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Bioinformatics Training


Since September 2018, I am an Associate Professor of Bioinformatics at the UCLouvain, in Belgium, and director of the Computational Biology and Bioinformatics (CBIO) group. I am located in the de Duve Institute, on the medical campus in Brussels, where I run a research group and teach at the faculty of pharmacy and biomedical sciences (FASB).

I am an avid open research advocate and make every possible effort to make my research reproducible and openly available. I am a Software Sustainability Institute fellow, a Data and Software Carpentry instructor, and an affiliated member of the Bioconductor project.

I am also involved in the Bullied Into Bad Science campaign, an initiative by and for early career researchers who aim for a fairer, more open and ethical research and publication environment. In 2017-2018, I was also part of the eLife Early-career advisory group and, since 2017, am a #ASAPbio ambassador.


I was a Senior Research Associate in the Department of Biochemistry at the University of Cambridge. It’s at the Cambridge Centre for Proteomics and the Computational Proteomics Unit (my former research group in Cambridge) that I started working on various aspects of quantitative and spatial proteomics, developing new methods and implementing computational tools with a strong emphasis on rigorous and reproducible data analysis. During my time in Cambridge, I have also a been a visiting scientist in the PRIDE team at the European Bioinformatics Institute and I the Department of Applied Mathematics and Theoretical Physics (DAMTP).

And even before that, during my MSc and PhD work, I studied micro-evolutionary genetic patterns of the Broom leaf beetle Gonioctena variabilis in Southern Europe (Gatto el al., 2008), the application of short interspersed mobile elements (SINEs) to study the evolution of cetaceans, and the applicability of the General Time Reversible nucleotide substitution model in the light of differential lineage sorting (Gatto el al., 2006). I also spend 3 years in industry working on genomic and transcriptomics data, in particular the microarray quality control (Shi et al., 2010).


Key publications: 

Crook OM, Davies CTR, Breckels LM, Christopher JA, Gatto L, Kirk PDW, Lilley KS Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE, Nature Communications volume 135948 (2022)doi:10.1038/s41467-022-33570-9 (Pre-print: biorXiv).

Lizcano-Perret B., Lardinois C., Wavreil F., Hauchamps P., Herinckx G., Sorgeloos F., Vertommen D., Gatto L., Michiels T. Cardiovirus leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic. bioRxiv 2022.06.16.496404; doi:10.1101/2022.06.16.496404.

Pollé O.G, Delfosse A., Martin M., Louis J., Gies I., den Brinker M., Seret N., Lebrethon M., Mouraux T., Gatto L., Lysy P.A. on behalf of the DIATAG Working Group Glycemic Variability Patterns Strongly Correlate with Partial Remission Status in Children with Newly Diagnosed Type 1 Diabetes. Diabetes Care 45(10):2360–2368 (2022). doi:10.2337/dc21-2543.

Moulis M., Runser S.V.M., Glorieux L. et al. Identification and implication of tissue-enriched ligands in epithelial–endothelial crosstalk during pancreas development. Sci Rep 12, 12498 (2022). doi:10.1038/s41598-022-16072-y.

Ward B, Yombi JC, Balligand J-L, Cani PD, Collet J-F, et al. HYGIEIA: HYpothesizing the Genesis of Infectious Diseases and Epidemics through an Integrated Systems Biology Approach. Viruses. 2022; 14(7):1373 doi:10.3390/v14071373.

Dewulf JP, Martin M, Marie S, Oguz F, Belkhir L, De Greef J, et alUrine metabolomics links dysregulation of the tryptophan-kynurenine pathway to inflammation and severity of COVID-19. Sci Rep. 12: 1–8 (2022). doi:10.1038/s41598-022-14292-w.

De Berdt P, Vanvarenberg K, Ucakar B, Bouzin C, Paquot A, Gratpain V, Loriot A, Payen V, Bearzatto B, Muccioli GG, Gatto L, Diogenes A, des Rieux A The human dental apical papilla promotes spinal cord repair through a paracrine mechanism Cell. Mol. Life Sci. 79, 252 (2022). doi:10.1007/s00018-022-04210-8.

Dontaine J, Bouali A, Daussin F et al. The intra-mitochondrial O-GlcNAcylation system rapidly modulates OXPHOS function and ROS release in the heart. Commun Biol 5, 349 (2022). doi:10.1038/s42003-022-03282-3

Delcorte O, Spourquet C, Lemoine P, Degosserie J, Van Der Smissen P, Dauguet N, Loriot A, Knauf JA, Gatto L, Marbaix E, Fagin JA, Pierreux CE. BRAFV600E Induction in Thyrocytes Triggers Important Changes in the miRNAs Content and the Populations of Extracellular Vesicles Released in Thyroid Tumor Microenvironment. Biomedicines. 2022; 10(4):755. doi:10.3390/biomedicines10040755

Rainer J, Vicini A, Salzer L, Stanstrup J, Badia JM, Neumann S, Stravs MA, Verri Hernandes V, Gatto L, Gibb S, Witting M. A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R. Metabolites. 2022; 12(2):173. doi:10.3390/metabo12020173

Teaching and Supervisions




  • Exploring, visualising and analysing proteomics data in R


  • R object-oriented programming and package development
  • Part III Systems Biology


  • Data Carpentry
  • R object-oriented programming and package development
  • Part III Systems Biology


  • R object-oriented programming and package development
  • Data Carpentry