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Statistical and Evolutionary Analysis of Biological Networks
Networks provide a very useful way to describe a wide range of different data types in biology, physics and elsewhere. Apart from providing a convenient tool to visualize highly dependent data, networks allow stringent mathematical and statistical analysis. In recent years, much progress has been achieved to interpret various types of biological network data such as transcriptomic, metabolomic and protein interaction data as well as epidemiological data. Of particular interest is to understand the organization, complexity and dynamics of biological networks and how these are influenced by network evolution and functionality. This book reviews and explores statistical, mathematical and evolut...
Modeling in Systems Biology
The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive o...
Data Management of Protein Interaction Networks
Current PPI databases do not offer sophisticated querying interfaces and especially do not integrate existing information about proteins. Current algorithms for PIN analysis use only topological information, while emerging approaches attempt to exploit the biological knowledge related to proteins and kinds of interaction, e.g. protein function, localization, structure, described in Gene Ontology or PDB. The book discusses technologies, standards and databases for, respectively, generating, representing and storing PPI data. It also describes main algorithms and tools for the analysis, comparison and knowledge extraction from PINs. Moreover, some case studies and applications of PINs are also discussed.
Analysis of Biological Networks
An introduction to biological networks and methods for their analysis Analysis of Biological Networks is the first book of its kind to provide readers with a comprehensive introduction to the structural analysis of biological networks at the interface of biology and computer science. The book begins with a brief overview of biological networks and graph theory/graph algorithms and goes on to explore: global network properties, network centralities, network motifs, network clustering, Petri nets, signal transduction and gene regulation networks, protein interaction networks, metabolic networks, phylogenetic networks, ecological networks, and correlation networks. Analysis of Biological Networ...
Integrative Bioinformatics
This book provides an overview of the history of integrative bioinformatics and the actual situation and the relevant tools. Subjects cover the essential topics, basic introductions, and latest developments; biological data integration and manipulation; modeling and simulation of networks; as well as a number of applications of integrative bioinformatics. It aims to provide basic introduction of biological information systems and guidance for the computational analysis of systems biology. This book covers a range of issues and methods that unveil a multitude of omics data integration and relevance that integrative bioinformatics has today. It contains a unique compilation of invited and selected articles from the Journal of Integrative Bioinformatics (JIB) and annual meetings of the International Symposium on Integrative Bioinformatics.
Graph Drawing
This book constitutes the thoroughly refereed post-proceedings of the 9th International Symposium on Graph Drawing, GD 2001, held in Vienna, Austria, in September 2001.The 32 revised full papers presented were carefully reviewed and selected from 66 paper submissions. Also included are a corrected version of a paper from the predecessor volume, short reports on the software systems exhibition, two papers of the special session on graph exchange formats, and a report on the annual graph drawing contests. The papers are organized in topical sections on hierarchical drawing, planarity, crossing theory, compaction, planar graphs, symmetries, interactive drawing, representations, aesthetics, 2D- and 3D-embeddings, data visualization, floor planning, and planar drawing.
Graph Drawing and Network Visualization
This two-volume set LNCS 14465-14466 constitutes the proceedings of the 31st International Symposium on Graph Drawing and Network Visualization, GD 2023, held in Isola delle Femmine, Palermo, Italy, in September 2023. The 31 full papers, 7 short papers, presented together with 2 invited talks, and one contest report, were thoroughly reviewed and selected from the 100 submissions. The abstracts of 11 posters presented at the conference can be found in the back matter of the volume. The contributions were organized in topical sections as follows: beyond planarity; crossing numbers; linear layouts; geometric aspects; visualization challenges; graph representations; graph decompositions; topological aspects; parameterized complexity for drawings; planar graphs; frameworks; algorithmics.
Transactions on Computational Systems Biology III
The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems-oriented point of view of biological phenomena. This, the third Transactions on Computational Systems Biology volume, edited by Emanuela Merelli, Pedro Pablo Gonzalez and Andrea Omicini, is devoted to considerably extended versions of selected papers presented at the International Workshop on Network Tools and Applications in Biology (NETTAB 2004), held at the University of Camerino, in Camerino, Italy, in September 2004. Dedicated especially to models and metaphors from biology to bioinformatics tools, the 10 papers selected for the special issue cover a wide range of bioinformatics research such as data visualisation, protein/RNA structure prediction, motif finding, modelling and simulation of protein interaction, genetic linkage analysis, and notations and models for systems biology.
Eye Tracking and Visual Analytics
Visualization and visual analytics are powerful concepts for exploring data from various application domains. The endless number of possible parameters and the many ways to combine visual variables as well as algorithms and interaction techniques create lots of possibilities for building such techniques and tools. The major goal of those tools is to include the human users with their tasks at hand, their hypotheses, and research questions to provide ways to find solutions to their problems or at least to hint them in a certain direction to come closer to a problem solution. However, due to the sheer number of design variations, it is unclear which technique is suitable for those tasks at han...
Graph Drawing
This book constitutes the thoroughly refereed post-proceedings of the 10th International Symposium on Graph Drawing, GD 2002, held in Irvine, CA, USA, in August 2002. The 24 revised full papers, 9 short papers, and 7 software demonstrations presented together with a report on the GD 2002 graph drawing contest were carefully reviewed and selected from a total of 48 regular paper submissions. All current aspects of graph drawing are addressed.
