Simultaneous optimization of both node and edge conservation in network alignment via WAVE

Y Sun, J Crawford, J Tang, T Milenković - Algorithms in Bioinformatics …, 2015 - Springer
Network alignment can be used to transfer functional knowledge between conserved
regions of different networks. Existing methods use a node cost function (NCF) to compare …

MAGNA++: maximizing accuracy in global network alignment via both node and edge conservation

V Vijayan, V Saraph, T Milenković - Bioinformatics, 2015 - academic.oup.com
Motivation: Network alignment aims to find conserved regions between different networks.
Existing methods aim to maximize total similarity over all aligned nodes (ie node …

MAGNA: maximizing accuracy in global network alignment

V Saraph, T Milenković - Bioinformatics, 2014 - academic.oup.com
Motivation: Biological network alignment aims to identify similar regions between networks
of different species. Existing methods compute node similarities to rapidly identify from …

Multiple network alignment via multiMAGNA++

V Vijayan, T Milenković - IEEE/ACM transactions on …, 2017 - ieeexplore.ieee.org
Network alignment (NA) aims to find a node mapping that identifies topologically or
functionally similar network regions between molecular networks of different species …

Aligning dynamic networks with DynaWAVE

V Vijayan, T Milenković - Proceedings of the 2018 ACM International …, 2018 - dl.acm.org
Network alignment (NA) aims to find similar (conserved) regions between networks. Until
recently, existing methods were limited to aligning static networks. However, real-world …

[HTML][HTML] From homogeneous to heterogeneous network alignment via colored graphlets

S Gu, J Johnson, FE Faisal, T Milenković - Scientific reports, 2018 - nature.com
Network alignment (NA) compares networks with the goal of finding a node mapping that
uncovers highly similar (conserved) network regions. Existing NA methods are …

Great: graphlet edge-based network alignment

J Crawford, T Milenković - 2015 IEEE International conference …, 2015 - ieeexplore.ieee.org
Network alignment aims to find regions of topological or functional similarities between
networks. In computational biology, it can be used to transfer biological knowledge from a …

SANA: simulated annealing far outperforms many other search algorithms for biological network alignment

N Mamano, WB Hayes - Bioinformatics, 2017 - academic.oup.com
Every alignment algorithm consists of two orthogonal components: an objective function M
measuring the quality of an alignment, and a search algorithm that explores the space of …

Glalign: A novel algorithm for local network alignment

M Milano, PH Guzzi… - IEEE/ACM transactions on …, 2018 - ieeexplore.ieee.org
Networks are successfully used as a modelling framework in many application domains. For
instance, Protein-Protein Interaction Networks (PPINs) model the set of interactions among …

[HTML][HTML] Fair evaluation of global network aligners

J Crawford, Y Sun, T Milenković - Algorithms for Molecular Biology, 2015 - Springer
Background Analogous to genomic sequence alignment, biological network alignment
identifies conserved regions between networks of different species. Then, function can be …