Reinhard C. Laubenbacher

According to our database, Reinhard C. Laubenbacher authored at least 70 papers between 1999 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Digital twins in medicine.

Reinhard C. Laubenbacher, Borna Mehrad, Ilya Shmulevich, Natalia A. Trayanova

Nat. Comput. Sci., 2024

Toward mechanistic medical digital twins: some use cases in immunology.

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

Frontiers Digit. Health, 2024

Control of Medical Digital Twins with Artificial Neural Networks.

Lucas Böttcher, Luis L. Fonseca, Reinhard C. Laubenbacher

CoRR, 2024

Metamodeling and Control of Medical Digital Twins.

Luis L. Fonseca, Lucas Böttcher, Borna Mehrad, Reinhard C. Laubenbacher

CoRR, 2024

2023

Collectively canalizing Boolean functions.

Claus Kadelka, Benjamin Keilty, Reinhard C. Laubenbacher

Adv. Appl. Math., 2023

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

Topological data analysis in biomedicine: A review.

Yara Skaf, Reinhard C. Laubenbacher

J. Biomed. Informatics, 2022

Stability of Linear Boolean Networks.

Karthik Chandrasekhar, Claus Kadelka, Reinhard C. Laubenbacher, David Murrugarra

CoRR, 2022

<i>SteadyCellPhenotype</i>: 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

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, Reinhard C. Laubenbacher

Proc. Natl. Acad. Sci. USA, 2021

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

2020

The Dynamics of Canalizing Boolean Networks.

Elijah Paul, Gleb Pogudin, William Qin, Reinhard C. Laubenbacher

Complex., 2020

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, João C. Setubal, B. M. Tyler, Reinhard C. Laubenbacher

BMC Bioinform., December, 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

Dynamics of semilattice networks with strongly connected dependency graph.

Alan Veliz-Cuba, Reinhard C. Laubenbacher

Autom., 2019

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

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

2017

Multistate nested canalizing functions and their networks.

Claus Kadelka, Yuan Li, Jack Kuipers, John O. Adeyeye, Reinhard C. Laubenbacher

Theor. Comput. Sci., 2017

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

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

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

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

Abdelrahman Hosny, Paola Vera-Licona, Reinhard C. Laubenbacher, Thibauld Favre

Bioinform., 2016

2015

Iron acquisition and oxidative stress response in aspergillus fumigatus.

Madison Brandon, Brad Howard, Christopher Lawrence, Reinhard C. Laubenbacher

BMC Syst. Biol., 2015

2014

Algebraic Models and Their Use in Systems Biology.

Reinhard C. Laubenbacher, Franziska Hinkelmann, David Murrugarra, Alan Veliz-Cuba

Proceedings of the Discrete and Topological Models in Molecular Biology, 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

Optimization of Agent-Based Models: Scaling Methods and Heuristic Algorithms.

Matthew Oremland, Reinhard C. Laubenbacher

J. Artif. Soc. Soc. Simul., 2014

Dimension Reduction of Large Sparse AND-NOT Network Models.

Alan Veliz-Cuba, Boris Aguilar, Reinhard C. Laubenbacher

Proceedings of the 5th International Workshop on Static Analysis and Systems Biology, 2014

Structure and dynamics of acyclic networks.

Alan Veliz-Cuba, David Murrugarra, Reinhard C. Laubenbacher

Discret. Event Dyn. Syst., 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

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

Evolving Collaboration Patterns in Medical Research.

Jason Cory Brunson, Xiaoyan Wang, Reinhard C. Laubenbacher

Proceedings of the AMIA 2014, 2014

2013

Boolean nested canalizing functions: A comprehensive analysis.

Yuan Li, John O. Adeyeye, David Murrugarra, Boris Aguilar, Reinhard C. Laubenbacher

Theor. Comput. Sci., 2013

Dimension Reduction of Large AND-NOT Network Models.

Alan Veliz-Cuba, Reinhard C. Laubenbacher, Boris Aguilar

CoRR, 2013

Finite fields in biology.

Franziska Hinkelmann, Reinhard C. Laubenbacher

Proceedings of the Handbook of Finite Fields., 2013

2012

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

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

Nested Canalyzing Functions And Their Average Sensitivities

Yuan Li, John O. Adeyeye, Reinhard C. Laubenbacher

CoRR, 2011

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

2010

Discretization of Time Series Data.

Elena S. Dimitrova, Paola Vera-Licona, John McGee, Reinhard C. Laubenbacher

J. Comput. Biol., 2010

A Mathematical Framework for Agent Based Models of Complex Biological Networks

Franziska Hinkelmann, David Murrugarra, Abdul Salam Jarrah, Reinhard C. Laubenbacher

CoRR, 2010

Polynomial algebra of discrete models in systems biology.

Alan Veliz-Cuba, Abdul Salam Jarrah, Reinhard C. Laubenbacher

Bioinform., 2010

2009

Agent Based Modeling, Mathematical Formalism for.

Reinhard C. Laubenbacher, Abdul Salam Jarrah, Henning S. Mortveit, S. S. Ravi

Proceedings of the Encyclopedia of Complexity and Systems Science, 2009

Computer Algebra in Systems Biology.

Reinhard C. Laubenbacher, Bernd Sturmfels

Am. Math. Mon., 2009

Computeralgebra in der Systembiologie.

Reinhard C. Laubenbacher, Bernd Sturmfels

Inform. Spektrum, 2009

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

A mathematical formalism for agent-based modeling

Reinhard C. Laubenbacher, Abdul Salam Jarrah, Henning S. Mortveit, S. S. Ravi

CoRR, 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

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

Proceedings of the Cellular Automata, 2008

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

Reverse-engineering of polynomial dynamical systems.

Abdul Salam Jarrah, Reinhard C. Laubenbacher, Brandilyn Stigler, Michael Eugene Stillman

Adv. Appl. Math., 2007

A Gröbner fan method for biochemical network modeling.

Elena S. Dimitrova, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Brandilyn Stigler

Proceedings of the Symbolic and Algebraic Computation, International Symposium, 2007

Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions.

Abdul Salam Jarrah, Reinhard C. Laubenbacher

Proceedings of the Algebraic Biology, Second International Conference, 2007

2006

Update schedules of sequential dynamical systems.

Reinhard C. Laubenbacher, Bodo Pareigis

Discret. Appl. Math., 2006

Monomial Dynamical Systems over Finite Fields.

Omar Colón-Reyes, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Bernd Sturmfels

Complex Syst., 2006

Sequential dynamical systems over words.

Luis David García-Puente, Abdul Salam Jarrah, Reinhard C. Laubenbacher

Appl. Math. Comput., 2006

2005

Perspectives on <i>A</i>-homotopy theory and its applications.

Hélène Barcelo, Reinhard C. Laubenbacher

Discret. Math., 2005

2004

PathSim visualizer: an Information-Rich Virtual Environment framework for systems biology.

Nicholas F. Polys, Doug A. Bowman, Chris North, Reinhard C. Laubenbacher, Karen Duca

Proceedings of the Proceeding of the Ninth International Conference on 3D Web Technology, 2004

An optimal control problem for in vitro virus competition.

Abdul Jarrah, Hussein Vastani, Karen Duca, Reinhard C. Laubenbacher

Proceedings of the 43rd IEEE Conference on Decision and Control, 2004

An analysis of a circadian model using the small-gain approach to monotone systems.

Abdul Jarrah, Hussein Vastani, Karen Duca, Reinhard C. Laubenbacher

Proceedings of the 43rd IEEE Conference on Decision and Control, 2004

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

Decomposition and simulation of sequential dynamical systems.

Reinhard C. Laubenbacher, Bodo Pareigis

Adv. Appl. Math., 2003

A computer algebra approach to biological systems.

Reinhard C. Laubenbacher

Proceedings of the Symbolic and Algebraic Computation, 2003

2001

Classification of Finite Dynamical Systems

Luis García, Abdul Salam Jarrah, Reinhard C. Laubenbacher

CoRR, 2001

Equivalence Relations on Finite Dynamical Systems.

Reinhard C. Laubenbacher, Bodo Pareigis

Adv. Appl. Math., 2001

Foundations of a Connectivity Theory for Simplicial Complexes.

Hélène Barcelo, Xenia H. Kramer, Reinhard C. Laubenbacher, Christopher Weaver

Adv. Appl. Math., 2001

Generic ideals and Moreno-Socías conjucture.

Edith Aguirre, Abdul Salam Jarrah, Reinhard C. Laubenbacher

Proceedings of the 2001 International Symposium on Symbolic and Algebraic Computation, 2001

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

Permanental Ideals.

Reinhard C. Laubenbacher, Irena Swanson

J. Symb. Comput., 2000

Special Issue on Symbolic Computation in Algebra, Analysis, and Geometry - Foreword of the Guest Editors.

Eduardo Cattani, Reinhard C. Laubenbacher

J. Symb. Comput., 2000

1999

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