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Songen Cao, Xiaoyi Lv, Yaxiong Ma, Xiaoke Ma

Yangruirui Zhou, Christopher A. Voigt, Douglas Densmore

David O’Reilly, William Shaw, Pauline Hilt, Rafael de Castro Aguiar, Sarah L. Astill, Ioannis Delis

David Kainer, Matthew Lane, Kyle A Sullivan, J Izaak Miller, Mikaela Cashman, Mallory Morgan, Ashley Cliff, Jonathon Romero, Angelica Walker, D Dakota Blair, Hari Chhetri, Yongqin Wang, Mirko Pavicic, Anna Furches, Jaclyn Noshay, Meghan Drake, A J Ireland, Ali Missaoui, Yun Kang, John C Sedbrook, Paramvir Dehal, Shane Canon, Daniel Jacobson

Arash Amini, Marina Paez, Lizhen Lin

Nuria Olvera, Jon Sánchez-Valle, Iker Núñez-Carpintero, Joselyn Rojas-Quintero, Guillaume Noell, Sandra Casas-Recasens, Alen Faiz, Philip Hansbro, Angela Guirao, Rosalba Lepore, Davide Cirillo, Alvar Agustí, Francesca Polverino, Alfonso Valencia, Rosa Faner

Siyuan Peng, Mingliang Yang, Zhijing Yang, Tianshui Chen, Jieming Xie, Guang Ma

Cécile Beust, Alberto Valdeolivas, Anthony Baptista, Galadriel Brière, Nicolas Lévy, Ozan Ozisik, Anaïs Baudot

Iker Núñez-Carpintero, Maria Rigau, Mattia Bosio, Emily O’Connor, Sally Spendiff, Yoshiteru Azuma, Ana Topf, Rachel Thompson, Peter A. C. ’t Hoen, Teodora Chamova, Ivailo Tournev, Velina Guergueltcheva, Steven Laurie, Sergi Beltran, Salvador Capella-Gutiérrez, Davide Cirillo, Hanns Lochmüller, Alfonso Valencia

Anthony Baptista, Galadriel Brière, Anaïs Baudot

Yuxuan Chen, Ruiqing Zheng, Jin Liu, Min Li

Roberta Marino, Yousef El Aalamat, Vanesa Bol, Michele Caselle, Giuseppe Del Giudice, Christophe Lambert, Duccio Medini, Tom M. A. Wilkinson, Alessandro Muzzi

Laishui Lv, Peng Hu, Dalal Bardou, Zijun Zheng, Ting Zhang

Madison Russell, Alber Aqil, Marie Saitou, Omer Gokcumen, Naoki Masuda

Lixia Pan, Wai Lim Ku, Qingsong Tang, Yaqiang Cao, Keji Zhao

Beibei Han, Yingmei Wei, Lai Kang, Qingyong Wang, Suru Feng

Pietro Hiram Guzzi, Giuseppe Tradigo, Pierangelo Veltri

Anthony Baptista, Aitor Gonzalez, Anaïs Baudot

Hakimeh Khojasteh, Alireza Khanteymoori, Mohammad Hossein Olyaee

Youjun Lu, Yongqiu Guan, Jiaying Wei, Yanjun Liang, Li Fu, Feiyu Zuo, Yunfeng Deng

Cagatay Dursun, Anne E. Kwitek, Serdar Bozdag

Iker Núñez-Carpintero, Marianyela Petrizzelli, Andrei Zinovyev, Davide Cirillo, Alfonso Valencia

Changzhou Ma, Qiang Lin, Yong Lin, Xiaoke Ma

Elva María Novoa-del-Toro, Efrén Mezura-Montes, Matthieu Vignes, Morgane Térézol, Frédérique Magdinier, Laurent Tichit, Anaïs Baudot

Violaine Saint-André

Beibei Han, Yingmei Wei, Xianghan Wang, Qingyong Wang

Sergio Antonio Alcalá-Corona, Santiago Sandoval-Motta, Jesús Espinal-Enríquez, Enrique Hernández-Lemus

Zengfa Dou, Xiaoke Ma

Ehsan Pournoor, Zaynab Mousavian, Abbas Nowzari-Dalini, Ali Masoudi-Nejad

Bihai Zhao, Sai Hu, Xiner Liu, Huijun Xiong, Xiao Han, Zhihong Zhang, Xueyong Li, Lei Wang

Hao Shi, Koon-Kiu Yan, Liang Ding, Chenxi Qian, Hongbo Chi, Jiyang Yu

Giuseppe Mangioni, Giuseppe Jurman, Manlio De Domenico

Dérick G. F. Borges, Roberto F. S. Andrade

Ehsan Pournoor, Zaynab Mousavian, Abbas Nowzari Dalini, Ali Masoudi-Nejad

Xueming Liu, Enrico Maiorino, Arda Halu, Kimberly Glass, Rashmi B. Prasad, Joseph Loscalzo, Jianxi Gao, Amitabh Sharma

Arda Halu, Manlio De Domenico, Alex Arenas, Amitabh Sharma

Alberto Valdeolivas, Laurent Tichit, Claire Navarro, Sophie Perrin, Gaëlle Odelin, Nicolas Levy, Pierre Cau, Elisabeth Remy, Anaïs Baudot

Daryl R. DeFord, Scott D. Pauls

Xiaoke Ma, Di Dong, Quan Wang

Sarvenaz Choobdar, Mehmet E. Ahsen, Jake Crawford, Mattia Tomasoni, Tao Fang, David Lamparter, Junyuan Lin, Benjamin Hescott, Xiaozhe Hu, Johnathan Mercer, Ted Natoli, Rajiv Narayan, Aravind Subramanian, Jitao D. Zhang, Gustavo Stolovitzky, Zoltán Kutalik, Kasper Lage, Donna K. Slonim, Julio Saez-Rodriguez, Lenore J. Cowen, Sven Bergmann, Daniel Marbach

Jennifer N. Kerkman, Andreas Daffertshofer, Leonardo L. Gollo, Michael Breakspear, Tjeerd W. Boonstra

Cangfeng Ding, Kan Li

Amir-Mohsen Karimi-Majd, Mohammad Fathian, Masoud Makrehchi

Gilles Didier, Alberto Valdeolivas, Anaïs Baudot

Ralucca Gera, Ryan Miller, Akrati Saxena, Miguel MirandaLopez, Scott Warnke

Xiaoke Ma, Zaiyi Liu, Zhongyuan Zhang, Xiaotai Huang, Wanxin Tang

Jaya Thomas, Dongmin Seo, Lee Sael

Junmei Xu, Runyu Jing, Yuan Liu, Yongcheng Dong, Zhining Wen, Menglong Li

Asep Maulana, Valerio Gemmetto, Diego Garlaschelli, Iryna Yevesyeva, Michael Emmerich

2025	Multi-Graph Contrastive Learning for Community Detection in Multi-Layer Networks IEEE Transactions on Emerging Topics in Computational Intelligence Songen Cao, Xiaoyi Lv, Yaxiong Ma, Xiaoke Ma
2025	Constraint-Based Sub-Graph Partitioning for Multi-Cellular Biological Networks IEEE Transactions on Computational Biology and Bioinformatics Yangruirui Zhou, Christopher A. Voigt, Douglas Densmore
2025	Quantifying the diverse contributions of hierarchical muscle interactions to motor function iScience David O’Reilly, William Shaw, Pauline Hilt, Rafael de Castro Aguiar, Sarah L. Astill, Ioannis Delis
2025	RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species GigaScience David Kainer, Matthew Lane, Kyle A Sullivan, J Izaak Miller, Mikaela Cashman, Mallory Morgan, Ashley Cliff, Jonathon Romero, Angelica Walker, D Dakota Blair, Hari Chhetri, Yongqin Wang, Mirko Pavicic, Anna Furches, Jaclyn Noshay, Meghan Drake, A J Ireland, Ali Missaoui, Yun Kang, John C Sedbrook, Paramvir Dehal, Shane Canon, Daniel Jacobson
2024	Hierarchical Stochastic Block Model for Community Detection in Multiplex Networks Bayesian Analysis Arash Amini, Marina Paez, Lizhen Lin
2024	Lung Tissue Multilayer Network Analysis Uncovers the Molecular Heterogeneity of Chronic Obstructive Pulmonary Disease American Journal of Respiratory and Critical Care Medicine Nuria Olvera, Jon Sánchez-Valle, Iker Núñez-Carpintero, Joselyn Rojas-Quintero, Guillaume Noell, Sandra Casas-Recasens, Alen Faiz, Philip Hansbro, Angela Guirao, Rosalba Lepore, Davide Cirillo, Alvar Agustí, Francesca Polverino, Alfonso Valencia, Rosa Faner
2024	A weighted prior tensor train decomposition method for community detection in multi-layer networks Neural Networks Siyuan Peng, Mingliang Yang, Zhijing Yang, Tianshui Chen, Jieming Xie, Guang Ma
2024	The Molecular Landscape of Premature Aging Diseases Defined by Multilayer Network Exploration Advanced Biology Cécile Beust, Alberto Valdeolivas, Anthony Baptista, Galadriel Brière, Nicolas Lévy, Ozan Ozisik, Anaïs Baudot
2024	Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes Nature Communications Iker Núñez-Carpintero, Maria Rigau, Mattia Bosio, Emily O’Connor, Sally Spendiff, Yoshiteru Azuma, Ana Topf, Rachel Thompson, Peter A. C. ’t Hoen, Teodora Chamova, Ivailo Tournev, Velina Guergueltcheva, Steven Laurie, Sergi Beltran, Salvador Capella-Gutiérrez, Davide Cirillo, Hanns Lochmüller, Alfonso Valencia
2024	Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond BMC Bioinformatics Anthony Baptista, Galadriel Brière, Anaïs Baudot
2024	scMLC: an accurate and robust multiplex community detection method for single-cell multi-omics data Briefings in Bioinformatics Yuxuan Chen, Ruiqing Zheng, Jin Liu, Min Li
2024	An integrative network-based approach to identify driving gene communities in chronic obstructive pulmonary disease npj Systems Biology and Applications Roberta Marino, Yousef El Aalamat, Vanesa Bol, Michele Caselle, Giuseppe Del Giudice, Christophe Lambert, Duccio Medini, Tom M. A. Wilkinson, Alessandro Muzzi
2023	Community Detection in Multilayer Networks Via Semi-Supervised Joint Symmetric Nonnegative Matrix Factorization IEEE Transactions on Network Science and Engineering Laishui Lv, Peng Hu, Dalal Bardou, Zijun Zheng, Ting Zhang
2023	Gene communities in co-expression networks across different tissues PLOS Computational Biology Madison Russell, Alber Aqil, Marie Saitou, Omer Gokcumen, Naoki Masuda
2022	scPCOR-seq enables co-profiling of chromatin occupancy and RNAs in single cells Communications Biology Lixia Pan, Wai Lim Ku, Qingsong Tang, Yaqiang Cao, Keji Zhao
2022	Attributed multiplex graph clustering: A heuristic clustering-aware network embedding approach Physica A: Statistical Mechanics and its Applications Beibei Han, Yingmei Wei, Lai Kang, Qingyong Wang, Suru Feng
2022	Using dual-network-analyser for communities detecting in dual networks BMC Bioinformatics Pietro Hiram Guzzi, Giuseppe Tradigo, Pierangelo Veltri
2022	Universal multilayer network exploration by random walk with restart Communications Physics Anthony Baptista, Aitor Gonzalez, Anaïs Baudot
2022	Comparing protein–protein interaction networks of SARS-CoV-2 and (H1N1) influenza using topological features Scientific Reports Hakimeh Khojasteh, Alireza Khanteymoori, Mohammad Hossein Olyaee
2022	Communications in Computer and Information Science Youjun Lu, Yongqiu Guan, Jiaying Wei, Yanjun Liang, Li Fu, Feiyu Zuo, Yunfeng Deng
2022	PhenoGeneRanker: Gene and Phenotype Prioritization Using Multiplex Heterogeneous Networks IEEE/ACM Transactions on Computational Biology and Bioinformatics Cagatay Dursun, Anne E. Kwitek, Serdar Bozdag
2021	The multilayer community structure of medulloblastoma iScience Iker Núñez-Carpintero, Marianyela Petrizzelli, Andrei Zinovyev, Davide Cirillo, Alfonso Valencia
2021	Identification of multi-layer networks community by fusing nonnegative matrix factorization and topological structural information Knowledge-Based Systems Changzhou Ma, Qiang Lin, Yong Lin, Xiaoke Ma
2021	A multi-objective genetic algorithm to find active modules in multiplex biological networks PLOS Computational Biology Elva María Novoa-del-Toro, Efrén Mezura-Montes, Matthieu Vignes, Morgane Térézol, Frédérique Magdinier, Laurent Tichit, Anaïs Baudot
2021	Computational biology approaches for mapping transcriptional regulatory networks Computational and Structural Biotechnology Journal Violaine Saint-André
2021	2021 IEEE International Conference on Unmanned Systems (ICUS) Beibei Han, Yingmei Wei, Xianghan Wang, Qingyong Wang
2021	Modularity in Biological Networks Frontiers in Genetics Sergio Antonio Alcalá-Corona, Santiago Sandoval-Motta, Jesús Espinal-Enríquez, Enrique Hernández-Lemus
2021	Inferring Functional Epigenetic Modules by Integrative Analysis of Multiple Heterogeneous Networks Frontiers in Genetics Zengfa Dou, Xiaoke Ma
2021	A propagation-based seed-centric local community detection for multilayer environment: The case study of colon adenocarcinoma PLOS ONE Ehsan Pournoor, Zaynab Mousavian, Abbas Nowzari-Dalini, Ali Masoudi-Nejad
2020	A Novel Computational Approach for Identifying Essential Proteins From Multiplex Biological Networks Frontiers in Genetics Bihai Zhao, Sai Hu, Xiner Liu, Huijun Xiong, Xiao Han, Zhihong Zhang, Xueyong Li, Lei Wang
2020	Network Approaches for Dissecting the Immune System iScience Hao Shi, Koon-Kiu Yan, Liang Ding, Chenxi Qian, Hongbo Chi, Jiyang Yu
2020	Multilayer Flows in Molecular Networks Identify Biological Modules in the Human Proteome IEEE Transactions on Network Science and Engineering Giuseppe Mangioni, Giuseppe Jurman, Manlio De Domenico
2020	Finding modular structure in multiplex networks by sequential intra-layer edge elimination The European Physical Journal B Dérick G. F. Borges, Roberto F. S. Andrade
2020	Identification of Key Components in Colon Adenocarcinoma Using Transcriptome to Interactome Multilayer Framework Scientific Reports Ehsan Pournoor, Zaynab Mousavian, Abbas Nowzari Dalini, Ali Masoudi-Nejad
2020	Robustness and lethality in multilayer biological molecular networks Nature Communications Xueming Liu, Enrico Maiorino, Arda Halu, Kimberly Glass, Rashmi B. Prasad, Joseph Loscalzo, Jianxi Gao, Amitabh Sharma
2019	The multiplex network of human diseases npj Systems Biology and Applications Arda Halu, Manlio De Domenico, Alex Arenas, Amitabh Sharma
2019	Random walk with restart on multiplex and heterogeneous biological networks Bioinformatics Alberto Valdeolivas, Laurent Tichit, Claire Navarro, Sophie Perrin, Gaëlle Odelin, Nicolas Levy, Pierre Cau, Elisabeth Remy, Anaïs Baudot
2019	Spectral clustering methods for multiplex networks Physica A: Statistical Mechanics and its Applications Daryl R. DeFord, Scott D. Pauls
2019	Community Detection in Multi-Layer Networks Using Joint Nonnegative Matrix Factorization IEEE Transactions on Knowledge and Data Engineering Xiaoke Ma, Di Dong, Quan Wang
2019	Assessment of network module identification across complex diseases Nature Methods Sarvenaz Choobdar, Mehmet E. Ahsen, Jake Crawford, Mattia Tomasoni, Tao Fang, David Lamparter, Junyuan Lin, Benjamin Hescott, Xiaozhe Hu, Johnathan Mercer, Ted Natoli, Rajiv Narayan, Aravind Subramanian, Jitao D. Zhang, Gustavo Stolovitzky, Zoltán Kutalik, Kasper Lage, Donna K. Slonim, Julio Saez-Rodriguez, Lenore J. Cowen, Sven Bergmann, Daniel Marbach
2018	Network structure of the human musculoskeletal system shapes neural interactions on multiple time scales Science Advances Jennifer N. Kerkman, Andreas Daffertshofer, Leonardo L. Gollo, Michael Breakspear, Tjeerd W. Boonstra
2018	Proceedings of the 15th ACM International Conference on Computing Frontiers Cangfeng Ding, Kan Li
2018	Consensus-based methodology for detection communities in multilayered networks Physica A: Statistical Mechanics and its Applications Amir-Mohsen Karimi-Majd, Mohammad Fathian, Masoud Makrehchi
2018	Identifying communities from multiplex biological networks by randomized optimization of modularity F1000Research Gilles Didier, Alberto Valdeolivas, Anaïs Baudot
2018	Identifying communities from multiplex biological networks by randomized optimization of modularity F1000Research Gilles Didier, Alberto Valdeolivas, Anaïs Baudot
2017	Proceedings of the 2017 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining 2017 Ralucca Gera, Ryan Miller, Akrati Saxena, Miguel MirandaLopez, Scott Warnke
2017	Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data BMC Bioinformatics Xiaoke Ma, Zaiyi Liu, Zhongyuan Zhang, Xiaotai Huang, Wanxin Tang
2016	Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders International Journal of Molecular Sciences Jaya Thomas, Dongmin Seo, Lee Sael
2016	A new strategy for exploring the hierarchical structure of cancers by adaptively partitioning functional modules from gene expression network Scientific Reports Junmei Xu, Runyu Jing, Yuan Liu, Yongcheng Dong, Zhining Wen, Menglong Li
2016	2016 IEEE Symposium Series on Computational Intelligence (SSCI) Asep Maulana, Valerio Gemmetto, Diego Garlaschelli, Iryna Yevesyeva, Michael Emmerich
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