Reinhard C. Laubenbacher

76 papers B 4Misc 1Journal 62Unranked 6

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Beyond Boolean Networks: New Tools for the Steady State Analysis of Multivalued Networks. SIAM J. Appl. Dyn. Syst. Juliana García Galofre, Mercedes Pérez Millán, Ayelén Galarza Rial, Reinhard C. Laubenbacher, Alicia Dickenstein
2025	J	`jnl`	Optimal control of agent-based models via surrogate modeling. PLoS Comput. Biol. Luis L. Fonseca, Lucas Böttcher, Borna Mehrad, Reinhard C. Laubenbacher
2024	J	`jnl`	Control of Medical Digital Twins with Artificial Neural Networks. CoRR Lucas Böttcher, Luis L. Fonseca, Reinhard C. Laubenbacher
2024	J	`jnl`	Digital twins in medicine. Nat. Comput. Sci. Reinhard C. Laubenbacher, Borna Mehrad, Ilya Shmulevich, Natalia A. Trayanova
2024	J	`jnl`	Metamodeling and Control of Medical Digital Twins. CoRR Luis L. Fonseca, Lucas Böttcher, Borna Mehrad, Reinhard C. Laubenbacher
2024	J	`jnl`	Toward mechanistic medical digital twins: some use cases in immunology. Frontiers Digit. Health Reinhard C. Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James A. Glazier, Tomás Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E. Yankeelov, Tjalf Ziemssen
2023	J	`jnl`	Collectively canalizing Boolean functions. Adv. Appl. Math. Claus Kadelka, Benjamin Keilty, Reinhard C. Laubenbacher
2022	J	`jnl`	Building digital twins of the human immune system: toward a roadmap. npj Digit. Medicine Reinhard C. Laubenbacher, Anna Niarakis, Tomás Helikar, Gary An, Bruce Shapiro, Rahuman S. Malik-Sheriff, T. J. Sego, Adam C. Knapp, Paul Macklin, James A. Glazier
2022	J	`jnl`	Stability of Linear Boolean Networks. CoRR Karthik Chandrasekhar, Claus Kadelka, Reinhard C. Laubenbacher, David Murrugarra
2022	J	`jnl`	Topological data analysis in biomedicine: A review. J. Biomed. Informatics Yara Skaf, Reinhard C. Laubenbacher
2021	J	`jnl`	A modular computational framework for medical digital twins. Proc. Natl. Acad. Sci. USA 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, Reinhard C. Laubenbacher
2021	J	`jnl`	Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies. PLoS Comput. Biol. David J. Wooten, Jorge Gómez Tejeda Zañudo, David Murrugarra, Austin M. Perry, Anna Dongari-Bagtzoglou, Reinhard C. Laubenbacher, Clarissa J. Nobile, Réka Albert
2020	J	`jnl`	Collectively canalizing Boolean functions. CoRR Claus Kadelka, Benjamin Keilty, Reinhard C. Laubenbacher
2020	J	`jnl`	The Dynamics of Canalizing Boolean Networks. Complex. Elijah Paul, Gleb Pogudin, William Qin, Reinhard C. Laubenbacher
2019	J	`jnl`	Dynamics of semilattice networks with strongly connected dependency graph. Autom. Alan Veliz-Cuba, Reinhard C. Laubenbacher
2019	J	`jnl`	Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors. PLoS Comput. Biol. Yingqian Ada Zhan, Charles Gregory Wray, Sandeep Namburi, Spencer T. Glantz, Reinhard C. Laubenbacher, Jeffrey H. Chuang
2019	J	`jnl`	PlantSimLab - a modeling and simulation web tool for plant biologists. BMC Bioinform. S. Ha, Elena S. Dimitrova, Stefan Hoops, Doaa Altarawy, Mitra Ansariola, D. Deb, Jane Glazebrook, R. Hillmer, Hossameldin Shahin, Fumiaki Katagiri, John McDowell, Molly Megraw, João C. Setubal, B. M. Tyler, Reinhard C. Laubenbacher
2019	J	`jnl`	The Dynamics of Canalizing Boolean Networks. CoRR Elijah Paul, Gleb Pogudin, William Qin, Reinhard C. Laubenbacher
2018	J	`jnl`	Applications of network analysis to routinely collected health care data: a systematic review. J. Am. Medical Informatics Assoc. Jason Cory Brunson, Reinhard C. Laubenbacher
2018	J	`jnl`	The innate immune response to ischemic injury: a multiscale modeling perspective. BMC Syst. Biol. Elena S. Dimitrova, Leslie A. Caromile, Reinhard C. Laubenbacher, Linda H. Shapiro
2017	J	`jnl`	Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective. PLoS Comput. Biol. 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
2017	J	`jnl`	Multistate nested canalizing functions and their networks. Theor. Comput. Sci. Claus Kadelka, Yuan Li, Jack Kuipers, John O. Adeyeye, Reinhard C. Laubenbacher
2016	J	`jnl`	A computational model of invasive aspergillosis in the lung and the role of iron. BMC Syst. Biol. Matthew Oremland, Kathryn R. Michels, Alexandra M. Bettina, Christopher Lawrence, Borna Mehrad, Reinhard C. Laubenbacher
2016	J	`jnl`	AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms. Bioinform. Abdelrahman Hosny, Paola Vera-Licona, Reinhard C. Laubenbacher, Thibauld Favre
2016	J	`jnl`	Identification of control targets in Boolean molecular network models via computational algebra. BMC Syst. Biol. David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Reinhard C. Laubenbacher
2015	J	`jnl`	Iron acquisition and oxidative stress response in aspergillus fumigatus. BMC Syst. Biol. Madison Brandon, Brad Howard, Christopher Lawrence, Reinhard C. Laubenbacher
2014	—	`ch.`	Algebraic Models and Their Use in Systems Biology. Discrete and Topological Models in Molecular Biology Reinhard C. Laubenbacher, Franziska Hinkelmann, David Murrugarra, Alan Veliz-Cuba
2014	J	`jnl`	An Algebra-Based Method for Inferring Gene Regulatory Networks. BMC Syst. Biol. Paola Vera-Licona, Abdul Salam Jarrah, Luis David García-Puente, John McGee, Reinhard C. Laubenbacher
2014	—	`conf`	Dimension Reduction of Large Sparse AND-NOT Network Models. SASB Alan Veliz-Cuba, Boris Aguilar, Reinhard C. Laubenbacher
2014	J	`jnl`	Evolutionary events in a mathematical sciences research collaboration network. Scientometrics Jason Cory Brunson, Steve Fassino, Antonio McInnes, Monisha Narayan, Brianna Richardson, Christopher Franck, Patrick Ion, Reinhard C. Laubenbacher
2014	Misc	`conf`	Evolving Collaboration Patterns in Medical Research. AMIA Jason Cory Brunson, Xiaoyan Wang, Reinhard C. Laubenbacher
2014	J	`jnl`	Optimization of Agent-Based Models: Scaling Methods and Heuristic Algorithms. J. Artif. Soc. Soc. Simul. Matthew Oremland, Reinhard C. Laubenbacher
2014	J	`jnl`	Steady state analysis of Boolean molecular network models via model reduction and computational algebra. BMC Bioinform. Alan Veliz-Cuba, Boris Aguilar, Franziska Hinkelmann, Reinhard C. Laubenbacher
2014	J	`jnl`	Structure and dynamics of acyclic networks. Discret. Event Dyn. Syst. Alan Veliz-Cuba, David Murrugarra, Reinhard C. Laubenbacher
2013	J	`jnl`	Boolean nested canalizing functions: A comprehensive analysis. Theor. Comput. Sci. Yuan Li, John O. Adeyeye, David Murrugarra, Boris Aguilar, Reinhard C. Laubenbacher
2013	J	`jnl`	Dimension Reduction of Large AND-NOT Network Models. CoRR Alan Veliz-Cuba, Reinhard C. Laubenbacher, Boris Aguilar
2013	—	`ch.`	Finite fields in biology. Handbook of Finite Fields Franziska Hinkelmann, Reinhard C. Laubenbacher
2012	J	`jnl`	Evolutionary Events in a Mathematical Sciences Research Collaboration Network CoRR Jason Cory Brunson, Steve Fassino, Antonio McInnes, Monisha Narayan, Brianna Richardson, Christopher Franck, Patrick Ion, Reinhard C. Laubenbacher
2012	J	`jnl`	Modeling stochasticity and variability in gene regulatory networks. EURASIP J. Bioinform. Syst. Biol. David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Seda Arat, Reinhard C. Laubenbacher
2011	J	`jnl`	ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra. BMC Bioinform. Franziska Hinkelmann, Madison Brandon, Bonny Guang, Rustin McNeill, Grigoriy Blekherman, Alan Veliz-Cuba, Reinhard C. Laubenbacher
2011	J	`jnl`	Nested Canalyzing Functions And Their Average Sensitivities CoRR Yuan Li, John O. Adeyeye, Reinhard C. Laubenbacher
2011	J	`jnl`	Parameter estimation for Boolean models of biological networks. Theor. Comput. Sci. Elena S. Dimitrova, Luis David García-Puente, Franziska Hinkelmann, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Brandilyn Stigler, Michael Eugene Stillman, Paola Vera-Licona
2010	J	`jnl`	A Mathematical Framework for Agent Based Models of Complex Biological Networks CoRR Franziska Hinkelmann, David Murrugarra, Abdul Salam Jarrah, Reinhard C. Laubenbacher
2010	J	`jnl`	Discretization of Time Series Data. J. Comput. Biol. Elena S. Dimitrova, Paola Vera-Licona, John McGee, Reinhard C. Laubenbacher
2010	J	`jnl`	Polynomial algebra of discrete models in systems biology. Bioinform. Alan Veliz-Cuba, Abdul Salam Jarrah, Reinhard C. Laubenbacher
2009	—	`ch.`	Agent Based Modeling, Mathematical Formalism for. Encyclopedia of Complexity and Systems Science Reinhard C. Laubenbacher, Abdul Salam Jarrah, Henning S. Mortveit, S. S. Ravi
2009	J	`jnl`	Computer Algebra in Systems Biology. Am. Math. Mon. Reinhard C. Laubenbacher, Bernd Sturmfels
2009	J	`jnl`	Computeralgebra in der Systembiologie. Inform. Spektrum Reinhard C. Laubenbacher, Bernd Sturmfels
2008	J	`jnl`	A mathematical formalism for agent-based modeling CoRR Reinhard C. Laubenbacher, Abdul Salam Jarrah, Henning S. Mortveit, S. S. Ravi
2008	J	`jnl`	Applications of the gröbner fan to gene network reconstruction (abstract only). ACM Commun. Comput. Algebra Elena S. Dimitrova, Brandilyn Stigler, Abdul Salam Jarrah, Reinhard C. Laubenbacher
2008	—	`conf`	Stabilizing and Destabilizing Effects of Embedding 3-Node Subgraphs on the State Space of Boolean Networks. ACRI Chikoo Oosawa, Michael A. Savageau, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Eduardo D. Sontag
2008	J	`jnl`	Using Formal Concept Analysis for microarray Data Comparison. J. Bioinform. Comput. Biol. V. Choi, Y. Huang, Vy Lam, D. Potter, Reinhard C. Laubenbacher, Karen Duca
2007	B	`conf`	A Gröbner fan method for biochemical network modeling. ISSAC Elena S. Dimitrova, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Brandilyn Stigler
2007	J	`jnl`	Computer algebra in systems biology CoRR Reinhard C. Laubenbacher, Bernd Sturmfels
2007	—	`conf`	Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions. AB Abdul Salam Jarrah, Reinhard C. Laubenbacher
2007	J	`jnl`	Reverse-engineering of polynomial dynamical systems. Adv. Appl. Math. Abdul Salam Jarrah, Reinhard C. Laubenbacher, Brandilyn Stigler, Michael Eugene Stillman
2007	J	`jnl`	Simulating Epstein-Barr virus infection with C-ImmSim. Bioinform. Filippo Castiglione, Karen Duca, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Donna Hochberg, David Thorley-Lawson
2007	B	`conf`	Using Formal Concept Analysis for Microarray Data Comparison. APBC V. Choi, Y. Huang, Vy Lam, D. Potter, Reinhard C. Laubenbacher, Karen Duca
2006	J	`jnl`	Monomial Dynamical Systems over Finite Fields. Complex Syst. Omar Colón-Reyes, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Bernd Sturmfels
2006	J	`jnl`	Sequential dynamical systems over words. Appl. Math. Comput. Luis David García-Puente, Abdul Salam Jarrah, Reinhard C. Laubenbacher
2006	J	`jnl`	Update schedules of sequential dynamical systems. Discret. Appl. Math. Reinhard C. Laubenbacher, Bodo Pareigis
2005	J	`jnl`	Perspectives on Discret. Math. Hélène Barcelo, Reinhard C. Laubenbacher
2004	—	`conf`	An analysis of a circadian model using the small-gain approach to monotone systems. CDC Abdul Jarrah, Hussein Vastani, Karen Duca, Reinhard C. Laubenbacher
2004	—	`conf`	An optimal control problem for in vitro virus competition. CDC Abdul Jarrah, Hussein Vastani, Karen Duca, Reinhard C. Laubenbacher
2004	—	`conf`	PathSim visualizer: an Information-Rich Virtual Environment framework for systems biology. Web3D Nicholas F. Polys, Doug A. Bowman, Chris North, Reinhard C. Laubenbacher, Karen Duca
2003	B	`conf`	A computer algebra approach to biological systems. ISSAC Reinhard C. Laubenbacher
2003	J	`jnl`	Decomposition and simulation of sequential dynamical systems. Adv. Appl. Math. Reinhard C. Laubenbacher, Bodo Pareigis
2003	J	`jnl`	The Sibirsky component of the center variety of polynomial differential systems. J. Symb. Comput. Abdul Salam Jarrah, Reinhard C. Laubenbacher, Valery G. Romanovski
2001	J	`jnl`	Classification of Finite Dynamical Systems CoRR Luis García, Abdul Salam Jarrah, Reinhard C. Laubenbacher
2001	J	`jnl`	Equivalence Relations on Finite Dynamical Systems. Adv. Appl. Math. Reinhard C. Laubenbacher, Bodo Pareigis
2001	J	`jnl`	Foundations of a Connectivity Theory for Simplicial Complexes. Adv. Appl. Math. Hélène Barcelo, Xenia H. Kramer, Reinhard C. Laubenbacher, Christopher Weaver
2001	B	`conf`	Generic ideals and Moreno-Socías conjucture. ISSAC Edith Aguirre, Abdul Salam Jarrah, Reinhard C. Laubenbacher
2000	J	`jnl`	An Algorithm for the Quillen-Suslin Theorem for Quotients of Polynomial Rings by Monomial Ideals. J. Symb. Comput. Reinhard C. Laubenbacher, Karen Schlauch
2000	J	`jnl`	Permanental Ideals. J. Symb. Comput. Reinhard C. Laubenbacher, Irena Swanson
2000	J	`jnl`	Special Issue on Symbolic Computation in Algebra, Analysis, and Geometry - Foreword of the Guest Editors. J. Symb. Comput. Eduardo Cattani, Reinhard C. Laubenbacher
1999	J	`jnl`	Monomial Orderings, Rewriting Systems, and Gröbner Bases for the Commutator Ideal of a Free Algebra. J. Symb. Comput. Susan M. Hermiller, Xenia H. Kramer, Reinhard C. Laubenbacher