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Contact Information

Office: Cherry Emerson 214.

Education

20182023

PhD student

Georgia Institute of Technology

Quantitative Biosciences Program

Home School of Biological Sciences

20122016

Undergaduate Program on Genomic Sciences

National Autonomous University of Mexico (UNAM)

Av. Universidad
Cuernavaca, Morelos 62100

Laboratory Experience

20182019

Teaching Assistant

Georgia Institute of Technology, Home School of Biological Sciences

Duties include:

  • I was a lab and recitation TA during fall 2018 and Spring 2019 semesters,  for the courses BIOL-1510  and BIOL-1520,  respectively.
Aug 2017Present

Weitz Group - Theoretical Ecology and Quantitative Biology

Georgia Institute of Technology, Home School of Biological Sciences

Current position: Graduate Research Assistant

Duties include:

  • Assist in the process of translation from MATLAB to MATLAB Live Editor for the use in the Foundations of Quantitative Biosciences course.
  • Visualize and organize Oceanographic time-series data obtained in 2015 cruises.
  • Develop an in-silico model of phage-antibiotic combination therapy against MDR infections.
  • Develop software to quantify statistical variation in biofilms exposed to different environments

Skills developed:

  • Improve MATLAB programming skills
  • In-depth understanding of microbial and viral ecology interactions.
  • Basic microbiology experimental tecqniques
  • Computational and Quantitative skills to model microbial and viral ecology interactions.
  • Data visualization using R and Plotly.
  • Image analysis
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, Alvaro San Millan. "Evaluating the effect of horizontal transmission on the stability of plasmids under different selection regimes". Mobile Genetics Elements, (2015).

2. Rodriguez-Gonzalez, R.A., Leung, C-Y., Chan, B., Turner, P.E., Weitz, J.S. Quantitative models of phage-antibiotic combination therapy. mSystems in review (2019).

Honors & Awards

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

2018:  Accepted as Ph.D. candidate for the Quantitative Biosciences graduate program at Georgia Tech 

2019:  Best poster award for presenting for the work, "Quantitative models of phage-antibiotic combination therapy", at the Evolution of Complex Life conference in May 2019.

Programming Skills

MATLAB
Python
R
Perl

Extracurricular activities

  • Evolution of Complex Life
    • Poster presentation
    • Atlanta, GA                                                                                                 May 2019
  • American Society for Microbiology (ASM Microbe) 

    Attendant.

    Atlanta, Georgia                                                                                               June 2018

  • 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
    • Mathematical Biology
    • Microbiology
    • Evolution
    • Metabolism
    • Systems Biology
    • Stochastic simulations
    • IBM

Languages

  • English

           Speak: high proficiency.

           Read/Write: high proficiency.

  • Spanish

          Native language.