Outcomes

Outcomes created during the M4DI project

Project HAL link: https://hal.science/search/index/q/*/anrProjectId_i/98247

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20 documents

Journal articles4 document
David P Hirst, Morgane Térézol, Laura Cantini, Paul Villoutreix, Matthieu Vignes, et al.. MOTL: enhancing multi-omics matrix factorization with transfer learning. Genome Biology, 2025, 26 (1), pp.224. ⟨10.1186/s13059-025-03675-7⟩. ⟨hal-05212749v2⟩
Nawel Benarba, Sara Bouchenak. Bias in Federated Learning: A Comprehensive Survey. ACM Computing Surveys, 2025, ⟨10.1145/3735125⟩. ⟨hal-05093158⟩
Amazigh Mokhtari, El Chérif Ibrahim, Arnaud Gloaguen, Claire-Cécile Barrot, David Cohen, et al.. Using multiomic integration to improve blood biomarkers of major depressive disorder: a case-control study. EBioMedicine, 2025, 113, pp.105569. ⟨10.1016/j.ebiom.2025.105569⟩. ⟨hal-04934910⟩
Elise Amblard, Vadim Bertrand, Hugo Barbot, Luis Martin Peña, Slim Karkar, et al.. A robust workflow to benchmark deconvolution of multi-omic data. Genome Biology, 2025, 26 (1), pp.429. ⟨10.1186/s13059-025-03897-9⟩. ⟨hal-05444478⟩

Conference papers5 document
Margot Derouin, Amazigh Mokhtari, El Chérif Ibrahim, Pierre-Eric Lutz, Raoul Belzeaux, et al.. Leveraging multi-omics integration to uncover childhood traumarelated mechanisms in bipolar disorder. JOBIM 2025, Jul 2025, Bordeaux, France. pp.228-229. ⟨hal-05344676⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Inferring cellular heterogeneity with mixture models for DNA methylation rates. JdS, Jun 2025, Marseille, France. ⟨hal-05065027⟩
H Barbot, D Causeur, Y Blum, M Richard. Inferring cellular heterogeneity with mixture models for DNA methylation rates. Journées de Statistique, Jun 2025, Marseille, France. ⟨hal-05489385⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Multi-omic statistical inference of cellular heterogeneity – JOBIM 2024. JOBIM 2024, Jun 2024, Toulouse, France. ⟨hal-04664788⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Multi-omic statistical inference of cellular heterogeneity – JdS 2024. JdS 2024, May 2024, Bordeaux, France. ⟨hal-04664748⟩

Poster communications4 document
Elouan Deffains, Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Evaluation of linear modeling assumptions in a simulation context for deconvolution of multi-omic data. Journée de Biologie In Silico de Rennes, Nov 2025, Rennes, France. . ⟨hal-05489405⟩
Florence Ghestem, Gaëlle Marenne, Emmanuelle Genin, Anne-Sophie Jannot, Anaïs Baudot, et al.. Knowledge graph to dissect genotype phenotype associations. IGES 2025 – Annual Meeting on International Genetic Epidemiology Society, Aug 2025, Cologne, Germany. 2025. ⟨hal-05333821⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Simulation of data-driven multi-omic benchmark data for cellular deconvolution methods evaluation. IGDR PhD symposium, Nov 2024, Rennes (Campus de Beaulieu), France. 2024. ⟨hal-04790951⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Multi-omic statistical inference of cellular heterogeneity – COBICA 2024. cobica2024 : Computational Biology of Cancer 2024, Mar 2024, Grenoble, France. ⟨hal-04664694⟩

Preprints, Working Papers6 document
Nicolas Homberg, Lucie Lamothe, Elise Amblard, Hugo Barbot, Morgane Térézol, et al.. How to organise a scientific competition to benchmark methods and algorithms in computational biology?. 2026. ⟨hal-05445539v2⟩
Siddharth Sabata, Jędrzej Kubica, Rishika Gupta, Lars Warren Ericson, Halimat Chisom Atanda, et al.. Addressing Background Genomic and Environmental Effects on Health through Accelerated Computing and Machine Learning: Results from the 2025 Hackathon at Carnegie Mellon University. 2025. ⟨hal-05274100⟩
Rahaf Ahmad, Michał Denkiewicz, Rishika Gupta, Sachin Gadakh, Jędrzej Kubica, et al.. AI for Computational Biology: Highlights from the first BioAI Hackathon at University of Warsaw. 2025. ⟨hal-05274112⟩
Silvia Grosso, Nawel Benarba, Sara Bouchenak, Roberto Esposito, Mirko Polato. A Survey on Multimodal Federated Learning. 2025. ⟨hal-05366356v2⟩
Océane Cassan, Julien Raynal, Christophe Vroland, Kayoko Yasuzawa, Tsukasa Kouno, et al.. A genome-wide, machine learning-guided exploration of the cis-regulatory code involved in neuronal differentiation. 2025. ⟨hal-05069585⟩
Mathys Grapotte, Christophe Vroland, Diego Garrido-Martín, Alessio Vignoli, Lisa Calero, et al.. Evidence of distal regulations orchestrated by RNAs initiating at short tandem repeats. 2025. ⟨hal-05030164⟩

Lectures1 document
Hugo Barbot. Reminder on hypothesis testing. Master. Rennes, France. 2025. ⟨hal-05065036⟩