SYSTEMS BIOMEDICINE

SYSTEMS BIOMEDICINE

TEAM LEADER
A. BAUDOT

CONTACT

Anaïs Baudot – DR2 CNRS

email: anais.baudot@univ-amu.fr

phone: 04 91 32 49 48

TEAM MEMBERS

  • ASSALI INES
  • BAUDOT ANAIS
  • BOULAIMEN YOUSSEF
  • CHASSAGNOL BASTIEN
  • GHESTEM FLORENCE
  • LOIRE BENJAMIN
  • PATERIA HARSHIT
  • PERE MARIELLE
  • PLATEAUX CLAIRE
  • SONG SOLENE
  • TEREZOL MORGANE
  • VILOUTREIX PAUL
  • ZEGHARI KENZA

ALUMNI

BAPTISTA ANTHONY

BARATTA PHILIPPE

BEN BOINA NADINE

BRIERE GALADRIEL

CHEVALIER CELINE

FANCHON ELIO

HIRST DAVID

KAUSAR SAMINA

LAMBERT JUDITH

NOVOA ELVA

OZISIK OZAN

VALDEOLIVAS ALBERTO

ZAKERI POOYA

SELECTED PUBLICATIONS

Baptista, A. et al. 2024

Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond

 

Beust, C. et al. 2024

The Molecular Landscape of Premature Aging Diseases Defined by Multilayer Network Exploration

 

Baptista, A. et al. 2022

Universal multilayer network exploration by random walk with restart

!!Open position for a bioinformatician/computational biologist!!

The Systems Biomedicine team devises computational strategies to transform the deluge of multimodal biomedical data into knowledge for genetic diseases.

The advances in high-throughput technologies are providing unprecedented opportunities to better understand human diseases. Recent years have in this context witnessed the accumulation of omics approaches and datasets. Novel technologies, such as single-cell or spatial omics, are constantly arising. Biomedicine is further transitioning from multiomics to multimodal datasets: data are not only available at the molecular omics level, as we now have access to signals and images, but also to various datasets related to disease phenotypes, health databases, or drug chemical similarities. The bottleneck now lies in the analysis and integration of these complex, large-scale and heterogeneous datasets. The Systems Biomedicine team bridges the gaps by harnessing digital expertise and developing novel computational approaches.
The Systems Biomedicine team is hosting the research group of Paul Villoutreix, laureate of an INSERM Chaire de Professeur Junior.
The Systems Biomedicine team works in close collaboration with the MABIOS team from the Marseille Mathematics Institute.
  • Systems Biomedicine / Baudot
Systems Biology, which consider biological systems as networks of interactions between biological components, offer a new approach to link the genotypes (e.g., the genes and the proteins, as the components of the systems) to the phenotypes (the merging properties of the systems), and in particular the diseased phenotypes. Our group is active in the fields of systems biology with both the development of mathematical and computational tools grounded on network theory and their application to biological questions, with the ultimate goal of untangling the genotype-phenotype relationships of human disorders. More info …
  • Learning meaningful representations of Life / Villoutreix
The Systems Biomedicine team is involved in various local, national and international projects. For instance, in Aix*Marseille University, we are active in the Marmara, Laënnec and Centuri institutes. At the national level, we are involved in the PEPR Santé Numérique, in particular in the M4DI and ai4scmed projects. At the international level, we are involved in the EJP-RD.
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Publication since 2021

Scientific papers (peer-reviewed) (N = 34)

2026

Fanchon E, Loire B, Trani JP, Magdinier F, Baudot A. Pylluminator: fast and scalable analysis of DNA methylation data in Python. Bioinformatics Advances. 2026;6(1):vbag146. doi: 10.1093/bioadv/vbag146

Brière G, Stosskopf T, Loire B, Baudot A. Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings. Bioinformatics. Accepted, August 2026.
2025

Hirst DP, Térézol M, Cantini L, Villoutreix P, Vignes M, Baudot A. MOTL: enhancing multi-omics matrix factorization with transfer learning. Genome Biology. 2025;26:224. doi: 10.1186/s13059-025-03675-7

Ben Boina N, Mossé B, Baudot A, Remy É. Refining Boolean models with the partial most permissive scheme. Bioinformatics. 2025;41(4):btaf123. doi: 10.1093/bioinformatics/btaf123

Lambert J, Leutenegger AL, Baudot A, Jannot AS. Improving patient clustering by incorporating structured variable label relationships in similarity measures. BMC Medical Research Methodology. 2025;25:72. doi: 10.1186/s12874-025-02459-8

Loo RTJ, Nasta F, Macchi M, Baudot A, Burstein F, Bove R, Greve M, Fröhlich H, Khalid S, Küderle A, Moore SL, Storms V, Torous J, Glaab E. Recommendations for Successful Development and Implementation of Digital Health Technology Tools. J Med Internet Res. 2025. doi: 10.2196/56747

Ogloblinsky MC, Conrad DF, Baudot A, Tournier-Lasserve E, FrEx Consortium, Génin E, Marenne G. Benchmark of computational methods to detect digenism in sequencing data. Eur J Hum Genet. 2025. doi: 10.1038/s41431-025-01834-9

Ozisik O, Kara NS, Abbassi-Daloii T, Térézol M, Kuijper EC, Queralt-Rosinach N, Jacobsen A, Sezerman OU, Roos M, Evelo CT, Baudot A, Ehrhart F, Mina E. A collaborative network analysis for the interpretation of transcriptomics data in Huntington’s disease. Scientific Reports. 2025. doi: 10.1038/s41598-025-85580-4

Toury L, Frankel D, Nael S, Abaji M, Le Goff L, Basset M, Airault C, Vernay B, Novoa-del-Toro EM, Bartoli C, Baudot A, Magdinier F, Kaspi E, Roll P. miR-140-5p Overexpression Contributes to Oxidative Stress and Mitochondrial Dysfunction in Hutchinson-Gilford Progeria Syndrome Fibroblasts Through NRF2 Pathway. Aging Cell. 2025. doi: 10.1111/acel.70276

De Bono C, Xu Y, Kausar S, Herbane M, Humbert C, Rafatov S, Missirian C, Moreno M, Shi W, Gitton Y, Lombardini A, Vanzetta I, Mazaud-Guittot S, Chédotal A, Baudot A, Zaffran S, Etchevers HC. Multi-modal refinement of the human heart atlas during the first gestational trimester. Development. 2025;152(5). doi: 10.1242/dev.204555

Kara NS, Ozisik O, Baudot A, Slachtova L. Investigating the Potential Roles of Environmental Exposures on the Pathology of Amyotrophic Lateral Sclerosis by Overlap Analysis. Neurotox Res. 2025;43(6):51. doi: 10.1007/s12640-025-00774-y

Wijnbergen D, Johari M, Ozisik O, ‘t Hoen PAC, Ehrhart F, Baudot A, Evelo CT, Udd B, Roos M, Mina E. Multi-omics analysis in inclusion body myositis identifies mir-16 responsible for HLA overexpression. Orphanet J Rare Dis. 2025;20(1):27. doi: 10.1186/s13023-024-03526-x

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Publication since 2021

Preprint (N = 8)

2026

Homberg N, Lamothe L, Amblard E, Barbot H, Térézol M, et al. (HADACA3 Consortium, incl. Baudot A), Blum Y, Richard M. How to organise a scientific competition to benchmark methods and algorithms in computational biology?. HAL preprint. 2026.

 

Berardelli S, Brière G, Loire B, Paoli FD, Gazzo A, Limongelli I, et al., Baudot A. PhenoXtract: combining Large Language Model and Knowledge Graph embedding to extract phenotypes from clinical descriptions. bioRxiv. 2026. doi: 10.64898/2026.06.22.733382

 

Barbot H, Amblard E, Homberg N, Lamothe L, Térézol M, et al. (HADACA3 Consortium, incl. Baudot A), Richard M. On the Promises and Limits of Multi-omics Integration for Deconvolution: The HADACA3 Benchmark. arXiv. 2026. arXiv:2606.05980.

 

Baratta P, Villoutreix P, Baudot A. Differential Analysis of Gene Spatial Organisation with Minkowski Functionals and Tensors. bioRxiv. 2026. doi: 10.64898/2026.05.12.724373

 

Torrejón E, Sleegers J, Matthiesen R, Macedo MP, Baudot A*, Machado de Oliveira R*. EV-Net: A computational framework to model extracellular vesicles-mediated communication. bioRxiv. 2026. doi: 10.64898/2026.04.02.716053

2025

Brière G, Beust C, Térézol M, Baudot A. Using Networks and Prior Knowledge to Uncover novel Rare Disease Phenotypes. medRxiv. 2025. doi: 10.1101/2025.04.02.25325098

 

Lepe-Soltero D, Artières T, Baudot A, Villoutreix P. MODIS: Multi-Omics Data Integration for Small and unpaired datasets. arXiv. 2025. arXiv:2503.18856.

2023

Kausar S, Asif M, Baudot A. scRNAseq_KNIME workflow: a customizable, locally executable, interactive and automated KNIME workflow for single-cell RNA-seq. bioRxiv. 2023. doi: 10.1101/2023.01.14.524084

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