Firas Hammami

PhD in Bioinformatics

Aix-Marseille Université


Hello there, I’m Firas Hammami. I have recently finished my PhD in Bioinformatics and Genomics at Aix-Marseille Université under the supervision of Elisabeth Remy (Institut de Mathématiques de Marseille, I2M) and Pierre Mandin (Laboratoire de Chimie Bactérienne, LCB).

I’m interested in the mathematical modelling approach (especially the logic formalism) and its application on biological systems, such as the regulation of the Iron Sulfur Cluster biogenesis in the bacterium Escherichia coli. The mathematical modelling approach allows me to better understand the complex regulations involved in biological processes, which i’m fond of!

On this website, you will see that I got passionnate about two more things: teaching and making videos. By the way, I was a founder of a collaboration for Bioinfuse (a french contest for the popularization of Bioinformatics), which won the 2017 edition.


  • Systems Biology
  • Logical Modelling
  • Bioinformatics
  • Developmental biology
  • Microbiology


  • PhD in Bioinformatics and Genomics, 2019

    Aix-Marseille Université

  • MSc in Bioinformatics, Structural Biology and Genomics, 2015

    Aix-Marseille Université

  • MSc in Life Sciences, 2014

    Université de Nice Sophia Antipolis






Video making

Sony Vegas / After Effects / Inkscape / GIMP

Logical modelling

GINsim / MaBoSS


Molecular Biology / Microbiology



Teaching Assistant

Aix-Marseille Université

Sep 2018 – Aug 2019 Marseille

Subject: Statistics for biologists (96h Courses/Tutorials/Practicals)

  • Mean, variance, standard deviation
  • Statistical law, probabilities (Normal law, Central Limit Theorem)
  • Comparison tests for 2 samples (Student, Wilcoxon-Mann-Whitney)
  • Comparison tests for k samples (ANOVA, Kruskall-Wallis)
  • Correlation test (Pearson)

Responsibilities include:

  • Preparing the exam subject
  • Preparing and giving courses

PhD student

Aix-Marseille Université

Oct 2015 – Dec 2019 Marseille

Used the logical modelling approach to understand Iron-Sulfur cluster biogenesis regulation depending of the environment (Iron/Oxygen) in Escherichia coli. A full description of the PhD thesis will be available soon.

Courses given during my PhD:

  • Object Oriented Programming - Master 2 Bioinformatics, Structural Biochemistry and Genomics (40h Tutorials/Practicals)
  • Statistical analysis of biological data - Master 1 Bioinformatics, Structural Biochemistry and Genomics (15h Course/Practicals)
  • Computer Science for biologists - L1 Biology (96h Tutorials/Practicals)
  • Applied Bioinformatics - L2 Biology (41h Tutorials/Practicals)


MSc student (Bioinformatics)

Aix-Marseille Université

Jan 2015 – Jun 2015 Marseille
Built a logical model to understand the regulation of erpA in Escherichia coli.

MSc student (Developmental biology)

Université de Nice Sophia-Antipolis

Jan 2014 – Jun 2014 Nice
Novel Nodal targets characterization using a transcriptome approach in the sea urchin Paracentrotus lividus.


Best video award

Popularization of Bioinformatics using a 5 minutes video (French)
See certificate

Recent Publications

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A wnt2 ortholog in the sea urchin Paracentrotus lividus

Summary Members of the wnt gene family encode secreted glycoproteins that mediate critical intercellular communications in metazoans. …