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Topological Pattern Discovery in Biological Systems and Its Applications

Topological Pattern Discovery in Biological Systems and Its Applications
Author: Ilan Smoly
Publisher:
Total Pages: 77
Release: 2016
Genre:
ISBN:
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"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.

Discriminative Pattern Discovery on Biological Networks

Discriminative Pattern Discovery on Biological Networks
Author: Fabio Fassetti
Publisher: Springer
Total Pages: 51
Release: 2017-09-01
Genre: Computers
ISBN: 3319634771
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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.

Pattern Discovery in Bioinformatics

Pattern Discovery in Bioinformatics
Author: Laxmi Parida
Publisher: CRC Press
Total Pages: 512
Release: 2007-07-04
Genre: Computers
ISBN: 1420010735
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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

Bioinformatics

Bioinformatics
Author: Dev Bukhsh Singh
Publisher: Academic Press
Total Pages: 512
Release: 2021-10-21
Genre: Medical
ISBN: 0323900054
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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

Database and Expert Systems Applications

Database and Expert Systems Applications
Author: Fernando Galindo
Publisher: Springer Science & Business Media
Total Pages: 993
Release: 2004-08-19
Genre: Computers
ISBN: 3540229361
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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

Theoretical Physics for Biological Systems

Theoretical Physics for Biological Systems
Author: Paola Lecca
Publisher: CRC Press
Total Pages: 106
Release: 2019-01-30
Genre: Medical
ISBN: 1351374311
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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.

Topological Data Analysis for Genomics and Evolution

Topological Data Analysis for Genomics and Evolution
Author: Raúl Rabadán
Publisher: Cambridge University Press
Total Pages: 521
Release: 2019-10-31
Genre: Science
ISBN: 1108753396
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Biology has entered the age of Big Data. The technical revolution has transformed the field, and extracting meaningful information from large biological data sets is now a central methodological challenge. Algebraic topology is a well-established branch of pure mathematics that studies qualitative descriptors of the shape of geometric objects. It aims to reduce questions to a comparison of algebraic invariants, such as numbers, which are typically easier to solve. Topological data analysis is a rapidly-developing subfield that leverages the tools of algebraic topology to provide robust multiscale analysis of data sets. This book introduces the central ideas and techniques of topological data analysis and its specific applications to biology, including the evolution of viruses, bacteria and humans, genomics of cancer and single cell characterization of developmental processes. Bridging two disciplines, the book is for researchers and graduate students in genomics and evolutionary biology alongside mathematicians interested in applied topology.

Biological Knowledge Discovery Handbook

Biological Knowledge Discovery Handbook
Author: Mourad Elloumi
Publisher: John Wiley & Sons
Total Pages: 1126
Release: 2015-02-04
Genre: Computers
ISBN: 1118853725
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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.

Topology with Applications

Topology with Applications
Author: S. A. Naimpally
Publisher: World Scientific Publishing Company
Total Pages: 0
Release: 2013
Genre: Proximity spaces
ISBN: 9789814407656
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The principal aim of this book is to introduce topology and its many applications viewed within a framework that includes a consideration of compactness, completeness, continuity, filters, function spaces, grills, clusters and bunches, hyperspace topologies, initial and final structures, metric spaces, metrization, nets, proximal continuity, proximity spaces, separation axioms, and uniform spaces.This book provides a complete framework for the study of topology with a variety of applications in science and engineering that include camouflage filters, classification, digital image processing, forgery detection, Hausdorff raster spaces, image analysis, microscopy, paleontology, pattern recognition, population dynamics, stem cell biology, topological psychology, and visual merchandising.It is the first complete presentation on topology with applications considered in the context of proximity spaces, and the nearness and remoteness of sets of objects. A novel feature throughout this book is the use of near and far, discovered by F Riesz over 100 years ago. In addition, it is the first time that this form of topology is presented in the context of a number of new applications.