- 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.

- What is Algebraic Biology? 13 pages. Updated Mar 18, 2020.

- Modeling the
*lac*operon in*E. coli*. 43 pages. Updated Mar 19, 2020. Worksheet.

- Algebraic models and finite dynamical systems. 23 pages. Updated Mar 31, 2020. Worksheet.

- Chemical reaction networks. 12 pages. Updated Mar 31, 2020. Worksheet.

- Bistability in ODE and algebraic models. 28 pages. Updated Mar 31, 2020. Worksheet

- Dilution, degradation, and time delays in algebraic models. 18 pages. Updated Mar 31, 2020. Worksheet.

- Reduction of algebraic models. 16 pages. Updated Mar 31, 2020. Worksheet

- Reverse engineering the wiring diagram. 39 pages. Updated Apr 7, 2018.

- Reverse engineering the model space. 29 pages. Updated Apr 5, 2018. Worksheet

- Fundamental axioms of mathematics, by Federico Ardilla
- The Lesson of Grace in Teaching, by Francis Su. Also available as a YouTube lecture.

- 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.