Topological Pattern Discovery in Biological Systems and Its Applications


Book Description

"In my research, I addressed this challenge by focusing on the discovery of meaningful patterns in biological systems. For this task, we developed new algorithms and tools for pattern discovery in biological networks, and analyzed regulatory networks of multiple species. The work described in this thesis is divided into three objectives. Each of these objectives was published as distinct scientific article."-- from abstract.




Pattern Discovery in Bioinformatics


Book Description

The computational methods of bioinformatics are being used more and more to process the large volume of current biological data. Promoting an understanding of the underlying biology that produces this data, Pattern Discovery in Bioinformatics: Theory and Algorithms provides the tools to study regularities in biological data. Taking a systema




Discriminative Pattern Discovery on Biological Networks


Book Description

This work provides a review of biological networks as a model for analysis, presenting and discussing a number of illuminating analyses. Biological networks are an effective model for providing insights about biological mechanisms. Networks with different characteristics are employed for representing different scenarios. This powerful model allows analysts to perform many kinds of analyses which can be mined to provide interesting information about underlying biological behaviors. The text also covers techniques for discovering exceptional patterns, such as a pattern accounting for local similarities and also collaborative effects involving interactions between multiple actors (for example genes). Among these exceptional patterns, of particular interest are discriminative patterns, namely those which are able to discriminate between two input populations (for example healthy/unhealthy samples). In addition, the work includes a discussion on the most recent proposal on discovering discriminative patterns, in which there is a labeled network for each sample, resulting in a database of networks representing a sample set. This enables the analyst to achieve a much finer analysis than with traditional techniques, which are only able to consider an aggregated network of each population.




Database and Expert Systems Applications


Book Description

DEXA 2004, the 15th International Conference on Database and Expert Systems Applications, was held August 30 ? September 3, 2004, at the University of Zaragoza, Spain. The quickly growing spectrum of database applications has led to the establisment of more specialized discussion platforms (DaWaK Conference, EC-Web Conference, EGOVConference, Trustbus Conference and DEXA Workshop: Every DEXA event has its own conference proceedings), which were held in parallel with the DEXA Conference also in Zaragoza. In your hands are the results of much effort. The work begins with the preparation of the submitted papers, which then go through the reviewing process. The accepted papers are revised to final versions by their authors and are then arranged within the conference program. All culminates in the conference itself. For this conference 304 papers were submitted, and I want to thank to all who contributed to it; they are the real base of the conference. The program committee and the supporting reviewers produced altogether 942 referee reports, in average 3,1 reports per paper, and selected 92 papers for presentation. At this point we would like to say many thanks to all the institutions that actively supported this conference and made it possible. These were: • University of Zaragoza • FAW • DEXA Association • Austrian Computer Society




Bioinformatics


Book Description

Bioinformatics: Methods and Applications provides a thorough and detailed description of principles, methods, and applications of bioinformatics in different areas of life sciences. It presents a compendium of many important topics of current advanced research and basic principles/approaches easily applicable to diverse research settings. The content encompasses topics such as biological databases, sequence analysis, genome assembly, RNA sequence data analysis, drug design, and structural and functional analysis of proteins. In addition, it discusses computational approaches for vaccine design, systems biology and big data analysis, and machine learning in bioinformatics.It is a valuable source for bioinformaticians, computer biologists, and members of biomedical field who needs to learn bioinformatics approaches to apply to their research and lab activities. - Covers basic and more advanced developments of bioinformatics with a diverse and interdisciplinary approach to fulfill the needs of readers from different backgrounds - Explains in a practical way how to decode complex biological problems using computational approaches and resources - Brings case studies, real-world examples and several protocols to guide the readers with a problem-solving approach







Pattern Recognition in Bioinformatics


Book Description

In the post-genomic era, a holistic understanding of biological systems and p- cesses,inalltheircomplexity,is criticalincomprehendingnature’schoreography of life. As a result, bioinformatics involving its two main disciplines, namely, the life sciences and the computational sciences, is fast becoming a very promising multidisciplinary research ?eld. With the ever-increasing application of lar- scalehigh-throughputtechnologies,suchasgeneorproteinmicroarraysandmass spectrometry methods, the enormous body of information is growing rapidly. Bioinformaticians are posed with a large number of di?cult problems to solve, arising not only due to the complexities in acquiring the molecular infor- tion but also due to the size and nature of the generated data sets and/or the limitations of the algorithms required for analyzing these data. Although the ?eld of bioinformatics is still in its embryonic stage, the recent advancements in computational and information-theoretic techniques are enabling us to c- ductvariousinsilicotestingandscreeningofmanylab-basedexperimentsbefore these are actually performed in vitro or in vivo. These in silico investigations are providing new insights for interpretation and establishing a new direction for a deeper understanding. Among the various advanced computational methods currently being applied to such studies, the pattern recognition techniques are mostly found to be at the core of the whole discovery process for apprehending the underlying biological knowledge. Thus, we can safely surmise that the - going bioinformatics revolution may, in future, inevitably play a major role in many aspects of medical practice and/or the discipline of life sciences.




Theoretical Physics for Biological Systems


Book Description

Quantum physics provides the concepts and their mathematical formalization that lend themselves to describe important properties of biological networks topology, such as vulnerability to external stress and their dynamic response to changing physiological conditions. A theory of networks enhanced with mathematical concepts and tools of quantum physics opens a new area of biological physics, the one of systems biological physics.




Biological Knowledge Discovery Handbook


Book Description

The first comprehensive overview of preprocessing, mining, and postprocessing of biological data Molecular biology is undergoing exponential growth in both the volume and complexity of biological data and knowledge discovery offers the capacity to automate complex search and data analysis tasks. This book presents a vast overview of the most recent developments on techniques and approaches in the field of biological knowledge discovery and data mining (KDD) providing in-depth fundamental and technical field information on the most important topics encountered. Written by top experts, Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data covers the three main phases of knowledge discovery (data preprocessing, data processing also known as data mining and data postprocessing) and analyzes both verification systems and discovery systems. BIOLOGICAL DATA PREPROCESSING Part A: Biological Data Management Part B: Biological Data Modeling Part C: Biological Feature Extraction Part D Biological Feature Selection BIOLOGICAL DATA MINING Part E: Regression Analysis of Biological Data Part F Biological Data Clustering Part G: Biological Data Classification Part H: Association Rules Learning from Biological Data Part I: Text Mining and Application to Biological Data Part J: High-Performance Computing for Biological Data Mining Combining sound theory with practical applications in molecular biology, Biological Knowledge Discovery Handbook is ideal for courses in bioinformatics and biological KDD as well as for practitioners and professional researchers in computer science, life science, and mathematics.




Biotechnology: Concepts, Methodologies, Tools, and Applications


Book Description

Biotechnology can be defined as the manipulation of biological process, systems, and organisms in the production of various products. With applications in a number of fields such as biomedical, chemical, mechanical, and civil engineering, research on the development of biologically inspired materials is essential to further advancement. Biotechnology: Concepts, Methodologies, Tools, and Applications is a vital reference source for the latest research findings on the application of biotechnology in medicine, engineering, agriculture, food production, and other areas. It also examines the economic impacts of biotechnology use. Highlighting a range of topics such as pharmacogenomics, biomedical engineering, and bioinformatics, this multi-volume book is ideally designed for engineers, pharmacists, medical professionals, practitioners, academicians, and researchers interested in the applications of biotechnology.