Monomial Orderings, Rewriting Systems, and Gröbner Bases for the Commutator Ideal of a Free Algebra. - Susan M. Hermiller; Xenia H. Kramer; Reinhard C. Laubenbacher (J. Symb. Comput., 1999)

Special Issue on Symbolic Computation in Algebra, Analysis, and Geometry - Foreword of the Guest Editors. - Eduardo Cattani; Reinhard C. Laubenbacher (J. Symb. Comput., 2000)

Permanental Ideals. - Reinhard C. Laubenbacher; Irena Swanson (J. Symb. Comput., 2000)

An Algorithm for the Quillen-Suslin Theorem for Quotients of Polynomial Rings by Monomial Ideals. - Reinhard C. Laubenbacher; Karen Schlauch (J. Symb. Comput., 2000)

Generic ideals and Moreno-Socías conjucture. - Edith Aguirre; Abdul Salam Jarrah; Reinhard C. Laubenbacher (ISSAC, 2001)

Foundations of a Connectivity Theory for Simplicial Complexes. - Hélène Barcelo; Xenia H. Kramer; Reinhard C. Laubenbacher; Christopher Weaver 002 (Adv. Appl. Math., 2001)

Equivalence Relations on Finite Dynamical Systems. - Reinhard C. Laubenbacher; Bodo Pareigis (Adv. Appl. Math., 2001)

Classification of Finite Dynamical Systems - Luis García; Abdul Salam Jarrah; Reinhard C. Laubenbacher (CoRR, 2001)

A computer algebra approach to biological systems. - Reinhard C. Laubenbacher (ISSAC, 2003)

Decomposition and simulation of sequential dynamical systems. - Reinhard C. Laubenbacher; Bodo Pareigis (Adv. Appl. Math., 2003)

The Sibirsky component of the center variety of polynomial differential systems. - Abdul Salam Jarrah; Reinhard C. Laubenbacher; Valery G. Romanovski (J. Symb. Comput., 2003)

An analysis of a circadian model using the small-gain approach to monotone systems. - Abdul Jarrah; Hussein Vastani; Karen Duca; Reinhard C. Laubenbacher (CDC, 2004)

An optimal control problem for in vitro virus competition. - Abdul Jarrah; Hussein Vastani; Karen Duca; Reinhard C. Laubenbacher (CDC, 2004)

PathSim visualizer: an Information-Rich Virtual Environment framework for systems biology. - Nicholas F. Polys; Doug A. Bowman; Chris North 001; Reinhard C. Laubenbacher; Karen Duca (Web3D, 2004)

Perspectives on A-homotopy theory and its applications. - Hélène Barcelo; Reinhard C. Laubenbacher (Discret. Math., 2005)

Sequential dynamical systems over words. - Luis David García-Puente; Abdul Salam Jarrah; Reinhard C. Laubenbacher (Appl. Math. Comput., 2006)

Monomial Dynamical Systems over Finite Fields. - Omar Colón-Reyes; Abdul Salam Jarrah; Reinhard C. Laubenbacher; Bernd Sturmfels (Complex Syst., 2006)

Update schedules of sequential dynamical systems. - Reinhard C. Laubenbacher; Bodo Pareigis (Discret. Appl. Math., 2006)

Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions. - Abdul Salam Jarrah; Reinhard C. Laubenbacher (AB, 2007)

A Gröbner fan method for biochemical network modeling. - Elena S. Dimitrova; Abdul Salam Jarrah; Reinhard C. Laubenbacher; Brandilyn Stigler (ISSAC, 2007)

Reverse-engineering of polynomial dynamical systems. - Abdul Salam Jarrah; Reinhard C. Laubenbacher; Brandilyn Stigler; Michael Eugene Stillman (Adv. Appl. Math., 2007)

Simulating Epstein-Barr virus infection with C-ImmSim. - Filippo Castiglione; Karen Duca; Abdul Salam Jarrah; Reinhard C. Laubenbacher; Donna Hochberg; David Thorley-Lawson (Bioinform., 2007)

Stabilizing and Destabilizing Effects of Embedding 3-Node Subgraphs on the State Space of Boolean Networks. - Chikoo Oosawa; Michael A. Savageau; Abdul Salam Jarrah; Reinhard C. Laubenbacher; Eduardo D. Sontag (ACRI, 2008)

Applications of the gröbner fan to gene network reconstruction (abstract only). - Elena S. Dimitrova; Brandilyn Stigler; Abdul Salam Jarrah; Reinhard C. Laubenbacher (ACM Commun. Comput. Algebra, 2008)

A mathematical formalism for agent-based modeling - Reinhard C. Laubenbacher; Abdul Salam Jarrah; Henning S. Mortveit; S. S. Ravi (CoRR, 2008)

Using Formal Concept Analysis for microarray Data Comparison. - V. Choi; Y. Huang; Vy Lam; D. Potter; Reinhard C. Laubenbacher; Karen Duca (J. Bioinform. Comput. Biol., 2008)

Computeralgebra in der Systembiologie. - Reinhard C. Laubenbacher; Bernd Sturmfels (Inform. Spektrum, 2009)

Computer Algebra in Systems Biology. - Reinhard C. Laubenbacher; Bernd Sturmfels (Am. Math. Mon., 2009)

Agent Based Modeling, Mathematical Formalism for. - Reinhard C. Laubenbacher; Abdul Salam Jarrah; Henning S. Mortveit; S. S. Ravi (Encyclopedia of Complexity and Systems Science, 2009)

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

A Mathematical Framework for Agent Based Models of Complex Biological Networks - Franziska Hinkelmann; David Murrugarra; Abdul Salam Jarrah; Reinhard C. Laubenbacher (CoRR, 2010)

Discretization of Time Series Data. - Elena S. Dimitrova; Paola Vera-Licona; John McGee; Reinhard C. Laubenbacher (J. Comput. Biol., 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)

Nested Canalyzing Functions And Their Average Sensitivities - Yuan Li; John O. Adeyeye; Reinhard C. Laubenbacher (CoRR, 2011)

Parameter estimation for Boolean models of biological networks. - Elena S. Dimitrova; Luis David García-Puente; Franziska Hinkelmann; Abdul Salam Jarrah; Reinhard C. Laubenbacher; Brandilyn Stigler; Michael Eugene Stillman; Paola Vera-Licona (Theor. Comput. Sci., 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)

Finite fields in biology. - Franziska Hinkelmann; Reinhard C. Laubenbacher (Handbook of Finite Fields, 2013)

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

Boolean nested canalizing functions: A comprehensive analysis. - Yuan Li; John O. Adeyeye; David Murrugarra; Boris Aguilar; Reinhard C. Laubenbacher (Theor. Comput. Sci., 2013)

Evolving Collaboration Patterns in Medical Research. - Jason Cory Brunson; Xiaoyan Wang; Reinhard C. Laubenbacher (AMIA, 2014)

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)

An Algebra-Based Method for Inferring Gene Regulatory Networks. - Paola Vera-Licona; Abdul Salam Jarrah; Luis David García-Puente; John McGee; Reinhard C. Laubenbacher (BMC Syst. Biol., 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)

Optimization of Agent-Based Models: Scaling Methods and Heuristic Algorithms. - Matthew Oremland; Reinhard C. Laubenbacher (J. Artif. Soc. Soc. Simul., 2014)

Evolutionary events in a mathematical sciences research collaboration network. - Jason Cory Brunson; Steve Fassino; Antonio McInnes; Monisha Narayan; Brianna Richardson; Christopher Franck; Patrick Ion; Reinhard C. Laubenbacher (Scientometrics, 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)

Iron acquisition and oxidative stress response in aspergillus fumigatus. - Madison Brandon; Brad Howard; Christopher Lawrence; Reinhard C. Laubenbacher (BMC Syst. Biol., 2015)

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms. - Abdelrahman Hosny; Paola Vera-Licona; Reinhard C. Laubenbacher; Thibauld Favre (Bioinform., 2016)

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)

A computational model of invasive aspergillosis in the lung and the role of iron. - Matthew Oremland; Kathryn R. Michels; Alexandra M. Bettina; Christopher Lawrence; Borna Mehrad; Reinhard C. Laubenbacher (BMC Syst. Biol., 2016)

Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective. - Julia Chifman; Seda Arat; Zhiyong Deng; Erica Lemler; James C. Pino; Leonard A. Harris; Michael A. Kochen; Carlos F. Lopez; Steven A. Akman; Frank M. Torti; Suzy V. Torti; Reinhard C. Laubenbacher (PLoS Comput. Biol., 2017)

Multistate nested canalizing functions and their networks. - Claus Kadelka; Yuan Li; Jack Kuipers; John O. Adeyeye; Reinhard C. Laubenbacher (Theor. Comput. Sci., 2017)

The innate immune response to ischemic injury: a multiscale modeling perspective. - Elena S. Dimitrova; Leslie A. Caromile; Reinhard C. Laubenbacher; Linda H. Shapiro (BMC Syst. Biol., 2018)

Applications of network analysis to routinely collected health care data: a systematic review. - Jason Cory Brunson; Reinhard C. Laubenbacher (J. Am. Medical Informatics Assoc., 2018)

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

Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors. - Yingqian Ada Zhan; Charles Gregory Wray; Sandeep Namburi; Spencer T. Glantz; Reinhard C. Laubenbacher; Jeffrey H. Chuang (PLoS Comput. Biol., 2019)

PlantSimLab - a modeling and simulation web tool for plant biologists. - S. Ha; Elena S. Dimitrova; Stefan Hoops; Doaa Altarawy; Mitra Ansariola; D. Deb; Jane Glazebrook; R. Hillmer; Hossameldin Shahin; Fumiaki Katagiri; J. McDowell; Molly Megraw; et al. (BMC Bioinform., 2019)

The Dynamics of Canalizing Boolean Networks. - Elijah Paul; Gleb Pogudin; William Qin; Reinhard C. Laubenbacher (Complex., 2020)

Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies. - David J. Wooten; Jorge Gómez Tejeda Zañudo; David Murrugarra; Austin M. Perry; Anna Dongari-Bagtzoglou; Reinhard C. Laubenbacher; Clarissa J. Nobile; Réka Albert (PLoS Comput. Biol., 2021)

A modular computational framework for medical digital twins. - Joseph Masison; Jonathan Beezley; Yu Mei; Henrique Assis Lopes Ribeiro; Adam C. Knapp; Luis Sordo Vieira; Bandita Adhikari; Yogesh Scindia; Michael Grauer; Brian Helba; William Schroeder; Borna Mehrad; et al. (Proc. Natl. Acad. Sci. USA, 2021)

SteadyCellPhenotype: a web-based tool for the modeling of biological networks with ternary logic. - Adam C. Knapp; Luis Sordo Vieira; Reinhard C. Laubenbacher; Julia Chifman (Bioinform., 2022)

Stability of Linear Boolean Networks. - Karthik Chandrasekhar; Claus Kadelka; Reinhard C. Laubenbacher; David Murrugarra (CoRR, 2022)

Topological data analysis in biomedicine: A review. - Yara Skaf; Reinhard C. Laubenbacher (J. Biomed. Informatics, 2022)

Building digital twins of the human immune system: toward a roadmap. - Reinhard C. Laubenbacher; Anna Niarakis; Tomás Helikar; Gary An; B. Shapiro; Rahuman S. Malik-Sheriff; T. J. Sego; Adam C. Knapp; Paul Macklin; James A. Glazier (npj Digit. Medicine, 2022)

Collectively canalizing Boolean functions. - Claus Kadelka; Benjamin Keilty; Reinhard C. Laubenbacher (Adv. Appl. Math., 2023)

Metamodeling and Control of Medical Digital Twins. - Luis L. Fonseca; Lucas Böttcher; Borna Mehrad; Reinhard C. Laubenbacher (CoRR, 2024)

Control of Medical Digital Twins with Artificial Neural Networks. - Lucas Böttcher; Luis L. Fonseca; Reinhard C. Laubenbacher (CoRR, 2024)

Toward mechanistic medical digital twins: some use cases in immunology. - Reinhard C. Laubenbacher; Fred Adler; Gary An; Filippo Castiglione; Stephen Eubank 002; Luis L. Fonseca; James A. Glazier; Tomás Helikar; Marti Jett-Tilton; Denise Kirschner; Paul Macklin; Borna Mehrad; et al. (Frontiers Digit. Health, 2024)

Digital twins in medicine. - Reinhard C. Laubenbacher; Borna Mehrad; Ilya Shmulevich; Natalia A. Trayanova (Nat. Comput. Sci., 2024)

Optimal control of agent-based models via surrogate modeling. - Luis L. Fonseca; Lucas Böttcher; Borna Mehrad; Reinhard C. Laubenbacher (PLoS Comput. Biol., 2025)