Anne J. Shiu
I am a Professor in the Department of Mathematics
at Texas A&M University.
 Email address: annejls at math dot tamu dot edu
 Office: Blocker 601 E
 My CV
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 20102011, I was an NSF Postdoctoral Fellow in the Department of Mathematics
at Duke University. During 20112014, I was an NSF Postdoc and L.E. Dickson Instructor in the Department of Mathematics at the University of Chicago.
Directed Reading Program
With
Jordy Lopez Garcia and Angelique Morvant,
I am organizing a
Directed Reading Program. Here is the poster.
Research Experience for Undergraduates:

The Department of Mathematics at Texas A&M hosted (online) an eightweek Research Experience for Undergraduates (REU) from
June 1 to July 24, 2020.
I mentored the program on Algebraic Methods in Computational Biology.
See details here.

Results and photos from our
2015 REU and
2016 REU
and
2017 REU,
2019 REU,
and
2020 REU, in which I mentored
the program on Algebraic Methods in Computational Biology.
Teaching:
Past Teaching:
Listed here.
Research interests:
Algebraic, geometric, and combinatorial approaches to mathematical biology; biochemical dynamical systems; neural coding; parameter identifiability; algebraic statistics; genomics.
Papers:

Wheels: A new criterion for nonconvexity of neural codes,
with
Laura Matusevich and Alexander Ruys de Perez.

Identifiability of linear compartmental tree models,
with
Cashous Bortner, Elizabeth Gross, Nicolette Meshkat, and Seth Sullivant. Submitted.

Absolute concentration robustness in networks with many conservation laws,
with Nicolette Meshkat and Angélica Torres.
Accepted to Vietnam Journal of Mathematics, special issue in honor of Bernd Sturmfels.

Identifiability of linear compartmental models: The impact of removing leaks and edges,
with Patrick Chan, Katherine Johnston, Aleksandra Sobieska, and Clare Spinner. Submitted.

Nondegenerate neural codes and obstructions to closedconvexity, with Patrick Chan, Katherine Johnston, Joseph Lent, and Alexander Ruys de Perez. Submitted.

Neural Codes With Three Maximal Codewords: Convexity and Minimal Embedding
Dimension, with Katherine Johnston and Clare Spinner. Accepted to Involve, a Journal of Mathematics.

Mixed volume of small reaction networks, with
Nida Obatake and Dilruba Sofia. Involve, a Journal of Mathematics,
13:5, pp. 845860 (2020).

Nonmonotonicity of closed convexity in neural codes, with Brianna Gambacini, R. Amzi Jeffs, and Sam Macdonald. Accepted to Vietnam Journal of Mathematics, special issue in honor of Bernd Sturmfels.

Dynamics of ERK regulation in the processive limit, with Carsten Conradi, Nida Obatake, and Xiaoxian Tang. Journal of Mathematical Biology, vol. 82, article 32 (2021).

Identifiability of linear compartmental models: The effect of moving inputs, outputs, and leaks, with Seth Gerberding and Nida Obatake. Linear and Multilinear Algebra, to appear.

Neural codes and the factor complex,
with Alexander Ruys de Perez and Laura Matusevich. Advances in Applied Mathematics, vol. 114, Article 101977 (2020).

Oscillations and bistability in a model of ERK regulation, with Nida Obatake, Xiaoxian Tang, and Angelica Torres. Journal of Mathematical Biology, vol. 79, no. 4, 1515–1549 (2019).

Joining and decomposing reaction networks, with Elizabeth Gross, Heather Harrington, and Nicolette Meshkat. Journal of Mathematical Biology, vol. 80, pp. 16831731 (2020).

Multistationarity in structured reaction networks, with Alicia Dickenstein, Mercedes Perez Millan, and Xiaoxian Tang. Bulletin
of Mathematical Biology, vol. 81, no. 5, 15271581 (2019).

Emergence of oscillations in a mixedmechanism phosphorylation system, with Carsten Conradi and Maya Mincheva. Bulletin
of Mathematical Biology, vol. 81, no. 6, 18291852 (2019). Supplementary Information.

Revisiting an intracellular regulatory network that exhibits oscillations, with Jonathan Tyler and Jay Walton. Journal of Mathematical Biology, vol. 78, no. 7, 23412368 (2019).

Linear compartmental models: inputoutput equations and operations that preserve identifiability, with Elizabeth Gross, Heather A. Harrington, and Nicolette Meshkat. SIAM Journal on Applied Mathematics, vol. 79, no. 4, 1423–1447 (2019).

Algebraic signatures of convex and nonconvex codes, with
Carina Curto, Elizabeth Gross,
Jack Jeffries, Katherine Morrison, Zvi Rosen, and Nora Youngs.
Journal of Pure and Applied Algebra, vol. 223, no. 9, 39193940 (2019).

Neural codes, decidability, and a new local obstruction to convexity,
with Aaron Chen and Florian Frick. SIAM Journal on Applied Algebra and Geometry, vol. 3, no. 1, 44−66 (2019).

Nondegenerate multistationarity in small reaction networks, with Timo de Wolff. Discrete & Continuous Dynamical Systems  B, vol. 24, no. 6, 26832700 (2019).

Identifiability of linear compartment models: the singular locus, with Elizabeth Gross and Nicolette Meshkat. Accepted to Advances in Applied Mathematics (2021).

Dynamics of posttranslational modification systems: recent progress and future directions, with Carsten Conradi. Invited Perspective. Biophysical Journal, vol. 114, issue 3, pp. 507515 (2018).

Gröbner bases of neural ideals, with Rebecca Garcia, Luis Garcia Puente, Ryan Kruse, Jessica Liu, Dane Miyata, Ethan Petersen, and Kaitlyn Phillipson. International Journal of Algebra and Computation, vol. 28, no. 4, pp. 553571 (2018).

An allencompassing global convergence result for processive multisite phosphorylation systems, with Mitchell Eithun. Mathematical Biosciences, vol. 291, pp. 19 (2017).

Which small reaction networks are multistationary?, with Badal Joshi. SIAM Journal on Applied Dynamical Systems, vol. 16, pp. 802833 (2017).

Obstructions to convexity in neural codes, with Caitlin Lienkaemper and Zev Woodstock. Advances in Applied Mathematics, vol. 85, pp. 3159 (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. 222238 (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. 6073 (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. 6997 (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. 4767 (2015).
 A global convergence result for processive multisite phosphorylation systems, with Carsten Conradi. Bulletin of Mathematical Biology 77:1, pp. 126155 (2015).
 A geometric approach to the global attractor conjecture, with Manoj Gopalkrishnan and Ezra Miller. SIAM J. Appl. Dyn. Syst., 13:2, pp. 758797 (2014).
 A projection argument for differential inclusions, with applications to persistence of massaction 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. 153178 (2013).
 Simplifying the Jacobian Criterion for precluding multistationarity in chemical reaction networks, with Badal Joshi. SIAM J. Appl. Math., 72:3, pp. 857876 (2012).
 Chemical reaction systems with
toric steady states, with Mercedes Perez Millan,
Alicia Dickenstein, and Carsten Conradi. Bulletin
of Mathematical Biology, 74:5, pp. 10271065 (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. 14481463 (2010).
 The dynamics of weakly reversible population processes near facets, with David F. Anderson. SIAM J. Appl. Math. 70:6, pp. 18401858 (2010).
 The smallest multistationary chemical reaction network. Proceedings of the Third International Conference, Algebraic Biology 2008, Castle of Hagenberg, Austria, July 31August 2, 2008. Lect. Notes Comput. Sc. 5147, pp. 172184 (2008).
 Toric dynamical systems, with Gheorghe Craciun, Alicia Dickenstein, and Bernd Sturmfels. Journal of Symbolic Computation 44, pp. 15511565 (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. 11171134 (2009).
 Three counterexamples on semigraphoids, with Raymond Hemmecke, Jason Morton, Bernd Sturmfels, Oliver Wienand. Combinatorics, Probability and Computing. 17:02, pp 239257 (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. 1215, 2006.
Link to my papers on the ArXiv.
Papers by undergraduate students under my mentorship:

On the identification of kinductively pierced codes using toric ideals
, Molly Hoch, Samuel Muthiah, and Nida Obatake. Submitted (in revision).

Strengthening relationships between neural ideals and receptive fields, Angelique Morvant. RoseHulman Undergraduate Mathematics Journal, 20:1 (2019), Article 8.

Conditions for Solvability in Chemical Reaction Networks at QuasiSteadyState, Mark Sweeney. Submitted.

Precluding Oscillations in MichaelisMenten Approximations of
Dualsite Phosphorylation Systems,
HwaiRay Tung. Mathematical Biosciences. 306, pp 5659 (2018).

Every Binary Code Can Be Realized by Convex Sets,
Megan K. Franke and Samuel Muthiah. Advances in Applied Mathematics. 99, pp 8393 (2018).

No oscillations in the MichaelisMenten approximation of the dual
futile cycle under a sequential and distributive mechanism,
Adriana Morales and Luna Bozeman. SIAM Undergraduate Research Online. 10, pp 2128 (2017).

ComplexBalanced Steady States of Chemical Reaction Networks that Contain an Eulerian Cycle,
Daniel Thielman (comentored by Christine Berkesch). Undergraduate thesis (Duke), Apr. 2012.
More about me:
My research group:
Photo (April 2019)
Ph.D. students:
Graduated Ph.D. students:

Alex Ruys de Perez (Ph.D. 2021, coadvised with Laura Matusevich), Postdoc, Dept. of Mathematics and Southeast Center for Mathematics and Biology, GA Tech

Jonathan Tyler (Ph.D. 2019, coadvised with Jay Walton), Postdoc, Dept. of Mathematics, University of Michigan
Postdocs:
Former Postdocs:

Xiaoxian Tang (20172019), Faculty, Dept. of Mathematics, Beihang University (China)
Editorial work:
Upcoming Workshops and Conferences:
Past Workshops and Conferences:
Listed here.
Events I am organizing:
Past events organized:
 With Sourav Chatterji, I organized a BerkeleyDavis 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 45, 2009 (Saturday  Sunday).
 With Raman Sanyal, I organized the Berkeley Discrete Math Seminar during Spring 2009.
 With Valerie Hower, I organized a minisymposium at the SIAM Math for Industry conference (October 911, 2009 in San Francisco). The minisymposium 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. 69, 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 1216, 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 2529, 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 14, 2013).
 I was one of the organizers of the 2015 Texas Algebraic Geometry Symposium, Texas A&M University (April 1012, 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 37, 2015).
 I was one of the organizers of the MiniTAGS workshop at Texas A&M (Saturdays, September 26, 2015 and October 24, 2015)

With Paulo LimaFilho and Jay Walton, I organized an IAMCS workshop on Contemporary Mathematical Challenges in the Life Sciences (May 1618, 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. 23, 2017).
 I was one of the organizers of the 2018
Texas Algebraic Geometry Symposium, Texas A&M University (Apr. 68, 2018). Conference poster courtesy of David Kerr.

With Brandy Stigler, I organized a special session on New Developments in Algebraic Biology at the
AWM Research Symposium 2019 at Rice University (April 67, 2019).
Upcoming Talks:

"Identifiability of linear compartment models", Industrial and Applied Mathematics Seminar, Texas A&M (Feb. 15, 2021).

"Finding Periodic Genes: From Mice to Mathematics", Biostatistics seminar, UC Davis (online), (May 24, 2021).

"Absolute concentration robustness in networks with many conservation laws",
minisymposium on "Advances in deterministic models of biochemical interaction networks"
at the
SMB Annual Meeting, online (Jun. 15, 2021 at 11:30 am Central).

"Identifiability and Operations on Linear Compartmental Models",
minisymposium on "Algebra and Geometry of Dynamic Models"
at the
SIAM Conference on Applied Algebraic Geometry 2021, Texas A&M (Aug. 18, 2021 at 1:40 PM Central)

"Absolute concentration robustness and multistationarity",
Mathematics of Reaction Networks (online) seminar (Sept. 16, 2021 at 10:00 AM Central)

"Identifiability of linear compartmental models", Applied CATS (Combinatorics, Algebra, Topology & Statistics) seminar, KTH Royal Institute of Technology (by Zoom, Nov. 30, 2021 at 16:15 CEST)
Past Talks:
Listed here.
Previous activities:
Older Projects:
Recognition:
 Association of Former Students Distinguished Achievement CollegeLevel Award in Teaching, 2019. Press release and photo.

Invited speaker for the 201819 Ethel AshworthTsutsui Memorial Lecture. Press release.
Current support:
Prior support:
 NSF Postdoctoral Fellowship, 20102013 (DMS1004380)
 NSF grant: "Biochemical reaction systems: multistationarity, persistence, and identifiability", 20132017 (DMS1312473, transferred to DMS1513364)
 Simons Foundation Collaboration Grant for Mathematicians, 20172018 (#521874)