ROGELIO ALBERTO RODRIGUEZ GONZALEZ

Av. Universidad
Cuernavaca, Morelos 62100

Associate Researcher I

Duties included:

• Collect Gene Expression and Proteomic data of Bacillus subtilis under different environmental conditions.
• Explore and Develop new approaches for integrating Gene Expression and/or Proteomic data into the metabolic model of Bacillus subtilis.
• Collect  Experimental growth rates and central carbon fluxes to validate the in silico model results.
• Explore parameter sensitivity of the integrated model to find key genetic components regulating metabolism.
• Analyze the correlation between Gene Expression and Growth under different carbon conditions in order to identify key regulatory components.
• Develop a bi-level optimization problem in order to find the minimum regulatory set that allows a model performance close to the experimental data.

Skills developed:

• Improve Python programming skills.
• More in-depth understanding of the relationship between gene regulation and metabolism.
• Use of MATLAB to set up and solve an LP problem for parameter sensitivity.
• Use of MATLAB and YALMIP to set up and solve a bi-level optimization problem.
  
• Parallel programming using Python.
• Develop Python tools to visualize model results (use of seaborn, matplotlib, plotly).

Intern

Duties included:

• Reproduce the EcoCyc-based metabolic model from Karp et al. A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database.
• Study enzyme localization in the context of Escherichia coli metabolic model.
• Construct the Transcription Factor - Enzyme network using metabolic and gene regulatory data.
• Developing a Bacillus subtilis  model that integrates metabolism and transcriptional regulation.

Skills developed:

• Exploration and filtering of metabolic data from Pathway Genome Databases.
• Develop of parsing tools using Pythond and Perl.
• Use of Pathway Tools software to manage metabolic data.
• Formulation of LP problems and use of RGLPK solver.
• Acquiring more in-depth understanding about Flux Balance Analysis (FBA).
• Managing metabolic tools in Matlab (Cobra toolbox) and Python (Cobrapy).
• Using tools derived from FBA:  pFBA,  FVA,  Mapping fluxes.
• Develop python software to construct the integrated model.
• Use of Cytoscape.
• Use of statistical libraries in Python (Fisher Test, Pearson correlation, Linear regression).

Intern

Duties included:

• Develop ODE-based model to describe population dynamics of a non-conjugative plasmid.

• Programming a numerical method to find the rate of horizontal transfer that conserves the plasmid in a bacterial population.
• Developing an application of the Gillespie Algorithm to account for noisy processes and study bacterial evolution in a chemostat.
• Optimize the previous model using tau-leap method.
• Use Knn algorithm to predict the optical density of  bacterial population using an experimental data set (13 days of different treatments with antibiotics).

Skills developed:

• R programming.
• Develop of Bisection method.
• Developing an application of the Gillespie Algorithm.
• Use of Knn algorithm as machine-learning algorithm.