Login
Theme

About

I am a senior research engineer at Aix-Marseille University and co-head of CB2M.

Career

I initially studied pure mathematics at university before moving into theoretical physics, where I obtained a PhD in 1999. This solid grounding in abstract reasoning and quantitative analysis has been a constant asset throughout my career.

After earning my PhD, I spent nine years working in professional software development, primarily focusing on algorithm design and development. This work allowed me to hone my technical expertise while cultivating my creativity and innovative spirit. One of the algorithms I developed resulted in the granting of an international patent, and several projects that required strong differentiation from the competition benefited from my thirst for novelty, optimization, and problem-solving, yielding results highly valued by both clients and colleagues.

With this experience in mind, I chose to return to my initial passion: scientific research. My curiosity and thirst for discovery, particularly in multidisciplinary contexts, remained a constant source of motivation and led me to focus on bioinformatics. This field, characterized by rapid evolution and increasing integration with disciplines such as theoretical physics and mathematics, perfectly matches my interests.

In 2014, I was appointed as a permanent research engineer at Aix-Marseille University (AMU). From 2014 to 2024, I worked jointly in two laboratories: the TAGC (Theories and Approaches of Genomic Complexity), a laboratory specialized in systems biology, and the CIML (Centre d'Immunologie de Marseille-Luminy), dedicated to immunology research. Sharing my time equally between these two environments allowed me to develop expertise at the interface of systems biology and immunology, with a particular focus on biological data analysis, modeling, and computational methods.

Since 2024, I have been fully dedicated to CIML. I am currently leading, with my colleague Sébastien Jaeger, the development of CB2M, the CIML's computational biology hub.

Internal cross-functional missions

Within the CIML, I participate in several responsibilities and missions:

  • On the laboratory council, I represent statutory IT staff.
  • I am a member of the IT Career unit.
  • I lead the working group on platform member authorship.
  • I actively participate in internal training activities intended for students and engineers.

Institutional external missions

I am a member of the Professional Equality Parity unit, a unit created at the instigation of the supervisory authorities to help improve gender equality within the CIML.

Publications

2025
Bavais J, Chevallier J, Spinelli L, van de Pavert SA, Puthier D, SciGeneX: enhancing transcriptional analysis through gene module detection in single-cell and spatial transcriptomics data. NAR Genom Bioinform 2025 Jun; 7(2): lqaf043.
2024
Mathilde Slivak, Sébastien A Choteau, Philippe Pierre, Lionel Spinelli, Andreas Zanzoni, Christine ..., InteractORF, predictions of human sORF functions from an interactome study, 2024.
2024
Mathilde Slivak, Sebastien Choteau, Philippe Pierre, Lionel Spinelli, Andreas Zanzoni, C. Brun, InteractORF, predictions of human sORF functions from an interactome study, JOBIM 2024 , SFBI, Jun 2024, Toulouse, France.
2023
Sabrina Baaklini, Alexandre Sarrabay, Camille Barthelemy, Laila Dahbi, Laurine Gil, Noushin Mossadeg..., A Single Cell Atlas of Diffuse Large B Cell Lymphomas Reveals Distinct Cellular States Predictive of Outcomes. <i>65th American Society of Hematology (ASH) Annual Meeting and Exhibition</i>, Dec 2023, San Diego, CA, United States. pp.848 - 848, <a target="_blank" href="https://dx.doi.org/10.1182/blood-2023-173929">⟨10.1182/blood-2023-173929⟩</a>.
2023
Arroyo Portilla C, Fenouil R, Wagner C, Luciani C, Lagier M, Da Silva C, Hidalgo-Villeda F, Spinelli..., Peyer's patch phagocytes acquire specific transcriptional programs that influence their maturation and activation profiles. Mucosal Immunol 2023 Aug; 16(4): 527-547.
2022
Sébastien A Choteau, Marceau Cristianini, Kevin Maldonado, Lilian Drets, Mégane Boujeant, Christin..., mimicINT: a workflow for microbe-host protein interaction inference, 2023.
2022
Pauline Brochet, Barbara Ianni, João PS Nunes, Amanda F Frade, Priscila C Teixeira, Charles Mady, ..., Blood DNA methylation marks discriminate Chagas cardiomyopathy disease clinical forms, <i>Frontiers in Immunology</i>, 2022, 13, <a target="_blank" href="https://dx.doi.org/10.3389/fimmu.2022.1020572">⟨10.3389/fimmu.2022.1020572⟩</a>.
2022
Gregoire C, Spinelli L, Villazala-Merino S, Gil L, Holgado MP, Moussa M, Dong C, Zarubica A, Fallet ..., Viral infection engenders bona fide and bystander subsets of lung-resident memory B cells through a permissive mechanism. Immunity 2022 Jul; 55(7): 1216-1233.e9.
2022
Julie Rebejac, Elisa Eme-Scolan, Laurie Arnaud Paroutaud, Sarah Kharbouche, Matei Teleman, Lionel Sp..., Meningeal macrophages protect against viral neuroinfection, <i>Immunity</i>, 2022, 55 (11), pp.2103-2117.e10. <a target="_blank" href="https://dx.doi.org/10.1016/j.immuni.2022.10.005">⟨10.1016/j.immuni.2022.10.005⟩</a>.
2022
Saswati Saha, Lionel Spinelli, Jaime Castro Mondragon, Anaïs Kervadec, Michaela Lynott, Laurent Kre..., Genetic architecture of natural variation of cardiac performance from flies to humans, <i>eLife</i>, 2022, 11, pp.e82459. <a target="_blank" href="https://dx.doi.org/10.7554/eLife.82459">⟨10.7554/eLife.82459⟩</a>.
2020
Wagner C, Bonnardel J, Da Silva C, Spinelli L, Portilla CA, Tomas J, Lagier M, Chasson L, Masse M, D..., Differentiation Paths of Peyer's Patch LysoDCs Are Linked to Sampling Site Positioning, Migration, and T Cell Priming. Cell Rep 2020 Apr; 31(1): 107479.
2018
Crinier A, Milpied P, Escalière B, Piperoglou C, Galluso J, Balsamo A, Spinelli L, Cervera-Marzal I..., High-Dimensional Single-Cell Analysis Identifies Organ-Specific Signatures and Conserved NK Cell Subsets in Humans and Mice. Immunity 2018 Nov; 49(5): 971-986.e5.
2018
Milpied P, Cervera-Marzal I, Mollichella ML, Tesson B, Brisou G, Traverse-Glehen A, Salles G, Spinel..., Human germinal center transcriptional programs are de-synchronized in B cell lymphoma. Nat Immunol 2018 Sep; 19(9): 1013-1024.
2017
Dalet A, Argüello RJ, Combes A, Spinelli L, Jaeger S, Fallet M, Vu Manh TP, Mendes A, Perego J, Rev..., Protein synthesis inhibition and GADD34 control IFN-β heterogeneous expression in response to dsRNA. EMBO J 2017 Mar; 36(6): 761-782.
2017
Perego J, Bourbon C, Chasson L, Laprie C, Spinelli L, Camosseto V, Gatti E, Pierre P, Guanabenz Prevents d-Galactosamine/Lipopolysaccharide-Induced Liver Damage and Mortality. Front Immunol 2017; 8(): 679.
2016
Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Frederic Koch, Muhammad Ahmad Maqbool, Touati Be..., Pasha: a versatile R package for piling chromatin HTS data, <i>Bioinformatics</i>, 2016, 32 (16), pp.2528 - 2530. <a target="_blank" href="https://dx.doi.org/10.1093/bioinformatics/btw206">⟨10.1093/bioinformatics/btw206⟩</a>.
2015
Spinelli L, Carpentier S, Montañana Sanchis F, Dalod M, Vu Manh TP, BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses. BMC Genomics 2015 Oct; 16():814.
2014
Ilaria Nardecchia, Lionel Spinelli, Jordane Preto, Matteo Gori, Elena Floriani, Sebastien Jaeger, Pi..., Experimental detection of long-distance interactions between biomolecules through their diffusion behavior: Numerical study, 2025.