David Murrugarra Share this page:

Research Interests:

• Systems Biology
• Bioinformatics
• Mathematical Biology

ResearchI develop computational tools for modeling, analysis, and control of signal transduction and gene regulatory networks. I have focused on discrete methods, which employ techniques from discrete mathematics, combinatorics, graph theory, and computational algebra. I am also developing efficient methods for optimal control of large probabilistic models using techniques from Markov decision processes and reinforcement learning. I am also interested in the computational prediction of RNA secondary structure using machine learning techniques.I am also interested on using deep learning techniques for classification problems in Systems Biology and Bioinformatics.PubMed Publications*: 

• Vieira, Sordo ;Laubenbacher, RC ;Murrugarra, D «Control of Intracellular Molecular Networks Using Algebraic Methods.» Bulletin of mathematical biology 82, 1 (2019): 2. Details. Full text
• Voss, Randal ;Murrugarra, D ;Jensen, TB ;Monaghan, JR «Transcriptional correlates of proximal-distal identify and regeneration timing in axolotl limbs.» Comparative biochemistry and physiology. Toxicology & pharmacology : CBP 208, (2018): 53-63. Details. Full text
• Rogers, E.;Murrugarra, D ;Heitsch, C «Conditioning and Robustness of RNA Boltzmann Sampling under Thermodynamic Parameter Perturbations.» Biophysical journal 113, 2 (2017): 321-329. Details. Full text
• Murrugarra, D ;Veliz-Cuba, A ;Aguilar, B ;Laubenbacher, R «Identification of control targets in Boolean molecular network models via computational algebra.» BMC systems biology 10, 1 (2016): 94. Details. Full text
• Murrugarra, D ;Dimitrova, ES «Molecular network control through boolean canalization.» EURASIP journal on bioinformatics & systems biology 2015, 1 (2015): 9. Details. Full text
• Kadelka, C ;Murrugarra, D ;Laubenbacher, R «Stabilizing gene regulatory networks through feedforward loops.» Chaos (Woodbury, N.Y.) 23, 2 (2013): 025107. Details. Full text
• Murrugarra, D ;Veliz-Cuba, A ;Aguilar, B ;Arat, S ;Laubenbacher, R «Modeling stochasticity and variability in gene regulatory networks.» EURASIP journal on bioinformatics & systems biology 2012, 1 (2012): 5. Details. Full text
• Murrugarra, D ;Laubenbacher, R «Regulatory patterns in molecular interaction networks.» Journal of theoretical biology 288, (2011): 66-72. Details. Full text
• Hinkelmann, F ;Murrugarra, D ;Jarrah, AS ;Laubenbacher, R «A mathematical framework for agent based models of complex biological networks.» Bulletin of mathematical biology 73, 7 (2011): 1583-602. Details. Full text
• Murrugarra, D ;Miller, J.;Mueller, AN «Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms.» Frontiers in neuroscience 10, (0): 513. Details. Full text

* Publications are automatically pulled from pubmed.gov based on a user-specific query. Results may include incorrect citations. See: Tutorial on improving PubMed results.