Random walk with restart on multiplex and heterogeneous biological networks

Bioinformatics
Alberto ValdeolivasAnaïs Baudot

Abstract

Recent years have witnessed an exponential growth in the number of identified interactions between biological molecules. These interactions are usually represented as large and complex networks, calling for the development of appropriated tools to exploit the functional information they contain. Random walk with restart (RWR) is the state-of-the-art guilt-by-association approach. It explores the network vicinity of gene/protein seeds to study their functions, based on the premise that nodes related to similar functions tend to lie close to each other in the networks. In this study, we extended the RWR algorithm to multiplex and heterogeneous networks. The walk can now explore different layers of physical and functional interactions between genes and proteins, such as protein-protein interactions and co-expression associations. In addition, the walk can also jump to a network containing different sets of edges and nodes, such as phenotype similarities between diseases. We devised a leave-one-out cross-validation strategy to evaluate the algorithms abilities to predict disease-associated genes. We demonstrate the increased performances of the multiplex-heterogeneous RWR as compared to several random walks on monoplex or heterogen...Continue Reading

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Citations

Apr 29, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Eunseon JeongJi Yeon Kim
Mar 5, 2020·Bioinformatics·Renming LiuArjun Krishnan
Jun 12, 2020·Journal of Translational Medicine·Francesco MessinaUNKNOWN COVID 19 INMI Network Medicine for IDs Study Group
Jun 9, 2020·Frontiers in Neuroscience·Kai WangXiaoguang Liu
Feb 18, 2020·Frontiers in Genetics·Bohyun LeeLei Xie
Nov 29, 2020·Nature Communications·Xueming LiuAmitabh Sharma
Dec 5, 2020·Briefings in Bioinformatics·Sezin Kircali AtaXiao-Li Li
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Apr 24, 2021·Scientific Reports·Léo Pio-LopezAnaïs Baudot
Apr 24, 2021·IScience·Iker Núñez-CarpinteroAlfonso Valencia
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Jul 22, 2021·Computational and Structural Biotechnology Journal·Milan PicardArnaud Droit
Apr 25, 2021·Genes, Brain, and Behavior·Rohan H C PalmerRobert W Williams
Jun 22, 2021·Bioinformatics·Mustafa Coşkun, Mehmet Koyutürk
Aug 31, 2021·PLoS Computational Biology·Elva María Novoa-Del-ToroAnaïs Baudot
Dec 4, 2021·Journal of Cachexia, Sarcopenia and Muscle·Camille LaberthonnièreFrédérique Magdinier

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