David Murrugarra
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A mathematical framework for agent based models of complex biological networks
F Hinkelmann, D Murrugarra, AS Jarrah, R Laubenbacher
Bulletin of mathematical biology 73 (7), 1583-1602, 2011
Modeling stochasticity and variability in gene regulatory networks
D Murrugarra, A Veliz-Cuba, B Aguilar, S Arat, R Laubenbacher
EURASIP Journal on Bioinformatics and Systems Biology 2012, 1-11, 2012
Identification of control targets in Boolean molecular network models via computational algebra
D Murrugarra, A Veliz-Cuba, B Aguilar, R Laubenbacher
BMC systems biology 10, 1-11, 2016
Boolean nested canalizing functions: A comprehensive analysis
Y Li, JO Adeyeye, D Murrugarra, B Aguilar, R Laubenbacher
Theoretical Computer Science 481, 24-36, 2013
Regulatory patterns in molecular interaction networks
D Murrugarra, R Laubenbacher
Journal of theoretical biology 288, 66-72, 2011
Evolution of cellular differentiation: from hypotheses to models
P Márquez-Zacarías, RM Pineau, M Gomez, A Veliz-Cuba, D Murrugarra, ...
Trends in Ecology & Evolution 36 (1), 49-60, 2021
The number of multistate nested canalyzing functions
D Murrugarra, R Laubenbacher
Physica D: Nonlinear Phenomena 241 (10), 929-938, 2012
Molecular network control through boolean canalization
D Murrugarra, ES Dimitrova
EURASIP Journal on Bioinformatics and Systems Biology 2015, 1-8, 2015
The spruce budworm and forest: a qualitative comparison of ODE and Boolean models
R Robeva, D Murrugarra
Letters in Biomathematics 3 (1), 75-92, 2016
Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies
DJ Wooten, JGT Zañudo, D Murrugarra, AM Perry, A Dongari-Bagtzoglou, ...
PLoS computational biology 17 (3), e1008690, 2021
Bifurcations in Boolean networks
C Kuhlman, H Mortveit, D Murrugarra, A Kumar
Discrete Mathematics & Theoretical Computer Science, 2011
Improving RNA secondary structure prediction via state inference with deep recurrent neural networks
D Willmott, D Murrugarra, Q Ye
Computational and Mathematical Biophysics 8 (1), 36-50, 2020
The nonlinearity of regulation in biological networks
S Manicka, K Johnson, M Levin, D Murrugarra
NPJ Systems Biology and Applications 9 (1), 10, 2023
Modeling the pancreatic cancer microenvironment in search of control targets
D Plaugher, D Murrugarra
Bulletin of Mathematical Biology 83 (11), 115, 2021
A near-optimal control method for stochastic boolean networks
B Aguilar, P Fang, R Laubenbacher, D Murrugarra
Letters in biomathematics 7 (1), 67, 2020
Control of intracellular molecular networks using algebraic methods
L Sordo Vieira, RC Laubenbacher, D Murrugarra
Bulletin of mathematical biology 82 (1), 2, 2020
Transcriptional correlates of proximal-distal identify and regeneration timing in axolotl limbs
SR Voss, D Murrugarra, TB Jensen, JR Monaghan
Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology …, 2018
Algebraic models and their use in systems biology
R Laubenbacher, F Hinkelmann, D Murrugarra, A Veliz-Cuba
Discrete and Topological Models in Molecular Biology, 443-474, 2013
Stabilizing gene regulatory networks through feedforward loops
C Kadelka, D Murrugarra, R Laubenbacher
Chaos: An Interdisciplinary Journal of Nonlinear Science 23 (2), 2013
Revealing the canalizing structure of Boolean functions: Algorithms and applications
E Dimitrova, B Stigler, C Kadelka, D Murrugarra
Automatica 146, 110630, 2022
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Articles 1–20