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ROGELIO ALBERTO RODRIGUEZ GONZALEZ

Contact Information

423 Parkway Dr NE                                                                                                    Mobile:  (+52)3121442079
Atlanta, GA 30308                                                                                                                       r[email protected]

Education

20122016

Undergaduate Program on Genomic Sciences

National Autonomous University of Mexico (UNAM)

Av. Universidad
Cuernavaca, Morelos 62100

Laboratory Experience

Aug 2017Present

Joshua Weitz Group - Theoretical Ecology and Quantitative Biology at Georgia Institute of Technology

School of Biology

Temporary Technician

Duties include:

  • Assist in the process of translation from MATLAB to MATLAB Live Editor for the use in the Foundations of Quantitative Biosciences course.
  • Extend, simulate, and analyze an immunophage model by including antibiotic dynamics.
  • Visualize and organize  Oceanographic time series data obtained in 2015 cruises.

Skills developed:

  • Improve MATLAB programming skills
  • In-depth understanding behind microbial and viral ecology interactions.
  • Ability to model microbial and viral ecology interactions.
  • Data visualization using R and Plotly.
Sep 2016Aug 2017

Pablo Meyer Lab- Icahn School of Medicine at Mount Sinai

Genetics and Genomic Sciences Department

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).

Sep 2015June 2016

Pablo Meyer lab - IBM Computational Biology Center

Computational Systems Biology

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).
Sep 2014Jun 2015

Rafael Peña-Miller lab - Center for Genomic Sciences

Microbial Systems Biology

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.

Publications

1. Rafael Peña-Miller, Rogelio Rodríguez-González, Craig R MacLean and Alvaro San Millan. "Evaluating the effect of horizontal transmission on the stability of plasmids under different selection regimes". Mobile Genetics Elements, (2015).

Honors & Awards

2014:   Award for being ranked in the top 3 among the second year students of the Undergraduate Program on Genomic Sciences

Programming Skills

Python
MATLAB
R
Perl

Extracurricular activities

  • NY/BIG Conference (Bacillus subtilis conference at NYU)Attendant.

        New York, New York                                                                                       June 2017

  • RECOMB/ISCB Conference on Regulatory and Systems Genomics, with Dream Challenges.

    Attendant.

    Philadelphia, Pennsylvania.                                                                     November  2015

  • Symposium "The Major Transitions In Evolution".

          Attendant.

          Mexico City.                                                                                                      March 2015    

  • XVI Autumn School and X National Meeting of Mathematical Biology.

           Scholarship holder.

           UNAM Science Faculty,  Juriquilla, Querétaro.        November 2014

            

Academic Interests

  • Computational Biology
  • Microbiology
  • Evolution
  • Whole-cell modeling
  • Metabolism
  • Transcriptional regulation
  • Systems Biology
  • Parallel computing
  • Machine learning
  • Stochastic simulations
  • FBA

Languages

  • English

           Speak: high proficiency.

           Read/Write: high proficiency.

  • Spanish

          Native language.