Marouen Ben Guebila

Instructor of Medicine, Dana-Farber Cancer Institute

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My research is at the interface of genomics, machine learning, and network biology. I often combine tools from these disciplines to address fundamental questions about the functioning of biological systems. I develop open-source, parallel software that leverages high-dimensional biological data to model regulatory genomics, small molecule dynamics, and metabolism in time and space.

Biology

  • Metabolic modeling in time and space
  • Gene regulatory networks
  • Protein–protein interactions
  • Kidney cancer
  • Pharmacogenomics

Methods

  • Optimization (linear & dynamic programming)
  • High-dimensional statistics
  • Machine learning
  • Recommender systems
  • Graphs & hypergraphs

Frameworks

Django Pydantic DSPy Vector database Bootstrap Nextflow JupyterHub CUDA OpenMP

Selected publications

  1. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
    Marouen Ben Guebila, Tian Wang, Camila M. Lopes‐Ramos, and 22 more authors
    Genome biology, 2023
    DOI HTML
  2. GRAND: a database of gene regulatory network models across human conditions
    Marouen Ben Guebila, Camila M. Lopes‐Ramos, Deborah Weighill, and 7 more authors
    Nucleic Acids Research, 2021
    DOI HTML
  3. ACHR.cu: GPU-accelerated sampling of metabolic networks
    Marouen Ben Guebila
    The Journal of Open Source Software, 2019
    DOI HTML

Funding & support

National Institutes of Health (NIH) Amazon Web Services (AWS) Phylo