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

- During Fall 2017, I am teaching Calculus I for Biological Sciences (Math 147, sections 501-502-503 and sections 507-508-509).

Listed here.

Algebraic, geometric, and combinatorial approaches to mathematical biology; biochemical dynamical systems; neural coding; algebraic statistics; genomics.

*Identifiability of linear compartment models: the singular locus*, with Elizabeth Gross and Nicolette Meshkat.*Dynamics of post-translational modification systems: recent progress and future directions*, with Carsten Conradi. Submitted.*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. 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.

- Special Session on "Applicable and Computational Algebraic Geometry" at the AMS Fall Central Section Meeting at University of North Texas, Denton TX (Sept. 9-10, 2017).
- SQuaRE at AIM (November 13-17, 2017)
- Nebraska Conference for Undergraduate Women in Mathematics, University of Nebraska Lincoln, (Jan. 26-28, 2018).
- CombinaTexas, Texas A&M University (Feb. 10-11, 2018)
- Texas Algebraic Geometry Symposium, Texas A&M University (Apr. 6-8, 2018)

Listed here.

- 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).

- "Identifiability of linear compartment models: the singular locus", Special Session on "Applicable and Computational Algebraic Geometry" at the AMS Fall Central Section Meeting at University of North Texas, Denton TX (Sept. 9, 2017 at 8:30 am).

Listed here.

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

- 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 at Berkeley, in which we assembled, annotated, and analyzed a newly sequenced genome.

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 2017-2022 (#521874)