Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems.

In recent years control theory has been applied to biological systems with the aim of identifying the minimum set of molecular interactions that can drive the network to a required state. However, in an intra-cellular network it is unclear how control can be achieved in practice. To address this limitation we use viral infection, specifically human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV), as a paradigm to model control of an infected cell.

Finding and analysing the minimum set of driver nodes required to control multilayer networks.

It is difficult to control multilayer networks in situations with real-world complexity. Here, we first define the multilayer control problem in terms of the minimum dominating set (MDS) controllability framework and mathematically demonstrate that simple formulas can be used to estimate the size of the minimum dominating set in multilayer (MDSM) complex networks. Second, we develop a new algorithm that efficiently identifies the MDSM in up to 6 layers, with several thousand nodes in each layer network.

Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets.

Controlling complex networks through a small number of controller vertices is of great importance in wide-ranging research fields. Recently, a new approach based on the minimum feedback vertex set (MFVS) has been proposed to find such vertices in directed networks in which the target states are restricted to steady states. However, multiple MFVS configurations may exist and thus the selection of vertices may depend on algorithms and input data representations.

Identification of genes and critical control proteins associated with inflammatory breast cancer using network controllability.

One of the most aggressive forms of breast cancer is inflammatory breast cancer (IBC), whose lack of tumour mass also makes a prompt diagnosis difficult. Moreover, genomic differences between common breast cancers and IBC have not been completely assessed, thus substantially limiting the identification of biomarkers unique to IBC. Here, we developed a novel statistical analysis of gene expression profiles corresponding to microdissected IBC, non-IBC (nIBC) and normal samples that enabled us to identify a set of genes significantly associated with a specific disease state.

Critical controllability analysis of directed biological networks using efficient graph reduction.

Network science has recently integrated key concepts from control theory and has applied them to the analysis of the controllability of complex networks. One of the proposed frameworks uses the Minimum Dominating Set (MDS) approach, which has been successfully applied to the identification of cancer-related proteins and in analyses of large-scale undirected networks, such as proteome-wide protein interaction networks. However, many real systems are better represented by directed networks.

Critical controllability in proteome-wide protein interaction network integrating transcriptome.

Recently, the number of essential gene entries has considerably increased. However, little is known about the relationships between essential genes and their functional roles in critical network control at both the structural (protein interaction network) and dynamic (transcriptional) levels, in part because the large size of the network prevents extensive computational analysis. Here, we present an algorithm that identifies the critical control set of nodes by reducing the computational time by 180 times and by expanding the computable network size up to 25 times, from 1,000 to 25,000 nodes.

The electric properties of low-magnetic-loss magnetic composites containing Zn-Ni-Fe particles.

Recently, magnetic composites consisting of magnetic particles dispersed in a polymer matrix have been widely discussed for miniaturizing high-frequency electronic components such as antennae. Previously, we investigated the influence of the manufacturing process on the homogeneous dispersion of magnetic particles in the polymer and on the magnetic properties of the magnetic composites. In order to miniaturize electronic components, it is crucial to be able to independently control the permeability and permittivity in magnetic composites.