Mahmoud Ahmed

Postdoc - Cancer Genomics

A Guided training on reproducible computational research

A training program for medical students on reproducible computational research funded by Medical Research Council (MRC) in South Korea

Capstone Title: Interaction of autophagy and oxidative stress products in cancer


Using the weighted-gene co-expression analysis to systematically investigate the potential interactions of autophagy and oxidative stress response gene products in the context of cancer with emphasis on quality reproducible analysis.


  • To familiarize the trainee with the essential tools for conducting an analysis
  • To run a case study analysis for autophagy and oxidative stress interactions in cance
  • To produce a reproducible report (article/presentation) summarizing the analysis


  • Week One
    • Reading and discussing an article similar to the target study
    • Introduction to the tools that will be used in the study
  • Week Two
    • Reproducing an analysis from an article and identifying essential building blocks of writing a reproducible analysis
    • Defining a question, choosing the dataset, and planning the analysis
  • Week Three
    • Refining the analysis and quality controlling the study
    • Producing the analysis finding in form of tables and graphs
  • Week Four
    • Writing the analysis in a basic research article format
    • Preparing the final trainee presentation



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