[Workshop] Multi-omics data integration with dimensionality reduction and multilayer network; applications to human genetic diseases

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Publié le 10 février 2021 – Mis à jour le 10 février 2021
Date(s)

le 8 avril 2021

From 10:00 to 11:30, online presentation followed by a workshop (via Zoom)
Lieu(x)

100% en ligne

Speakers

  • Laura Cantini (CNRS permanent researcher at IBENS - Institut de Biologie de l’Ecole Normale Supérieure)
  • Anaïs Baudot (CNRS researcher in Systems Biology at the MMG - Marseille Medical genetic Unit)

Abstract

The technological advances and accumulation of biomedical datasets are yielding unprecedented opportunities to better understand genetic diseases, but necessitate proper exploration and integration methods to unravel a complete picture of biological systems.

In this mini-workshop, we will discuss the computational strategies we recently developed, using i) multilayer networks to integrate a large range of interactions, and associated exploration algorithms and ii) dimensionality reduction to extract biological knowledge simultaneously from multiple omics. On the application side, we will illustrate our approaches with the analysis of cancer and rare genetic diseases.

Selected related publications & preprints

Cantini, L., Zakeri, P., Hernandez, C., Naldi, A., Thieffry, D., Remy, E., Baudot, A., 2021. Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer. Nature Communications 12. https://doi.org/10.1038/s41467-020-20430-7

Novoa-del-Toro, E.-M., Mezura-Montes, E., Vignes, M., Magdinier, F., Tichit, L., Baudot, A., 2020. A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks. bioRxiv 2020.05.25.114215. https://doi.org/10.1101/2020.05.25.114215

Pio-Lopez, L., Valdeolivas, A., Tichit, L., Remy, É., Baudot, A., 2020. MultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach. arXiv:2008.10085.

Kang, Yoonjee, Denis Thieffry, and Laura Cantini. "Evaluating the reproducibility of single-cell gene regulatory network inference algorithms." bioRxiv (2020).

Valdeolivas, A., Tichit, L., Navarro, C., Perrin, S., Odelin, G., Levy, N., Cau, P., Remy, E., Baudot, A., 2018. Random Walk with Restart on Multiplex and Heterogeneous Biological Networks. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty637

Format and Registration

Online presentation followed by a workshop. To register, please send an email to