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David Murrugarra

Biography:

I am an associate professor in the Department of Mathematics at the University of Kentucky. I do research in Mathematical Biology with an emphasis in Systems Biology and Computational Biology. I got my PhD in Mathematics from Virginia Tech. I was a postdoc in the School of Mathematics at Georgia Tech before moving to UK in 2014. For more information visit my webpage.

Research Interests:
Mathematical Biology
Systems Biology
Computational Biology
Research

I develop computational tools for modeling, analysis, and control of gene 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 working in the development of methods for the computational prediction of RNA secondary structure using machine learning techniques. For more information, including a list of publications,  please visit my personal webpage.

Outreach
PubMed Publications*: 
  • P Márquez-Zacarías; RM Pineau; M Gómez; A Veliz-Cuba; D Murrugarra; WC Ratcliff; KJ Niklas"Evolution of Cellular Differentiation: From Hypotheses to Models."Trends in ecology & evolution36.1(2021):49-60.Details. Full text
  • DJ Wooten; JGT Zañudo; D Murrugarra; AM Perry; A Dongari-Bagtzoglou; R Laubenbacher; CJ Nobile; R Albert"Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies."PLoS computational biology17.3(2021):e1008690.Details. Full text
  • D Plaugher; D Murrugarra"Modeling the Pancreatic Cancer Microenvironment in Search of Control Targets."Bulletin of mathematical biology83.11(2021):115.Details. Full text
  • B Aguilar; P Fang; R Laubenbacher; D Murrugarra"A Near-Optimal Control Method for Stochastic Boolean Networks."Letters in biomathematics7.1(2020):67-80.Details.
  • Sordo Vieira; RC Laubenbacher; D Murrugarra"Control of Intracellular Molecular Networks Using Algebraic Methods."Bulletin of mathematical biology82.1(2019):2.Details. Full text
  • Randal Voss; D Murrugarra; TB Jensen; Monaghan JR"Transcriptional correlates of proximal-distal identify and regeneration timing in axolotl limbs."Comparative biochemistry and physiology. Toxicology & pharmacology : CBP208.(2018):53-63.Details. Full text
  • E Rogers; D Murrugarra; C Heitsch"Conditioning and Robustness of RNA Boltzmann Sampling under Thermodynamic Parameter Perturbations."Biophysical journal113.2(2017):321-329.Details. Full text
  • D Murrugarra; A Veliz-Cuba; B Aguilar; R Laubenbacher"Identification of control targets in Boolean molecular network models via computational algebra."BMC systems biology10.1(2016):94.Details. Full text
  • D Murrugarra; ES Dimitrova"Molecular network control through boolean canalization."EURASIP journal on bioinformatics & systems biology2015.1(2015):9.Details. Full text
  • C Kadelka; D Murrugarra; R Laubenbacher"Stabilizing gene regulatory networks through feedforward loops."Chaos (Woodbury, N.Y.)23.2(2013):025107.Details. Full text
  • D Murrugarra; A Veliz-Cuba; B Aguilar; S Arat; R Laubenbacher"Modeling stochasticity and variability in gene regulatory networks."EURASIP journal on bioinformatics & systems biology2012.1(2012):5.Details. Full text
  • D Murrugarra; R Laubenbacher"Regulatory patterns in molecular interaction networks."Journal of theoretical biology288.(2011):66-72.Details. Full text
  • F Hinkelmann; D Murrugarra; AS Jarrah; R Laubenbacher"A mathematical framework for agent based models of complex biological networks."Bulletin of mathematical biology73.7(2011):1583-602.Details. Full text
  • D Murrugarra; J Miller; AN Mueller"Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms."Frontiers in neuroscience10.(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.