Natalie 2.0: sparse global network alignment as a special case of quadratic assignment

DOI10.3390/A8041035zbMATH Open1461.90065OpenAlexW2173355656WikidataQ60142893 ScholiaQ60142893MaRDI QIDQ1736730FDOQ1736730

Authors: Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau 

Publication date: 26 March 2019

Published in: Algorithms (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.3390/a8041035

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zbMATH Keywords

network analysisgraph matchingbioinformaticsglobal network alignmentnetwork comparison

Mathematics Subject Classification ID

Graph algorithms (graph-theoretic aspects) (05C85) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10) Discrete location and assignment (90B80)

Cites Work

• Title not available (Why is that?)
• Reducibility among combinatorial problems
• Theoretical Improvements in Algorithmic Efficiency for Network Flow Problems
• Paths, Trees, and Flowers
• Algorithms for the Assignment and Transportation Problems
• The traveling-salesman problem and minimum spanning trees: Part II
• Lagrangean relaxation. (With comments and rejoinder).
• Title not available (Why is that?)
• A Heuristic Method for the Set Covering Problem
• The quadratic assignment problem
• Algorithm engineering for optimal alignment of protein structure distance matrices

Cited In (8)

• A heuristic algorithm to align protein interaction networks
• Lagrangian relaxations for multiple network alignment
• Scalable algorithms for multiple network alignment
• PBNA: an improved probabilistic biological network alignment method
• Simultaneous optimization of both node and edge conservation in network alignment via WAVE
• Network alignment by discrete Ollivier-Ricci flow
• ELRUNA: elimination rule-based network alignment
• Exact \(p\)-values for global network alignments via combinatorial analysis of shared GO terms. \textit{REFANGO}: \textit{R}igorous \textit{E}valuation of \textit{F}unctional \textit{A}lignments of \textit{N}etworks using \textit{G}ene \textit{O}ntology

Uses Software

• SPINAL
• GHOST
• Natalie
• IsoRank
• KEGG
• STRING
• HubAlign
• NETAL
• MAGNA++
• NatalieQ
• L-GRAAL

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