Graph Theory and Networks in Biology

In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape

Algorithms in nature: the convergence of systems biology and computational thinking

Biologists rely on computational methods to analyze and integrate large data sets, while several computational methods were inspired by the high-level design principles of biological systems. This Perspectives discusses the recent convergence of these two ways of thinking

Rhythmic dynamics and synchronization via dimensionality reduction : application to human gait

Reliable characterization of locomotor dynamics of human walking is vital to understanding the neuromuscular control of human locomotion and disease diagnosis. However, the inherent oscillation and ubiquity of noise in such non-strictly periodic signals pose great challenges to current methodologies. To this end, we exploit the state-of-the-art technology in pattern recognition and, specifically, dimensionality reduction techniques, and propose to reconstruct and characterize the dynamics accurately on the cycle scale of the signal. This is achieved by deriving a low-dimensional representation of the cycles through global optimization, which effectively preserves the topology of the cycles that are embedded in a high-dimensional Euclidian space. Our approach demonstrates a clear advantage in capturing the intrinsic dynamics and probing the subtle synchronization patterns from uni/bivariate oscillatory signals over traditional methods. Application to human gait data for healthy subjects and diabetics reveals a significant difference in the dynamics of ankle movements and ankle-knee coordination, but not in knee movements. These results indicate that the impaired sensory feedback from the feet due to diabetes does not influence the knee movement in general, and that normal human walking is not critically dependent on the feedback from the peripheral nervous system

Biologically Inspired Near Extinct System Reconstruction

Recovery software system operations from a state of extensive damage without human intervention is a challenging problem as it may need to be based on a different infrastructure from the one that the system was originally designed for and deployed on (i.e., computational and communication devices) and significant reorganization of system functionalities. In this paper, we introduce a bio-inspired approach for reconstructing nearly extinct complex software systems. Our approach is based on encoding a computational DNA (co-DNA) of a system and computational analogues of biological processes to enable the transmission of co-DNA over computational devices and, through it, the transformation of these devices into system cells that can realise chunks of the system functionality, and spread further its reconstruction process

Natural clustering: the modularity approach

We show that modularity, a quantity introduced in the study of networked systems, can be generalized and used in the clustering problem as an indicator for the quality of the solution. The introduction of this measure arises very naturally in the case of clustering algorithms that are rooted in Statistical Mechanics and use the analogy with a physical system.Comment: 11 pages, 5 figure enlarged versio

Process Calculi Abstractions for Biology

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-

A Quorum Sensing Inspired Algorithm for Dynamic Clustering

Quorum sensing is a decentralized biological process, through which a community of cells with no global awareness coordinate their functional behaviors based solely on cell-medium interactions and local decisions. This paper draws inspirations from quorum sensing and colony competition to derive a new algorithm for data clustering. The algorithm treats each data as a single cell, and uses knowledge of local connectivity to cluster cells into multiple colonies simultaneously. It simulates auto-inducers secretion in quorum sensing to tune the influence radius for each cell. At the same time, sparsely distributed core cells spread their influences to form colonies, and interactions between colonies eventually determine each cell's identity. The algorithm has the flexibility to analyze not only static but also time-varying data, which surpasses the capacity of many existing algorithms. Its stability and convergence properties are established. The algorithm is tested on several applications, including both synthetic and real benchmarks data sets, alleles clustering, community detection, image segmentation. In particular, the algorithm's distinctive capability to deal with time-varying data allows us to experiment it on novel applications such as robotic swarms grouping and switching model identification. We believe that the algorithm's promising performance would stimulate many more exciting applications