MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation

Bioinformatics
V VijayanTijana Milenković

Abstract

Network alignment aims to find conserved regions between different networks. Existing methods aim to maximize total similarity over all aligned nodes (i.e. node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Thus, we recently introduced MAGNA (Maximizing Accuracy in Global Network Alignment) to directly maximize edge conservation while producing alignments and showed its superiority over the existing methods. Here, we extend the original MAGNA with several important algorithmic advances into a new MAGNA++ framework. MAGNA++ introduces several novelties: (i) it simultaneously maximizes any one of three different measures of edge conservation (including our recent superior [Formula: see text] measure) and any desired node conservation measure, which further improves alignment quality compared with maximizing only node conservation or only edge conservation; (ii) it speeds up the original MAGNA algorithm by parallelizing it to automatically use all available resources, as well as by reimplementing the edge conservation measures more efficiently; (iii) it provides a friendly graphical user interface for easy use by domain (e.g. biological...Continue Reading

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Citations

Jul 1, 2016·Bioinformatics·Lei MengTijana Milenković
Jul 19, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Somaye HashemifarJinbo Xu
Jan 8, 2017·Briefings in Bioinformatics·Pietro Hiram Guzzi, Tijana Milenkovic
Oct 25, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jiaxiang HuangLijia Ma
Jan 5, 2018·Bioinformatics·Vipin Vijayan, Tijana Milenkovic
Aug 3, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Shahin MohammadiAnanth Grama
Aug 23, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Vipin Vijayan, Tijana Milenkovic
Jul 3, 2020·PloS One·Shawn Gu, Tijana Milenković
Dec 14, 2016·BMC Bioinformatics·Ehsan KazemiHassan Pezeshgi Modarres
Jun 29, 2018·Bioinformatics·Karel Kalecky, Young-Rae Cho
Mar 2, 2019·Bioinformatics·Noël Malod-Dognin, Nataša Pržulj
Mar 5, 2020·Scientific Reports·Marianna MilanoPietro Hiram Guzzi
Apr 21, 2017·Scientific Reports·Noël Malod-DogninNataša Pržulj
Jun 4, 2015·EURASIP Journal on Bioinformatics & Systems Biology·Fazle E FaisalTijana Milenković
Jun 16, 2017·BMC Bioinformatics·Marianna MilanoMario Cannataro
Jun 14, 2019·BMC Genomics·Rasha ElheshaTamer Kahveci
May 24, 2019·Frontiers in Genetics·Walter NelsonRoded Sharan
Feb 13, 2020·Briefings in Bioinformatics·Zhaoqian LiuBingqiang Liu
Aug 23, 2018·Scientific Reports·Shawn GuTijana Milenković
Sep 9, 2017·Bioinformatics·V VijayanT Milenkovic
Oct 10, 2020·Computational and Structural Biotechnology Journal·Cheng-Yu Ma, Chung-Shou Liao
Sep 10, 2019·Drug Discovery Today·Wilson Wen Bin GohGuillaume Thibault
Nov 6, 2020·BMC Bioinformatics·Umair AyubHammad Naveed
Mar 18, 2021·BMC Bioinformatics·Katie OvensIan McQuillan
Sep 17, 2021·Medical & Biological Engineering & Computing·Elham Mahdipour, Mohammad Ghasemzadeh

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