GONZALEZ Aitor

Location
TGML Platform
Telephone
+33 (0)491 82 87 11
Fonction
Associate Professor
Status
Faculty staff
Diseases, phenotypes & models
Cancer
Human
in silico
Research axes
A.1 - Bioinformatics and Genomics of Molecular Networks
A.1.1 - Bioinformatics of Regulatory Sequences
A.1.3 - Bioinformatics of gene regulation underlying phenotypic traits

Last updated: 2025-04-30

Scientific and Administrative Responsibilities

Current:

  • Co-responsible for Bioinformatics, TGML Sequencing Platform, Marseille (Since Jan 2024) - TGML Platform
  • Elected Member, Faculty of Sciences Medical Council, Aix-Marseille UniversitĂ© (Since Sep 2023)
  • Member, Faculty of Sciences AI Working Group, Aix-Marseille UniversitĂ© (Since 2024)

 

Previous:

  • Member, National University Council (CNU Section 65 - Cell Biology) (2023)
  • Member, MARMARA Institute (Rare Diseases) Training Committee (2021)
  • Coordinator, Master Bioinformatics (Software Development and Data Analysis track), Aix-Marseille UniversitĂ© (2018-2024)
  • Member, Institute for Cancer and Immunology (ICI) Training Committee (2021-2024)

Research Interests

My research focuses on understanding how gene expression is regulated, particularly through computational approaches. Key areas include:

  • Analysis and prediction of human gene regulatory sequences and variants: Investigating non-coding variants (e.g., eQTLs), their association with complex phenotypes, pleiotropy, and their enrichment in regulatory elements.
  • Development of bioinformatics software and machine learning models: Creating tools for analyzing genomic data and predicting regulatory function (e.g., TAGOOS, VTAM, LedPred).
  • Analysis of high-throughput sequencing data: Developing and applying pipelines for RNA-seq, metabarcoding, and other omics data.
  • Modeling and analysis of gene regulatory networks: Using logical and differential equation models to understand network dynamics, particularly in development (e.g., Drosophila wing, mouse somitogenesis).

Research Highlight:

  • Habilitation Ă  Diriger des Recherches (HDR), Aix-Marseille UniversitĂ© (Nov 2020): Bioinformatics of Gene Regulatory Networks.

Software Development

I have developed or contributed to several bioinformatics tools:

  • GWAS2EQTL: Database of colocalized GWAS variants and eQTLs (Link)
  • VTAM: A robust pipeline for validating metabarcoding data using internal controls (GitHub)
  • TAGOOS: Genome-wide supervised learning of non-coding loci associated with complex phenotypes (Docs)
  • LedPred: R/Bioconductor package to predict regulatory sequences using SVMs (Bioconductor)
  • MultiXrank: Heterogeneous multilayer network exploration by random walk with restart (Collaboration) (GitHub)
  • GINsim: Software for qualitative modeling, simulation, and analysis of regulatory networks (Early contribution) (Link)
  • WopMars: Workflow Python Manager for Reproducible Science (GitHub)

Teaching

My teaching activities cover various aspects of bioinformatics, programming, and statistics at Aix-Marseille Université (Faculty of Sciences, Polytech Marseille) and internationally (e.g., Saint Joseph University of Beirut). Topics include:

  • Bioinformatics: Sequence Analysis, Biological Networks & Regulation, Omics Data Analysis (Genomics, Transcriptomics), Genetic Variant Analysis, Computational Biology.
  • Programming: Introduction to Programming (Netlogo), Python, Web Development (Django), Reproducible Analysis.
  • Statistics & Machine Learning: Biostatistics, Advanced Biostatistics, Machine Learning for Biology.

Teaching levels: Bachelor (Licence), Master, PhD programs, DESU (University Diploma).

Collaborators

Current:

  • BĂ©atrice Loriod (TAGC-TGML)
  • Denis Puthier (TAGC-TGML)
  • Pascale Paul (TAGC)
  • Pascal Rihet (TAGC)

 

Previous:

  • AnaĂŻs Baudot (MMG)
  • Emese MeglĂ©cz (IMBE)

Address

Aix-Marseille Université | Lab TAGC/INSERM U1090
163, avenue de Luminy - case 928
13288 Marseille cedex 09
 

External URLs

Author publications