. R., Matusevich, L. F., & Shiu, A.
(2020).
Neural codes and the factor complex. Advances in Applied Mathematics.
114, 101977-101977.
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Obatake, N., Shiu, A., Tang, X., & Torres, A.
(2019).
Oscillations and bistability in a model of ERK regulation. 79(4), 1515-1549.
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Curto, C., Gross, E., Jeffries, J., Morrison, K., Rosen, Z., Shiu, A., & Youngs, N.
(2019).
Algebraic signatures of convex and non-convex codes. 223(9), 3919-3940.
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Tyler, J., Shiu, A., & Walton, J.
(2019).
Revisiting a synthetic intracellular regulatory network that exhibits oscillations. 78(7), 2341-2368.
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Conradi, C., Mincheva, M., & Shiu, A.
(2019).
Emergence of Oscillations in a Mixed-Mechanism Phosphorylation System. 81(6), 1829-1852.
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Dickenstein, A., Milln, M. P., Shiu, A., & Tang, X.
(2019).
Multistationarity in Structured Reaction Networks. 81(5), 1527-1581.
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Gross, E., Harrington, H., Meshkat, N., & Shiu, A.
(2019).
LINEAR COMPARTMENTAL MODELS: INPUT-OUTPUT EQUATIONS AND OPERATIONS THAT PRESERVE IDENTIFIABILITY. SIAM Journal on Applied Mathematics.
79(4), 1423-1447.
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Shiu, A., & de Wolff, T.
(2019).
NONDEGENERATE MULTISTATIONARITY IN SMALL REACTION NETWORKS. 24(6), 2683-2700.
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Chen, A., Frick, F., & Shiu, A.
(2019).
Neural Codes, Decidability, and a New Local Obstruction to Convexity. SIAM Journal on Applied Algebra and Geometry.
3(1), 44-66.
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Garcia, R., Puente, L., Kruse, R., Liu, J., Miyata, D., Petersen, E., Phillipson, K., & Shiu, A.
(2018).
Grobner bases of neural ideals. International Journal of Algebra and Computation.
28(4), 553-571.
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Conradi, C., & Shiu, A.
(2018).
Dynamics of Posttranslational Modification Systems: Recent Progress and Future Directions. 114(3), 507-515.
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Lienkaemper, C., Shiu, A., & Woodstock, Z.
(2017).
Obstructions to convexity in neural codes. Advances in Applied Mathematics.
85, 31-59.
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Curto, C., Gross, E., Jeffries, J., Morrison, K., Omar, M., Rosen, Z., Shiu, A., & Youngs, N.
(2017).
What Makes a Neural Code Convex?. SIAM Journal on Applied Algebra and Geometry.
1(1), 222-238.
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Joshi, B., & Shiu, A.
(2017).
Which Small Reaction Networks Are Multistationary?. SIAM Journal on Applied Dynamical Systems.
16(2), 802-833.
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Felix, B., Shiu, A., & Woodstock, Z.
(2016).
Analyzing multistationarity in chemical reaction networks using the determinant optimization method. Applied Mathematics and Computation.
287, 60-73.
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Mueller, S., Feliu, E., Regensburger, G., Conradi, C., Shiu, A., & Dickenstein, A.
(2016).
Sign Conditions for Injectivity of Generalized Polynomial Maps with Applications to Chemical Reaction Networks and Real Algebraic Geometry. Foundations of Computational Mathematics.
16(1), 69-97.
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Joshi, B., & Shiu, A.
(2015).
A Survey of Methods for Deciding Whether a Reaction Network is Multistationary. Mathematical Modelling of Natural Phenomena (MMNP).
10(5), 47-67.
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Conradi, C., & Shiu, A.
(2015).
A global convergence result for processive multisite phosphorylation systems. Bulletin of Mathematical Biology.
77(1), 126-155.
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Gopalkrishnan, M., Miller, E., & Shiu, A.
(2014).
A Geometric Approach to the Global Attractor Conjecture. SIAM Journal on Applied Dynamical Systems.
13(2), 758-797.
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Gopalkrishnan, M., Miller, E., & Shiu, A.
(2013).
A Projection Argument for Differential Inclusions, with Applications to Persistence of Mass-Action Kinetics. Symmetry, Integrability and Geometry: Methods and Applications.
9.
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Joshi, B., & Shiu, A.
(2013).
Atoms of multistationarity in chemical reaction networks. Journal of Mathematical Chemistry.
51(1), 153-178.
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Prez Milln, M., Dickenstein, A., Shiu, A., & Conradi, C.
(2012).
Chemical reaction systems with toric steady states. Bulletin of Mathematical Biology.
74(5), 1027-1065.
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Joshi, B., & Shiu, A.
(2012).
SIMPLIFYING THE JACOBIAN CRITERION FOR PRECLUDING MULTISTATIONARITY IN CHEMICAL REACTION NETWORKS. SIAM Journal on Applied Mathematics.
72(3), 857-876.
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Shiu, A., & Sturmfels, B.
(2010).
Siphons in chemical reaction networks. Bulletin of Mathematical Biology.
72(6), 1448-1463.
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Anderson, D. F., & Shiu, A.
(2010).
THE DYNAMICS OF WEAKLY REVERSIBLE POPULATION PROCESSES NEAR FACETS. SIAM Journal on Applied Mathematics.
70(6), 1840-1858.
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Craciun, G., Dickenstein, A., Shiu, A., & Sturmfels, B.
(2009).
Toric dynamical systems. Journal of Symbolic Computation.
44(11), 1551-1565.
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Morton, J., Pachter, L., Shiu, A., Sturmfels, B., & Wienand, O.
(2009).
CONVEX RANK TESTS AND SEMIGRAPHOIDS. SIAM Journal on Discrete Mathematics.
23(3), 1117-1134.
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Dequant, M., Ahnert, S., Edelsbrunner, H., Fink, T., Glynn, E. F., Hattem, G., ... Pourqui, O.
(2008).
Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS ONE.
3(8), e2856-e2856.
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Hemmecke, R., Morton, J., Shiu, A., Sturmfels, B., & Wienand, O.
(2008).
Three counter-examples on semi-graphoids. Combinatorics, Probability and Computing.
17(2), 239-257.
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Morton, J., Pachter, L., Shiu, A., & Sturmfels, B.
(2007).
The cyclohedron test for finding periodic genes in time course expression studies. Statistical Applications in Genetics and Molecular Biology.
6(1), Article-21.
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Kaihnsa, N., Nguyen, T., & Shiu, A.
Absolute concentration robustness and multistationarity in reaction networks: Conditions for coexistence. European Journal of Applied Mathematics.
1-35.
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Joshi, B., Kaihnsa, N., Nguyen, T. D., & Shiu, A.
(2023).
Prevalence of Multistationarity and Absolute Concentration Robustness in Reaction Networks. SIAM Journal on Applied Mathematics.
83(6), 2260-2283.
-
conference paper
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Shiu, A.
(2008).
The smallest multistationary mass-preserving chemical reaction network. Lecture Notes in Computer Science.
172-184.
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Morton, J., Pachter, L., Shiu, A., Sturmfels, B., & Wienand, O.
(2006).
Geometry of rank tests. 207-214.
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Shiu, A.
(2008).
The smallest multistationary mass-preserving chemical reaction network. Lecture Notes in Computer Science.
172-184.
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institutional repository document
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Puente, L., Gross, E., Harrington, H. A., Johnston, M., Meshkat, N., Milln, M. P., & Shiu, A.
(2023).
Absolute concentration robustness: Algebra and geometry
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Puente, L., Gross, E., Harrington, H. A., Johnston, M., Meshkat, N., Milln, M. P., & Shiu, A.
(2023).
Absolute concentration robustness: Algebra and geometry
Research
principal investigator on
- CAREER: Biochemical Reaction Systems: From Structure to Dynamics awarded by National Science Foundation - (Arlington, Virginia, United States) 2018 - 2023
- REU Site: Undergraduate Research in the Mathematical Sciences and their Applications awarded by National Science Foundation - (Arlington, Virginia, United States) 2018 - 2021
- REU Site: Undergraduate Research in the Mathematical Sciences and Their Applications -- awarded by National Science Foundation - (Arlington, Virginia, United States) 2015 - 2019
- Biochemical reaction systems: multistationarity, persistence, and identifiability awarded by National Science Foundation - (Arlington, Virginia, United States) 2014 - 2017
co-principal investigator on
Teaching
teaching activities
- BIOL285 Directed Studies Instructor
- MATH147 Calc I Biol Sci Instructor
- MATH171 Hnr-calculus I Instructor
- MATH220 Foundations Of Math Instructor
- MATH285 Directed Studies Instructor
- MATH300 Foundations Of Math Instructor
- MATH302 Discrete Mathematics Instructor
- MATH416 Modern Algebra Ii Instructor
- MATH469 Intro Mathematical Biol Instructor
- MATH491 Hnr-research Instructor
- MATH491 Research Instructor
- MATH653 Algebra I Instructor
- MATH669 Seminar Math Biology Instructor
- MATH684 Prof Internship Instructor
- MATH685 Directed Studies Instructor
- MATH691 Research Instructor
Works By Students
chaired theses and dissertations
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Barton, Andrea (2023-04). An Extension of Descartes' Rule of Signs to Multiple Variables, with Applications to Models of Biological Systems.
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Obatake, Nida Kazi (2021-05). On the stability and number of steady states of chemical reaction networks.
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Ruys De Perez, Alexander Mark (2021-04). New Tools for Classifying Convex Neural Codes: The Factor Complex and the Wheel.
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Tyler, Jonathan P. (2019-07). Mathematical Modeling of Biological Clocks.
Background
education and training
- Ph.D. in Mathematics, University of California, Berkeley - (Berkeley, California, United States) 2010
- B.S. in Mathematics, University of Chicago - (Chicago, Illinois, United States) 2005
awards and honors
Contact
first name
- Anne
has last name
- Shiu
mailing address
-
Texas A&M University
Mathematics
3368 TAMU
College Station, TX 77843-3368
USA
Other
In the News
- annejls@tamu.edu