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Undergaduate Program on Genomic Sciences

National Autonomous University of Mexico (UNAM)

Av. Universidad
Cuernavaca, Morelos 62100

Laboratory Experience

Sep 2016Sep 2017

Associate Researcher I - Mount Sinai

Genetics and Genomic Sciences Department

Duties included:

  • Develop new approaches for  integrating transcriptional data into the metabolic model.
  • Collect new experimental data to evaluate model performance.
  • Improve computer performance of the model simulations.
  • Explore parameter sensitivity of the integrated model to find key genetic components regulating metabolism.
  • Develop a dynamical version of the integrated model using Ordinary Differential Equations.
  • Study enzyme localization in the context  Bacillus subtilis metabolism.

Skills developed:

  • Improve my Python programming skills.
  • More in-depth understanding of transcriptional regulation and metabolism.
  • Use of seaborn library, for data exploration and visualization.
  • Use of MATLAB to reformulate an LP problem and calculate parameter sensitivity
  • Parallel programming using Python.
  • Develop Python software tools to visualize model results.

Sep 2015June 2016

Pablo Meyer - IBM Computational Biology Center

Computational Systems Biology


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 Genomics Sciences

Microbial Systems Biology


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.


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


Extracurricular activities

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

             Scholarship holder.

             UNAM Science Faculty,  Juriquilla, Querétaro Campus.      November 2014


  • Symposium "The Major Transitions In Evolution".


          Mexico City.                                                                                                    March 2015    

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


    Philadelphia, Pennsylvania.                                                                     November  2015

Academic Interests

  • Whole-Cell Models
  • Evolution
  • Metabolism
  • Transcriptional regulation
  • Computer science
  • Computational Biology
  • Cell-to-Cell communication
  • Systems Biology
  • Parallel computing
  • Machine learning
  • Stochastic simulations
  • FBA


  • English

           Speak: high proficiency.

           Read/Write: high proficiency.

  • Spanish

          Native language.

Personal Interests

  • Play Soccer
  • Play Basketball
  • Reading
  • Listen to music
  • Walk and Explore
  • Biking