Abstract: One of the most challenging tasks in computational biology is the integration of complementary biological data produced from different experimental sources. Our goal here is to combine expression data and biological networks to identify “active modules”, i.e. subnetworks of interacting genes/proteins associated with expression changes in different biological contexts. We developed MOGAMUN, a multi-objective genetic algorithm that finds dense subnetworks with an overall deregulation. We compared the performance of MOGAMUN with 3 state-of-the-art methods (jActiveModules [3],COSINE [4] and PinnacleZ [5]), on simulated expression datasets, where MOGAMUN showed the best performances. We also applied MOGAMUN to identify active modules for a rare monogenic disease, Facioscapulohumeral muscular dystrophy (FSHD). We found active modules that represent both known and new cellular processes associated with the hallmarks of the FSHD disorder. MOGAMUN is available as a Bioconductor package.


[1] Deb, K. et al. (2002). A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE transactions on evolutionary computation, 6, 182-197. [2] Valdeolivas et al. (2018). Random walk with restart on multiplex and heterogeneous biological networks. Bioinformatics, 35(3), 497-505. [3] Ideker, T., Ozier, O., Schwikowski, B., & Siegel, A. F. (2002). Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics,18(suppl_1), S233-S240. [4] Ma, H., Schadt, E. E., Kaplan, L. M., & Zhao, H. (2011). COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. Bioinformatics,27(9), 1290-1298. [5] Chuang, H. Y., Lee, E., Liu, Y. T., Lee, D., & Ideker, T. (2007). Network based classification of breast cancer ‐ metastasis. Molecular systems biology,3(1)

Bioinfo4Women seminars / BSC Life Session

Venue: Online seminar - Zoom

Date: 08/07/2021

Time: 12:00 CEST

Host: Barcelona Supercomputing Center

A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks


Elva Novoa

Postdoc at Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300 Toulouse, France

Sex differences in genetic architecture in UK Biobank



Elena Bernabéu

PhD student at The Roslin Institute, University of Edinburgh

Abstract: Sex is arguably the most important differentiating characteristic in most mammalian species, separating populations into different groups, with varying behaviors, morphologies, and physiologies based on their complement of sex chromosomes, amongst other factors. In humans, despite males and females sharing nearly identical genomes, there are differences between the sexes in complex traits and in the risk of a wide array of diseases. Gene by sex interactions (GxS) are thought to account for some of these differences. However, the extent and basis of these interactions are poorly understood.

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