Polynomial algebra of discrete models in systems biology. - Alan Veliz-Cuba; Abdul Salam Jarrah; Reinhard C. Laubenbacher (Bioinform., 2010)

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra. - Franziska Hinkelmann; Madison Brandon; Bonny Guang; Rustin McNeill; Grigoriy Blekherman; Alan Veliz-Cuba; Reinhard C. Laubenbacher (BMC Bioinform., 2011)

On the relationship of steady states of continuous and discrete models - Alan Veliz-Cuba; Joseph Arthur; Laura Hochstetler; Victoria Klomps; Erikka Korpi (CoRR, 2011)

Boolean Models Can Explain Bistability in the lac Operon. - Alan Veliz-Cuba; Brandilyn Stigler (J. Comput. Biol., 2011)

Modeling stochasticity and variability in gene regulatory networks. - David Murrugarra; Alan Veliz-Cuba; Boris Aguilar; Seda Arat; Reinhard C. Laubenbacher (EURASIP J. Bioinform. Syst. Biol., 2012)

An Algebraic Approach to Reverse Engineering Finite Dynamical Systems Arising from Biology. - Alan Veliz-Cuba (SIAM J. Appl. Dyn. Syst., 2012)

Dimension Reduction of Large AND-NOT Network Models. - Alan Veliz-Cuba; Reinhard C. Laubenbacher; Boris Aguilar (CoRR, 2013)

Steady state analysis of Boolean molecular network models via model reduction and computational algebra. - Alan Veliz-Cuba; Boris Aguilar; Franziska Hinkelmann; Reinhard C. Laubenbacher (BMC Bioinform., 2014)

Structure and dynamics of acyclic networks. - Alan Veliz-Cuba; David Murrugarra; Reinhard C. Laubenbacher (Discret. Event Dyn. Syst., 2014)

Dimension Reduction of Large Sparse AND-NOT Network Models. - Alan Veliz-Cuba; Boris Aguilar; Reinhard C. Laubenbacher (SASB, 2014)

Algebraic Models and Their Use in Systems Biology. - Reinhard C. Laubenbacher; Franziska Hinkelmann; David Murrugarra; Alan Veliz-Cuba (Discrete and Topological Models in Molecular Biology, 2014)

Networks that learn the precise timing of event sequences. - Alan Veliz-Cuba; Harel Z. Shouval; Kresimir Josic; Zachary P. Kilpatrick (J. Comput. Neurosci., 2015)

Sources of Variability in a Synthetic Gene Oscillator. - Alan Veliz-Cuba; Andrew J. Hirning; Adam A. Atanas; Faiza Hussain; Flavia Vancia; Kresimir Josic; Matthew R. Bennett (PLoS Comput. Biol., 2015)

Identification of control targets in Boolean molecular network models via computational algebra. - David Murrugarra; Alan Veliz-Cuba; Boris Aguilar; Reinhard C. Laubenbacher (BMC Syst. Biol., 2016)

The Number of Fixed Points of AND-OR Networks with Chain Topology. - Alan Veliz-Cuba; Lauren Geiser (CoRR, 2016)

Stochastic Models of Evidence Accumulation in Changing Environments. - Alan Veliz-Cuba; Zachary P. Kilpatrick; Kresimir Josic (SIAM Rev., 2016)

Evidence Accumulation and Change Rate Inference in Dynamic Environments. - Adrian E. Radillo; Alan Veliz-Cuba; Kresimir Josic; Zachary P. Kilpatrick (Neural Comput., 2017)

Bistability and oscillations in co-repressive synthetic microbial consortia. - Mehdi Sadeghpour; Alan Veliz-Cuba; Gábor Orosz; Kresimir Josic; Matthew R. Bennett (Quant. Biol., 2017)

Dynamics of semilattice networks with strongly connected dependency graph. - Alan Veliz-Cuba; Reinhard C. Laubenbacher (Autom., 2019)

An information theoretic approach for the inference of Boolean networks and functions from data: BoCSE. - David Murrugarra; Alan Veliz-Cuba (Patterns, 2022)

Algebraic network reconstruction of discrete dynamical systems. - Heather A. Harrington; Mike Stillman; Alan Veliz-Cuba (Adv. Appl. Math., 2024)

Algebraic Experimental Design: Theory and Computation. - Elena S. Dimitrova; Cameron H. Fredrickson; Nicholas A. Rondoni; Brandilyn Stigler; Alan Veliz-Cuba (SIAM J. Appl. Algebra Geom., 2024)

A Unified Approach to Reverse Engineering and Data Selection for Unique Network Identification. - Alan Veliz-Cuba; Vanessa Newsome-Slade; Elena S. Dimitrova (SIAM J. Appl. Dyn. Syst., 2024)