Reinhard C. Laubenbacher

Publication Activity (10 Years)

Years Active: 1999-2024
Publications (10 Years): 26

Top Topics

Immune Response

Boolean Networks

Mathematical Modeling

Top Venues

BMC Syst. Biol.

PLoS Comput. Biol.

Publications

Reinhard C. Laubenbacher, Borna Mehrad, Ilya Shmulevich, Natalia A. Trayanova
Digital twins in medicine. Nat. Comput. Sci. 4 (3) (2024)
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
Toward mechanistic medical digital twins: some use cases in immunology. Frontiers Digit. Health 6 (2024)
Lucas Böttcher, Luis L. Fonseca, Reinhard C. Laubenbacher
Control of Medical Digital Twins with Artificial Neural Networks. CoRR (2024)
Luis L. Fonseca, Lucas Böttcher, Borna Mehrad, Reinhard C. Laubenbacher
Metamodeling and Control of Medical Digital Twins. CoRR (2024)
Claus Kadelka, Benjamin Keilty, Reinhard C. Laubenbacher
Collectively canalizing Boolean functions. Adv. Appl. Math. 145 (2023)
Adam C. Knapp, Luis Sordo Vieira, Reinhard C. Laubenbacher, Julia Chifman
: a web-based tool for the modeling of biological networks with ternary logic. Bioinform. 38 (8) (2022)
Karthik Chandrasekhar, Claus Kadelka, Reinhard C. Laubenbacher, David Murrugarra
Stability of Linear Boolean Networks. CoRR (2022)
Yara Skaf, Reinhard C. Laubenbacher
Topological data analysis in biomedicine: A review. J. Biomed. Informatics 130 (2022)
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
Building digital twins of the human immune system: toward a roadmap. npj Digit. Medicine 5 (2022)
David J. Wooten, Jorge Gómez Tejeda Zañudo, David Murrugarra, Austin M. Perry, Anna Dongari-Bagtzoglou, Reinhard C. Laubenbacher, Clarissa J. Nobile, Réka Albert
Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies. PLoS Comput. Biol. 17 (3) (2021)
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
A modular computational framework for medical digital twins. Proc. Natl. Acad. Sci. USA 118 (20) (2021)
Elijah Paul, Gleb Pogudin, William Qin, Reinhard C. Laubenbacher
The Dynamics of Canalizing Boolean Networks. Complex. 2020 (2020)
Claus Kadelka, Benjamin Keilty, Reinhard C. Laubenbacher
Collectively canalizing Boolean functions. CoRR (2020)
Alan Veliz-Cuba, Reinhard C. Laubenbacher
Dynamics of semilattice networks with strongly connected dependency graph. Autom. 99 (2019)
Elijah Paul, Gleb Pogudin, William Qin, Reinhard C. Laubenbacher
The Dynamics of Canalizing Boolean Networks. CoRR (2019)
S. Ha, Elena S. Dimitrova, S. Hoops, Doaa Altarawy, Mitra Ansariola, D. Deb, Jane Glazebrook, R. Hillmer, Hossameldin Shahin, Fumiaki Katagiri, J. McDowell, Molly Megraw, J. Setubal, B. M. Tyler, Reinhard C. Laubenbacher
PlantSimLab - a modeling and simulation web tool for plant biologists. BMC Bioinform. 20 (1) (2019)
Yingqian Ada Zhan, Charles Gregory Wray, Sandeep Namburi, Spencer T. Glantz, Reinhard C. Laubenbacher, Jeffrey H. Chuang
Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors. PLoS Comput. Biol. 15 (6) (2019)
Jason Cory Brunson, Reinhard C. Laubenbacher
Applications of network analysis to routinely collected health care data: a systematic review. J. Am. Medical Informatics Assoc. 25 (2) (2018)
Elena S. Dimitrova, Leslie A. Caromile, Reinhard C. Laubenbacher, Linda H. Shapiro
The innate immune response to ischemic injury: a multiscale modeling perspective. BMC Syst. Biol. 12 (1) (2018)
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
Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective. PLoS Comput. Biol. 13 (2) (2017)
Claus Kadelka, Yuan Li, Jack Kuipers, John O. Adeyeye, Reinhard C. Laubenbacher
Multistate nested canalizing functions and their networks. Theor. Comput. Sci. 675 (2017)
David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Reinhard C. Laubenbacher
Identification of control targets in Boolean molecular network models via computational algebra. BMC Syst. Biol. 10 (2016)
Abdelrahman Hosny, Paola Vera-Licona, Reinhard C. Laubenbacher, Thibauld Favre
AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms. Bioinform. 32 (15) (2016)
Matthew Oremland, Kathryn R. Michels, Alexandra M. Bettina, Christopher Lawrence, Borna Mehrad, Reinhard C. Laubenbacher
A computational model of invasive aspergillosis in the lung and the role of iron. BMC Syst. Biol. 10 (2016)
Madison Brandon, Brad Howard, Christopher Lawrence, Reinhard C. Laubenbacher
Iron acquisition and oxidative stress response in aspergillus fumigatus. BMC Syst. Biol. 9 (2015)
Alan Veliz-Cuba, Boris Aguilar, Reinhard C. Laubenbacher
Dimension Reduction of Large Sparse AND-NOT Network Models. Electron. Notes Theor. Comput. Sci. 316 (2015)
Alan Veliz-Cuba, Boris Aguilar, Franziska Hinkelmann, Reinhard C. Laubenbacher
Steady state analysis of Boolean molecular network models via model reduction and computational algebra. BMC Bioinform. 15 (2014)
Paola Vera-Licona, Abdul Salam Jarrah, Luis David García-Puente, John McGee, Reinhard C. Laubenbacher
An Algebra-Based Method for Inferring Gene Regulatory Networks. BMC Syst. Biol. 8 (2014)
Jason Cory Brunson, Steve Fassino, Antonio McInnes, Monisha Narayan, Brianna Richardson, Christopher Franck, Patrick Ion, Reinhard C. Laubenbacher
Evolutionary events in a mathematical sciences research collaboration network. Scientometrics 99 (3) (2014)
Matthew Oremland, Reinhard C. Laubenbacher
Optimization of Agent-Based Models: Scaling Methods and Heuristic Algorithms. J. Artif. Soc. Soc. Simul. 17 (2) (2014)
Jason Cory Brunson, Xiaoyan Wang, Reinhard C. Laubenbacher
Evolving Collaboration Patterns in Medical Research. AMIA (2014)
Alan Veliz-Cuba, David Murrugarra, Reinhard C. Laubenbacher
Structure and dynamics of acyclic networks. Discret. Event Dyn. Syst. 24 (4) (2014)
Yuan Li, John O. Adeyeye, David Murrugarra, Boris Aguilar, Reinhard C. Laubenbacher
Boolean nested canalizing functions: A comprehensive analysis. Theor. Comput. Sci. 481 (2013)
Alan Veliz-Cuba, Reinhard C. Laubenbacher, Boris Aguilar
Dimension Reduction of Large AND-NOT Network Models. CoRR (2013)
David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Seda Arat, Reinhard C. Laubenbacher
Modeling stochasticity and variability in gene regulatory networks. EURASIP J. Bioinform. Syst. Biol. 2012 (2012)
Jason Cory Brunson, Steve Fassino, Antonio McInnes, Monisha Narayan, Brianna Richardson, Christopher Franck, Patrick Ion, Reinhard C. Laubenbacher
Evolutionary Events in a Mathematical Sciences Research Collaboration Network CoRR (2012)
Franziska Hinkelmann, Madison Brandon, Bonny Guang, Rustin McNeill, Grigoriy Blekherman, Alan Veliz-Cuba, Reinhard C. Laubenbacher
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra. BMC Bioinform. 12 (2011)
Yuan Li, John O. Adeyeye, Reinhard C. Laubenbacher
Nested Canalyzing Functions And Their Average Sensitivities CoRR (2011)
Elena S. Dimitrova, Luis David García-Puente, Franziska Hinkelmann, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Brandilyn Stigler, Michael Eugene Stillman, Paola Vera-Licona
Parameter estimation for Boolean models of biological networks. Theor. Comput. Sci. 412 (26) (2011)
Franziska Hinkelmann, David Murrugarra, Abdul Salam Jarrah, Reinhard C. Laubenbacher
A Mathematical Framework for Agent Based Models of Complex Biological Networks CoRR (2010)
Elena S. Dimitrova, Paola Vera-Licona, John McGee, Reinhard C. Laubenbacher
Discretization of Time Series Data. J. Comput. Biol. 17 (6) (2010)
Alan Veliz-Cuba, Abdul Salam Jarrah, Reinhard C. Laubenbacher
Polynomial algebra of discrete models in systems biology. Bioinform. 26 (13) (2010)
Reinhard C. Laubenbacher, Bernd Sturmfels
Computer Algebra in Systems Biology. Am. Math. Mon. 116 (10) (2009)
Reinhard C. Laubenbacher, Bernd Sturmfels
Computeralgebra in der Systembiologie. Inform. Spektrum 32 (1) (2009)
Reinhard C. Laubenbacher, Abdul Salam Jarrah, Henning S. Mortveit, S. S. Ravi
A mathematical formalism for agent-based modeling CoRR (2008)
Elena S. Dimitrova, Brandilyn Stigler, Abdul Salam Jarrah, Reinhard C. Laubenbacher
Applications of the gröbner fan to gene network reconstruction (abstract only). ACM Commun. Comput. Algebra 42 (1-2) (2008)
Chikoo Oosawa, Michael A. Savageau, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Eduardo D. Sontag
Stabilizing and Destabilizing Effects of Embedding 3-Node Subgraphs on the State Space of Boolean Networks. ACRI (2008)
V. Choi, Y. Huang, Vy Lam, D. Potter, Reinhard C. Laubenbacher, Karen Duca
Using Formal Concept Analysis for microarray Data Comparison. J. Bioinform. Comput. Biol. 6 (1) (2008)
Abdul Salam Jarrah, Reinhard C. Laubenbacher
Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions. AB (2007)
Elena S. Dimitrova, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Brandilyn Stigler
A Gröbner fan method for biochemical network modeling. ISSAC (2007)
Reinhard C. Laubenbacher, Bernd Sturmfels
Computer algebra in systems biology CoRR (2007)
Filippo Castiglione, Karen Duca, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Donna Hochberg, David Thorley-Lawson
Simulating Epstein-Barr virus infection with C-ImmSim. Bioinform. 23 (11) (2007)
V. Choi, Y. Huang, Vy Lam, D. Potter, Reinhard C. Laubenbacher, Karen Duca
Using Formal Concept Analysis for Microarray Data Comparison. APBC (2007)
Abdul Salam Jarrah, Reinhard C. Laubenbacher, Brandilyn Stigler, Michael Eugene Stillman
Reverse-engineering of polynomial dynamical systems. Adv. Appl. Math. 39 (4) (2007)
Luis David García-Puente, Abdul Salam Jarrah, Reinhard C. Laubenbacher
Sequential dynamical systems over words. Appl. Math. Comput. 174 (1) (2006)
Omar Colón-Reyes, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Bernd Sturmfels
Monomial Dynamical Systems over Finite Fields. Complex Syst. 16 (4) (2006)
Reinhard C. Laubenbacher, Bodo Pareigis
Update schedules of sequential dynamical systems. Discret. Appl. Math. 154 (6) (2006)
Hélène Barcelo, Reinhard C. Laubenbacher
-homotopy theory and its applications. Discret. Math. 298 (1-3) (2005)
Nicholas F. Polys, Doug A. Bowman, Chris North, Reinhard C. Laubenbacher, Karen Duca
PathSim visualizer: an Information-Rich Virtual Environment framework for systems biology. Web3D (2004)
Abdul Jarrah, Hussein Vastani, Karen Duca, Reinhard C. Laubenbacher
An analysis of a circadian model using the small-gain approach to monotone systems. CDC (2004)
Abdul Jarrah, Hussein Vastani, Karen Duca, Reinhard C. Laubenbacher
An optimal control problem for in vitro virus competition. CDC (2004)
Reinhard C. Laubenbacher, Bodo Pareigis
Decomposition and simulation of sequential dynamical systems. Adv. Appl. Math. 30 (4) (2003)
Abdul Salam Jarrah, Reinhard C. Laubenbacher, Valery G. Romanovski
The Sibirsky component of the center variety of polynomial differential systems. J. Symb. Comput. 35 (5) (2003)
Reinhard C. Laubenbacher
A computer algebra approach to biological systems. ISSAC (2003)
Luis García, Abdul Salam Jarrah, Reinhard C. Laubenbacher
Classification of Finite Dynamical Systems CoRR (2001)
Edith Aguirre, Abdul Salam Jarrah, Reinhard C. Laubenbacher
Generic ideals and Moreno-Socías conjucture. ISSAC (2001)
Reinhard C. Laubenbacher, Bodo Pareigis
Equivalence Relations on Finite Dynamical Systems. Adv. Appl. Math. 26 (3) (2001)
Hélène Barcelo, Xenia H. Kramer, Reinhard C. Laubenbacher, Christopher Weaver
Foundations of a Connectivity Theory for Simplicial Complexes. Adv. Appl. Math. 26 (2) (2001)
Eduardo Cattani, Reinhard C. Laubenbacher
Special Issue on Symbolic Computation in Algebra, Analysis, and Geometry - Foreword of the Guest Editors. J. Symb. Comput. 29 (4-5) (2000)
Reinhard C. Laubenbacher, Karen Schlauch
An Algorithm for the Quillen-Suslin Theorem for Quotients of Polynomial Rings by Monomial Ideals. J. Symb. Comput. 30 (5) (2000)
Reinhard C. Laubenbacher, Irena Swanson
Permanental Ideals. J. Symb. Comput. 30 (2) (2000)
Susan M. Hermiller, Xenia H. Kramer, Reinhard C. Laubenbacher
Monomial Orderings, Rewriting Systems, and Gröbner Bases for the Commutator Ideal of a Free Algebra. J. Symb. Comput. 27 (2) (1999)