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Genomic Signal Processing by Ilya Shmulevich,Edward R. Dougherty Pdf
Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathematical definitions and propositions for the main elements of GSP and by paying attention to the validity of models relative to the data. Ilya Shmulevich and Edward Dougherty cover real-world situations and explain their mathematical modeling in relation to systems biology and systems medicine. Genomic Signal Processing makes a major contribution to computational biology, systems biology, and translational genomics by providing a self-contained explanation of the fundamental mathematical issues facing researchers in four areas: classification, clustering, network modeling, and network intervention.
Genomic Signal Processing and Statistics by Edward R. Dougherty Pdf
Recent advances in genomic studies have stimulated synergetic research and development in many cross-disciplinary areas. Processing the vast genomic data, especially the recent large-scale microarray gene expression data, to reveal the complex biological functionality, represents enormous challenges to signal processing and statistics. This perspective naturally leads to a new field, genomic signal processing (GSP), which studies the processing of genomic signals by integrating the theory of signal processing and statistics. Written by an international, interdisciplinary team of authors, this invaluable edited volume is accessible to students just entering this emergent field, and to researchers, both in academia and in industry, in the fields of molecular biology, engineering, statistics, and signal processing. The book provides tutorial-level overviews and addresses the specific needs of genomic signal processing students and researchers as a reference book. The book aims to address current genomic challenges by exploiting potential synergies between genomics, signal processing, and statistics, with special emphasis on signal processing and statistical tools for structural and functional understanding of genomic data. The first part of this book provides a brief history of genomic research and a background introduction from both biological and signal-processing/statistical perspectives, so that readers can easily follow the material presented in the rest of the book. In what follows, overviews of state-of-the-art techniques are provided. We start with a chapter on sequence analysis, and follow with chapters on feature selection, classification, and clustering of microarray data. We then discuss the modeling, analysis, and simulation of biological regulatory networks, especially gene regulatory networks based on Boolean and Bayesian approaches. Visualization and compression of gene data, and supercomputer implementation of genomic signal processing systems are also treated. Finally, we discuss systems biology and medical applications of genomic research as well as the future trends in genomic signal processing and statistics research.
Genomic Signal Processing and Statistics by Anonim Pdf
This book provides tutorial-level overviews and addresses the specific needs of genomic signal processing students and researchers as a reference book. It aims to address current genomic challenges by exploiting potential synergies between genomics, signal processing, and statistics, with special emphasis on signal processing and statistical tools for structural and functional understanding of genomic data.
Computational and Statistical Approaches to Genomics by Wei Zhang,Ilya Shmulevich Pdf
The second edition of this book adds eight new contributors to reflect a modern cutting edge approach to genomics. It contains the newest research results on genomic analysis and modeling using state-of-the-art methods from engineering, statistics, and genomics. These tools and models are then applied to real biological and clinical problems. The book’s original seventeen chapters are also updated to provide new initiatives and directions.
Genomic Sequence Analysis for Exon Prediction Using Adaptive Signal Processing Algorithms by Md. Zia Ur Rahman,Srinivasareddy Putluri Pdf
This book addresses the issue of improving the accuracy in exon prediction in DNA sequences using various adaptive techniques based on different performance measures that are crucial in disease diagnosis and therapy. First, the authors present an overview of genomics engineering, structure of DNA sequence and its building blocks, genetic information flow in a cell, gene prediction along with its significance, and various types of gene prediction methods, followed by a review of literature starting with the biological background of genomic sequence analysis. Next, they cover various theoretical considerations of adaptive filtering techniques used for DNA analysis, with an introduction to adaptive filtering, properties of adaptive algorithms, and the need for development of adaptive exon predictors (AEPs) and structure of AEP used for DNA analysis. Then, they extend the approach of least mean squares (LMS) algorithm and its sign-based realizations with normalization factor for DNA analysis. They also present the normalized logarithmic-based realizations of least mean logarithmic squares (LMLS) and least logarithmic absolute difference (LLAD) adaptive algorithms that include normalized LMLS (NLMLS) algorithm, normalized LLAD (NLLAD) algorithm, and their signed variants. This book ends with an overview of the goals achieved and highlights the primary achievements using all proposed techniques. This book is intended to provide rigorous use of adaptive signal processing algorithms for genetic engineering, biomedical engineering, and bioinformatics and is useful for undergraduate and postgraduate students. This will also serve as a practical guide for Ph.D. students and researchers and will provide a number of research directions for further work. Features Presents an overview of genomics engineering, structure of DNA sequence and its building blocks, genetic information flow in a cell, gene prediction along with its significance, and various types of gene prediction methods Covers various theoretical considerations of adaptive filtering techniques used for DNA analysis, introduction to adaptive filtering, properties of adaptive algorithms, need for development of adaptive exon predictors (AEPs), and structure of AEP used for DNA analysis Extends the approach of LMS algorithm and its sign-based realizations with normalization factor for DNA analysis Presents the normalized logarithmic-based realizations of LMLS and LLAD adaptive algorithms that include normalized LMLS (NLMLS) algorithm, normalized LLAD (NLLAD) algorithm, and their signed variants Provides an overview of the goals achieved and highlights the primary achievements using all proposed techniques Dr. Md. Zia Ur Rahman is a professor in the Department of Electronics and Communication Engineering at Koneru Lakshmaiah Educational Foundation (K. L. University), Guntur, India. His current research interests include adaptive signal processing, biomedical signal processing, genetic engineering, medical imaging, array signal processing, medical telemetry, and nanophotonics. Dr. Srinivasareddy Putluri is currently a Software Engineer at Tata Consultancy Services Ltd., Hyderabad. He received his Ph.D. degree (Genomic Signal Processing using Adaptive Signal Processing algorithms) from the Department of Electronics and Communication Engineering at Koneru Lakshmaiah Educational Foundation (K. L. University), Guntur, India. His research interests include genomic signal processing and adaptive signal processing. He has published 15 research papers in various journals and proceedings. He is currently a reviewer of publishers like the IEEE Access and IGI.
Signal Processing and Machine Learning for Biomedical Big Data by Ervin Sejdic,Tiago H. Falk Pdf
Within the healthcare domain, big data is defined as any ``high volume, high diversity biological, clinical, environmental, and lifestyle information collected from single individuals to large cohorts, in relation to their health and wellness status, at one or several time points.'' Such data is crucial because within it lies vast amounts of invaluable information that could potentially change a patient's life, opening doors to alternate therapies, drugs, and diagnostic tools. Signal Processing and Machine Learning for Biomedical Big Data thus discusses modalities; the numerous ways in which this data is captured via sensors; and various sample rates and dimensionalities. Capturing, analyzing, storing, and visualizing such massive data has required new shifts in signal processing paradigms and new ways of combining signal processing with machine learning tools. This book covers several of these aspects in two ways: firstly, through theoretical signal processing chapters where tools aimed at big data (be it biomedical or otherwise) are described; and, secondly, through application-driven chapters focusing on existing applications of signal processing and machine learning for big biomedical data. This text aimed at the curious researcher working in the field, as well as undergraduate and graduate students eager to learn how signal processing can help with big data analysis. It is the hope of Drs. Sejdic and Falk that this book will bring together signal processing and machine learning researchers to unlock existing bottlenecks within the healthcare field, thereby improving patient quality-of-life. Provides an overview of recent state-of-the-art signal processing and machine learning algorithms for biomedical big data, including applications in the neuroimaging, cardiac, retinal, genomic, sleep, patient outcome prediction, critical care, and rehabilitation domains. Provides contributed chapters from world leaders in the fields of big data and signal processing, covering topics such as data quality, data compression, statistical and graph signal processing techniques, and deep learning and their applications within the biomedical sphere. This book’s material covers how expert domain knowledge can be used to advance signal processing and machine learning for biomedical big data applications.
Parametric Statistical Change Point Analysis by Jie Chen,Arjun K. Gupta Pdf
This revised and expanded second edition is an in-depth study of the change point problem from a general point of view, as well as a further examination of change point analysis of the most commonly used statistical models. Change point problems are encountered in such disciplines as economics, finance, medicine, psychology, signal processing, and geology, to mention only several. More recently, change point analysis has been found in extensive applications related to analyzing biomedical imaging data and gene expression data. Extensive examples throughout the text emphasize key concepts and different methodologies used. New examples of change point analysis in modern molecular biology and other fields such as finance and air traffic control have been added to this second edition.
Introduction to Genomic Signal Processing with Control by Aniruddha Datta,Edward R. Dougherty Pdf
Studying large sets of genes and their collective function requires tools that can easily handle huge amounts of information. Recent research indicates that engineering approaches for prediction, signal processing, and control are well suited for studying multivariate interactions. A tutorial guide to the current engineering research in genomics, Introduction to Genomic Signal Processing with Control provides a state-of-the-art account of the use of control theory to obtain intervention strategies for gene regulatory networks. The book builds up the necessary molecular biology background with a basic review of organic chemistry and an introduction of DNA, RNA, and proteins, followed by a description of the processes of transcription and translation and the genetic code that is used to carry out the latter. It discusses control of gene expression, introduces genetic engineering tools such as microarrays and PCR, and covers cell cycle control and tissue renewal in multi-cellular organisms. The authors then delineate how the engineering approaches of classification and clustering are appropriate for carrying out gene-based disease classification. This leads naturally to expression prediction, which in turn leads to genetic regulatory networks. The book concludes with a discussion of control approaches that can be used to alter the behavior of such networks in the hope that this alteration will move the network from a diseased state to a disease-free state. Written by recognized leaders in this emerging field, the book provides the exact amount of molecular biology required to understand the engineering applications. It is a self-contained resource that spans the diverse disciplines of molecular biology and electrical engineering.
