David Murrugarra

DMU228's picture
  • Associate Professor
  • Mathematics
murrugarra@uky.edu
771 Patterson Office Tower, Office Hours: MWF 11AM-12PM, and by appointment.
8592574734
Personal website
Research Interests:
  • Mathematical Biology
  • Systems Biology
  • Computational Biology
Research
I develop computational tools for modeling, analysis, and control of regulatory networks. 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.
 
PubMed Publications*: 
  • Plaugher, D ;Murrugarra, D "Modeling the Pancreatic Cancer Microenvironment in Search of Control Targets." Bulletin of mathematical biology 83, 11 (2021): 115. Details. Full text
  • Márquez-Zacarías, P ;Pineau, RM ;Gómez, M ;Veliz-Cuba, A ;Murrugarra, D ;Ratcliff, WC ;Niklas, KJ "Evolution of Cellular Differentiation: From Hypotheses to Models." Trends in ecology & evolution 36, 1 (2021): 49-60. Details. Full text
  • Wooten, DJ ;Zañudo, JGT ;Murrugarra, D ;Perry, AM ;Dongari-Bagtzoglou, A ;Laubenbacher, R ;Nobile, CJ ;Albert, R "Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies." PLoS computational biology 17, 3 (2021): e1008690. Details. Full text
  • Aguilar, B ;Fang, P ;Laubenbacher, R ;Murrugarra, D "A Near-Optimal Control Method for Stochastic Boolean Networks." Letters in biomathematics 7, 1 (2020): 67-80. Details.
  • 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.