Publications depuis 2020

Anaïs Baudot — mis à jour juillet 2026

Anaïs Baudot  |  Membre de l'équipe

Articles scientifiques (peer-reviewed) (n = 35)

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

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

2024

Baptista A, Brière G, Baudot A. Random Walk with Restart on multilayer networks: from node prioritisation to supervised link prediction and beyond. BMC Bioinformatics. 2024;25:70.

Térézol M, Baudot A, Ozisik O. ODAMNet: a Python package to identify molecular relationships between chemicals and rare diseases using overlap, active module and random walk approaches. SoftwareX. 2024;26:101701. doi: 10.1016/j.softx.2024.101701

Beust C, Valdeolivas A, Baptista A, Brière G, Lévy N, Ozisik O, Baudot A. The Molecular Landscape of Premature Aging Diseases Defined by Multilayer Network Exploration. Advanced Biology. 2024. doi: 10.1002/adbi.202400134

Ozisik O, Gorokhova S, Cerino M, Bartoli M, Baudot A. System-level analysis of genes mutated in muscular dystrophies reveals a functional pattern associated with muscle weakness distribution. Scientific Reports. 2024. doi: 10.1038/s41598-024-60761-9

Bayjanov JR, Doornbos C, Ozisik O, Shin W, Queralt-Rosinach N, Wijnbergen D, Saulnier-Blache JS, Schanstra JP, Buffin-Meyer B, Klein J, Fernández JM, Kaliyaperumal R, Baudot A, 't Hoen PAC, Ehrhart F. Integrative analysis of multi-omics data reveals importance of collagen and the PI3K-AKT signalling pathway in CAKUT. Scientific Reports. 2024. doi: 10.1038/s41598-024-71721-8

Zitnik M, Li MM, Wells A, Glass K, Gysi DM, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, et al.. Current and future directions in network biology. Bioinformatics Advances. 2024;4(1):vbae099. doi: 10.1093/bioadv/vbae099

Argiro L, Chevalier C, Choquet C, Nandkishore N, Ghata A, Baudot A, Zaffran S, Lescroart F. Gastruloids are competent to specify both cardiac and skeletal muscle lineages. Nat Commun. 2024;15:10172. doi: 10.1038/s41467-024-54466-w

Ogloblinsky MC, Bocher O, Aloui C, Leutenegger AL, Ozisik O, Baudot A, Tournier-Lasserve E, Castillo-Madeen H, Lewinsohn D, Conrad DF, Génin E, Marenne G. PSAP-Genomic-Regions: A Method Leveraging Population Data to Prioritize Coding and Non-Coding Variants in Whole Genome Sequencing for Rare Disease Diagnosis. Genet Epidemiol. 2024;49(1):e22593. doi: 10.1002/gepi.22593

van Karnebeek CDM, O'Donnell-Luria A, Baynam G, Baudot A, et al.. Leaving no patient behind! Expert recommendation in the use of innovative technologies for diagnosing rare diseases. Orphanet J Rare Dis. 2024;19(1):357. doi: 10.1186/s13023-024-03361-0

2023

Lescouzères L, Hassen-Khodja C, Baudot A, Bordignon B, Bomont P. A multilevel screening pipeline in zebrafish identifies therapeutic drugs for GAN. EMBO Mol Med. 2023;e16267.

Lambert J, Leutenegger AL, Jannot AS, Baudot A. Tracking clusters of patients over time enables extracting information from medico-administrative databases. J Biomed Inform. 2023;139:104309.

Baptista A, Sánchez-García RJ, Baudot A, Bianconi G. Zoo guide to network embedding. J Phys Complex. 2023;4(4). doi: 10.1088/2632-072X/ad0e23

Laberthonnière C, Delourme M, Chevalier R, Dion C, Ganne B, Hirst D, Caron L, Perrin P, Adélaïde J, Chaffanet M, Xue S, Nguyen K, Reversade B, Déjardin J, Baudot A, Robin JD, Magdinier F. In skeletal muscle and neural crest cells, SMCHD1 regulates biological pathways relevant for Bosma syndrome and facioscapulohumeral dystrophy phenotype. Nucleic Acids Res. 2023;51(14):7269-7287. doi: 10.1093/nar/gkad523

2022

Baptista A, Gonzalez A, Baudot A. Universal multilayer network exploration by random walk with restart. Communications Physics. 2022;5:170.

Ozisik O, Térézol M, Baudot A. orsum: a Python package for filtering and comparing enrichment analyses using a simple principle. BMC Bioinformatics. 2022;23(1):293.

Ozisik O, Ehrhart F, Evelo CT, Mantovani A, Baudot A. Overlap of vitamin A and vitamin D target genes with CAKUT-related processes. F1000Res. 2022;10:395.

Frankel D, Delecourt V, Novoa-del-Toro EM, Robin JD, Airault C, Bartoli C, Baudot A, et al.. miR-376a-3p and miR-376b-3p overexpression in Hutchinson-Gilford progeria fibroblasts inhibits cell proliferation and induces premature senescence. iScience. 2022;103757.

Lambert J, Leutenegger AL, Jannot AS, Baudot A. Tracking Temporal Clusters from Patient Networks. Stud Health Technol Inform. 2022;294:155-156. doi: 10.3233/SHTI220427

2021

Laberthonnière C, Novoa-del-Toro EM, Chevalier R, Broucqsault N, Rao VV, Trani JP, Baudot A, et al.. AKT Signaling Modifies the Balance between Cell Proliferation and Migration in Neural Crest Cells from Patients Affected with Bosma Arhinia and Microphthalmia Syndrome. Biomedicines. 2021;9(7):751.

Laberthonnière C, Novoa-del-Toro E, Delourme M, Chevalier R, Broucqsault N, Mazaleyrat K, Baudot A, et al.. Facioscapulohumeral dystrophy weakened sarcomeric contractility is mimicked in induced pluripotent stem cells-derived innervated muscle fibres. J Cachexia Sarcopenia Muscle. 2021.

Novoa-del-Toro EM, Mezura-Montes E, Vignes M, Térézol M, Magdinier F, Tichit L, Baudot A. A multi-objective genetic algorithm to find active modules in multiplex biological networks. PLoS Comput Biol. 2021;17(8):e1009263.

Pio-Lopez L, Valdeolivas A, Tichit L, Remy É, Baudot A. MultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach. Scientific Reports. 2021.

Cantini L, Zakeri P, Hernandez C, Naldi A, Thieffry D, Remy E, Baudot A. Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer. Nature Communications. 2021;12.

2020

Sánchez-Valle J, Tejero H, Fernández JM, Juan D, Capella-Gutiérrez S, Al-Shahrour F, Tabarés-Seisdedos R, Baudot A*, Pancaldi V*, Valencia A*. Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships. Nat Commun. 2020;11(1):2854.

Prépublications (preprints) (n = 9)

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.

Brière G, Stosskopf T, Loire B, Baudot A. Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings. bioRxiv. 2025. doi: 10.1101/2025.01.23.634511

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