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

DOI10.3390/A8041035MaRDI QIDQ1736730zbMATH OpenOpenAlexWikidataFDO

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

Publication date 26 March 2019

Published in Algorithms (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

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

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)

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Cites work

• scientific article; zbMATH DE number 714527 (Why is no real title available?)
• scientific article; zbMATH DE number 3231692 (Why is no real title available?)
• A Heuristic Method for the Set Covering Problem
• Algorithm engineering for optimal alignment of protein structure distance matrices
• Algorithms for the Assignment and Transportation Problems
• Lagrangean relaxation. (With comments and rejoinder).
• Paths, Trees, and Flowers
• Reducibility among combinatorial problems
• The quadratic assignment problem
• The traveling-salesman problem and minimum spanning trees: Part II
• Theoretical Improvements in Algorithmic Efficiency for Network Flow Problems

Cited in

(8)

• PBNA: an improved probabilistic biological network alignment method
• Scalable algorithms for multiple network alignment
• Network alignment by discrete Ollivier-Ricci flow
• Simultaneous optimization of both node and edge conservation in network alignment via WAVE
• A heuristic algorithm to align protein interaction networks
• 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
• Lagrangian relaxations for multiple network alignment

Describes a project that uses

Uses Software

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

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