Mathematical and Algorithmic Analysis of Network and Biological Data

This is the handbook for the KONECT project, the \emph{Koblenz Network Collection}, a scientific project to collect, analyse, and provide network datasets for researchers in all related fields of research, by the Namur Center for Complex Systems (naXys) at the University of Namur, Belgium, with web hosting provided by the Institute for Web Science and Technologies (WeST) at the University of Koblenz--Landau, Germany.

This paper surveys and discusses recent work adapting partial differential equation (PDE) models to discrete structures.

Complex networks or graphs are ubiquitous in sciences and engineering: biological networks, brain networks, transportation networks, social networks, and the World Wide Web, to name a few. Spectral graph theory provides a set of useful techniques and models for understanding `patterns of interconnectedness' in a graph. Our prime focus in this paper is on the following question: Is there a unified explanation and description of the fundamental spectral graph methods? There are...

In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large scale metabolic networks inside three organisms, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus. We also study the dynamics of the large scale genetic network controlling E. coli metabolism. We have tried to explain the ob...

In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction networks, nonlinear dynamics in gene regulatory networks and in particular the design of synthetic genetic networks using the concepts and techniques of nonlinear physics and lastly the effect of stochasticity on the dynamics. The examples chose...

We survey and introduce concepts and tools located at the intersection of information theory and network biology. We show that Shannon's information entropy, compressibility and algorithmic complexity quantify different local and global aspects of synthetic and biological data. We show examples such as the emergence of giant components in Erdos-Renyi random graphs, and the recovery of topological properties from numerical kinetic properties simulating gene expression data. We...

In an era of unprecedented deluge of (mostly unstructured) data, graphs are proving more and more useful, across the sciences, as a flexible abstraction to capture complex relationships between complex objects. One of the main challenges arising in the study of such networks is the inference of macroscopic, large-scale properties affecting a large number of objects, based solely on the microscopic interactions between their elementary constituents. Statistical physics, precis...

Algebraic statistics uses tools from algebra (especially from multilinear algebra, commutative algebra and computational algebra), geometry and combinatorics to provide insight into knotty problems in mathematical statistics. In this survey we illustrate this on three problems related to networks, namely network models for relational data, causal structure discovery and phylogenetics. For each problem we give an overview of recent results in algebraic statistics with emphasis...

Graph theory provides a primary tool for analyzing and designing computer communication networks. In the past few decades, Graph theory has been used to study various types of networks, including the Internet, wide Area Networks, Local Area Networks, and networking protocols such as border Gateway Protocol, Open shortest Path Protocol, and Networking Networks. In this paper, we present some key graph theory concepts used to represent different types of networks. Then we descr...

We present the spectrum of the (normalized) graph Laplacian as a systematic tool for the investigation of networks, and we describe basic properties of eigenvalues and eigenfunctions. Processes of graph formation like motif joining or duplication leave characteristic traces in the spectrum. This can suggest hypotheses about the evolution of a graph representing biological data. To this data, we analyze several biological networks in terms of rough qualitative data of their sp...