Algebraic biology

Slides
Worksheet on algebraic models
Worksheet on place fields and neural ideals
M. Macauley and N. Youngs. The case for algebraic biology: from research to education. Bull. Math. Biol., 82(115), 2020.
M. Macauley and R. Robeva. Algebraic models, pseudomonomials, and inverse problems in algebraic biology. Lett. Biomath. 7(1):81--104, 2020.

Mathematical Concepts and Methods in Modern Biology: using modern discrete models, edited by Raina Robeva and Terrell Hodge. Academic Press, 2013. Freely available with ScienceDirect subscription.
Algebraic and Discrete Mathematical Methods for Modern Biology, edited by Raina Robeva. Academic Press, 2015. Freely available with ScienceDirect subscription.
Algebraic and Combinatorial Computational Biology, edited by Raina Robeva and Matthew Macauley. Academic Press, 2018. Freely available with ScienceDirect, subscription.
Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks, by Ilya Shmulevich and Edward R. Dougherty. SIAM, 2010.
Biological Feedback, by René Thomas and Thomas D'Ari. CRC Press, 1990 (updated 2006).
Ideals, Varieties, and Algorithms: An Introduction to Computational Algebraic Geometry and Commutative Algebra, by David A. Cox, John Little, and Donal O'Shea. Spring, 2015 (4th edition).

TURING: Algorithms for Computational with Finite Dynamical Systems. List of algorithms on AlgoRun.
Sage: free open-source mathematics software. Can be downloaded or run online.
Singular: free open-source computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory. Can be downloaded or run online.
Macaulay2: free open-source software for computational algebraic geometry and commutative algebra. Can be downloaded or run online.
The gfan package for computing the Gröbner fan of an ideal in Singular.
GINsim (Gene Interaction Network simulation), a computer tool for modeling and simulation of Boolean and logical networks.

The various lac operon models for entry in Cyclone.
The toy 3-variable lac operon model of Robeva in Macaulay2
The 9-variable lac operon model of Robeva in Macaulay2
The 10-variable lac operon model of Veliz-Cuba/Stigler that exhibits bistability in Macaulay2
The Reduction of a 5-variable Boolean model.

M. Macauley and N. Youngs. The case for algebraic biology: from research to education. Under review, 2020.
A. Veliz-Cuba and B. Stigler. Boolean Models Can Explain Bistability in the lac Operon. J. Comput. Biol., 2011, 783-794.