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Journal Articles
- 2024
[j49]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)- [j48]Reinhard C. Laubenbacher, Borna Mehrad, Ilya Shmulevich, Natalia A. Trayanova:
Digital twins in medicine. Nat. Comput. Sci. 4(3): 184-191 (2024) - 2023
- [j47]Claus Kadelka, Benjamin Keilty, Reinhard C. Laubenbacher:
Collectively canalizing Boolean functions. Adv. Appl. Math. 145: 102475 (2023) - 2022
- [j46]Adam C. Knapp, Luis Sordo Vieira, Reinhard C. Laubenbacher, Julia Chifman:
SteadyCellPhenotype: a web-based tool for the modeling of biological networks with ternary logic. Bioinform. 38(8): 2369-2370 (2022) - [j45]Yara Skaf, Reinhard C. Laubenbacher:
Topological data analysis in biomedicine: A review. J. Biomed. Informatics 130: 104082 (2022) - [j44]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) - 2021
- [j43]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) - [j42]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): e2024287118 (2021) - 2020
- [j41]Elijah Paul, Gleb Pogudin, William Qin, Reinhard C. Laubenbacher:
The Dynamics of Canalizing Boolean Networks. Complex. 2020: 3687961:1-3687961:14 (2020) - 2019
- [j40]Alan Veliz-Cuba, Reinhard C. Laubenbacher:
Dynamics of semilattice networks with strongly connected dependency graph. Autom. 99: 167-174 (2019) - [j39]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:
PlantSimLab - a modeling and simulation web tool for plant biologists. BMC Bioinform. 20(1): 508 (2019) - [j38]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) - 2018
- [j37]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): 50:1-50:13 (2018) - [j36]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): 210-221 (2018) - 2017
- [j35]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) - [j34]Claus Kadelka, Yuan Li, Jack Kuipers, John O. Adeyeye, Reinhard C. Laubenbacher:
Multistate nested canalizing functions and their networks. Theor. Comput. Sci. 675: 1-14 (2017) - 2016
- [j33]Abdelrahman Hosny, Paola Vera-Licona, Reinhard C. Laubenbacher, Thibauld Favre:
AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms. Bioinform. 32(15): 2396-2398 (2016) - [j32]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: 34 (2016) - [j31]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: 94 (2016) - 2015
- [j30]Madison Brandon, Brad Howard, Christopher Lawrence, Reinhard C. Laubenbacher:
Iron acquisition and oxidative stress response in aspergillus fumigatus. BMC Syst. Biol. 9: 19 (2015) - 2014
- [j29]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: 221 (2014) - [j28]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: 37 (2014) - [j27]Alan Veliz-Cuba, David Murrugarra, Reinhard C. Laubenbacher:
Structure and dynamics of acyclic networks. Discret. Event Dyn. Syst. 24(4): 647-658 (2014) - [j26]Matthew Oremland, Reinhard C. Laubenbacher:
Optimization of Agent-Based Models: Scaling Methods and Heuristic Algorithms. J. Artif. Soc. Soc. Simul. 17(2) (2014) - [j25]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): 973-998 (2014) - 2013
- [j24]Yuan Li, John O. Adeyeye, David Murrugarra, Boris Aguilar, Reinhard C. Laubenbacher:
Boolean nested canalizing functions: A comprehensive analysis. Theor. Comput. Sci. 481: 24-36 (2013) - 2012
- [j23]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: 5 (2012) - 2011
- [j22]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: 295 (2011) - [j21]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): 2816-2826 (2011) - 2010
- [j20]Alan Veliz-Cuba, Abdul Salam Jarrah, Reinhard C. Laubenbacher:
Polynomial algebra of discrete models in systems biology. Bioinform. 26(13): 1637-1643 (2010) - [j19]Elena S. Dimitrova, Paola Vera-Licona, John McGee, Reinhard C. Laubenbacher:
Discretization of Time Series Data. J. Comput. Biol. 17(6): 853-868 (2010) - 2009
- [j18]Reinhard C. Laubenbacher, Bernd Sturmfels:
Computeralgebra in der Systembiologie. Inform. Spektrum 32(1): 27-32 (2009) - [j17]Reinhard C. Laubenbacher, Bernd Sturmfels:
Computer Algebra in Systems Biology. Am. Math. Mon. 116(10): 882-891 (2009) - 2008
- [j16]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): 69 (2008) - [j15]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): 65-75 (2008) - 2007
- [j14]Abdul Salam Jarrah, Reinhard C. Laubenbacher, Brandilyn Stigler, Michael Eugene Stillman:
Reverse-engineering of polynomial dynamical systems. Adv. Appl. Math. 39(4): 477-489 (2007) - [j13]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): 1371-1377 (2007) - 2006
- [j12]Luis David García-Puente, Abdul Salam Jarrah, Reinhard C. Laubenbacher:
Sequential dynamical systems over words. Appl. Math. Comput. 174(1): 500-510 (2006) - [j11]Omar Colón-Reyes, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Bernd Sturmfels:
Monomial Dynamical Systems over Finite Fields. Complex Syst. 16(4) (2006) - [j10]Reinhard C. Laubenbacher, Bodo Pareigis:
Update schedules of sequential dynamical systems. Discret. Appl. Math. 154(6): 980-994 (2006) - 2005
- [j9]Hélène Barcelo, Reinhard C. Laubenbacher:
Perspectives on A-homotopy theory and its applications. Discret. Math. 298(1-3): 39-61 (2005) - 2003
- [j8]Reinhard C. Laubenbacher, Bodo Pareigis:
Decomposition and simulation of sequential dynamical systems. Adv. Appl. Math. 30(4): 655-678 (2003) - [j7]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): 577-589 (2003) - 2001
- [j6]Hélène Barcelo, Xenia H. Kramer, Reinhard C. Laubenbacher, Christopher Weaver:
Foundations of a Connectivity Theory for Simplicial Complexes. Adv. Appl. Math. 26(2): 97-128 (2001) - [j5]Reinhard C. Laubenbacher, Bodo Pareigis:
Equivalence Relations on Finite Dynamical Systems. Adv. Appl. Math. 26(3): 237-251 (2001) - 2000
- [j4]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): 483 (2000) - [j3]Reinhard C. Laubenbacher, Irena Swanson:
Permanental Ideals. J. Symb. Comput. 30(2): 195-205 (2000) - [j2]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): 555-571 (2000) - 1999
- [j1]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): 133-141 (1999)
Conference and Workshop Papers
- 2014
- [c11]Jason Cory Brunson, Xiaoyan Wang, Reinhard C. Laubenbacher:
Evolving Collaboration Patterns in Medical Research. AMIA 2014 - [c10]Alan Veliz-Cuba, Boris Aguilar, Reinhard C. Laubenbacher:
Dimension Reduction of Large Sparse AND-NOT Network Models. SASB 2014: 83-95 - 2008
- [c9]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: 100-107 - 2007
- [c8]Abdul Salam Jarrah, Reinhard C. Laubenbacher:
Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions. AB 2007: 15-22 - [c7]V. Choi, Y. Huang, Vy Lam, D. Potter, Reinhard C. Laubenbacher, Karen Duca:
Using Formal Concept Analysis for Microarray Data Comparison. APBC 2007: 57-66 - [c6]Elena S. Dimitrova, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Brandilyn Stigler:
A Gröbner fan method for biochemical network modeling. ISSAC 2007: 122-126 - 2004
- [c5]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: 575-578 - [c4]Abdul Jarrah, Hussein Vastani, Karen Duca, Reinhard C. Laubenbacher:
An optimal control problem for in vitro virus competition. CDC 2004: 579-584 - [c3]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: 7-14 - 2003
- [c2]Reinhard C. Laubenbacher:
A computer algebra approach to biological systems. ISSAC 2003: 5-6 - 2001
- [c1]Edith Aguirre, Abdul Salam Jarrah, Reinhard C. Laubenbacher:
Generic ideals and Moreno-Socías conjucture. ISSAC 2001: 21-23
Parts in Books or Collections
- 2014
- [p2]Reinhard C. Laubenbacher, Franziska Hinkelmann, David Murrugarra, Alan Veliz-Cuba:
Algebraic Models and Their Use in Systems Biology. Discrete and Topological Models in Molecular Biology 2014: 443-474 - 2013
- [p1]Franziska Hinkelmann, Reinhard C. Laubenbacher:
Finite fields in biology. Handbook of Finite Fields 2013: 825-834
Reference Works
- 2009
- [r1]Reinhard C. Laubenbacher, Abdul Salam Jarrah, Henning S. Mortveit, S. S. Ravi:
Agent Based Modeling, Mathematical Formalism for. Encyclopedia of Complexity and Systems Science 2009: 160-176
Informal and Other Publications
- 2024
- [i12]Luis L. Fonseca, Lucas Böttcher, Borna Mehrad, Reinhard C. Laubenbacher:
Metamodeling and Control of Medical Digital Twins. CoRR abs/2402.05750 (2024) - [i11]Lucas Böttcher, Luis L. Fonseca, Reinhard C. Laubenbacher:
Control of Medical Digital Twins with Artificial Neural Networks. CoRR abs/2403.13851 (2024) - 2022
- [i10]Karthik Chandrasekhar, Claus Kadelka, Reinhard C. Laubenbacher, David Murrugarra:
Stability of Linear Boolean Networks. CoRR abs/2209.02044 (2022) - 2020
- [i9]Claus Kadelka, Benjamin Keilty, Reinhard C. Laubenbacher:
Collectively canalizing Boolean functions. CoRR abs/2008.13741 (2020) - 2019
- [i8]Elijah Paul, Gleb Pogudin, William Qin, Reinhard C. Laubenbacher:
The Dynamics of Canalizing Boolean Networks. CoRR abs/1902.00056 (2019) - 2013
- [i7]Alan Veliz-Cuba, Reinhard C. Laubenbacher, Boris Aguilar:
Dimension Reduction of Large AND-NOT Network Models. CoRR abs/1311.6868 (2013) - 2012
- [i6]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 abs/1203.5158 (2012) - 2011
- [i5]Yuan Li, John O. Adeyeye, Reinhard C. Laubenbacher:
Nested Canalyzing Functions And Their Average Sensitivities. CoRR abs/1111.7217 (2011) - 2010
- [i4]Franziska Hinkelmann, David Murrugarra, Abdul Salam Jarrah, Reinhard C. Laubenbacher:
A Mathematical Framework for Agent Based Models of Complex Biological Networks. CoRR abs/1006.0408 (2010) - 2008
- [i3]Reinhard C. Laubenbacher, Abdul Salam Jarrah, Henning S. Mortveit, S. S. Ravi:
A mathematical formalism for agent-based modeling. CoRR abs/0801.0249 (2008) - 2007
- [i2]Reinhard C. Laubenbacher, Bernd Sturmfels:
Computer algebra in systems biology. CoRR abs/0712.4248 (2007) - 2001
- [i1]Luis García, Abdul Salam Jarrah, Reinhard C. Laubenbacher:
Classification of Finite Dynamical Systems. CoRR math.DS/0112216 (2001)
Coauthor Index
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last updated on 2024-10-07 22:18 CEST by the dblp team
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