Systemic Approaches In Bioinformatics And Computational Systems Biology

Author : Lecca, Paola
Publisher : IGI Global
Page : 471 pages
File Size : 46,6 Mb
Release : 2011-12-31
Category : Medical
ISBN : 9781613504369

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Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances by Lecca, Paola Pdf

The convergence of biology and computer science was initially motivated by the need to organize and process a growing number of biological observations resulting from rapid advances in experimental techniques. Today, however, close collaboration between biologists, biochemists, medical researchers, and computer scientists has also generated remarkable benefits for the field of computer science. Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances presents new techniques that have resulted from the application of computer science methods to the organization and interpretation of biological data. The book covers three subject areas: bioinformatics, computational biology, and computational systems biology. It focuses on recent, systemic approaches in computer science and mathematics that have been used to model, simulate, and more generally, experiment with biological phenomena at any scale.

Author : Paola Lecca,Dan Tulpan
Publisher : Unknown
Page : 336 pages
File Size : 54,8 Mb
Release : 2024-06-10
Category : Electronic
ISBN : OCLC:794546073

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Systemic Approaches in Bioinformatics and Computational Systems Biology by Paola Lecca,Dan Tulpan Pdf

Author : Sangdun Choi
Publisher : Springer Science & Business Media
Page : 549 pages
File Size : 48,6 Mb
Release : 2008-05-17
Category : Science
ISBN : 9781597455312

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Introduction to Systems Biology by Sangdun Choi Pdf

This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors offer a broad overview of the field using key examples and typical approaches to experimental design. The volume begins with an introduction to systems biology and then details experimental omics tools. Other sections introduce the reader to challenging computational approaches. The final sections provide ideas for theoretical and modeling optimization in systemic biological researches. The book is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.

Author : Hamid R Arabnia,Quoc Nam Tran
Publisher : Morgan Kaufmann
Page : 670 pages
File Size : 51,8 Mb
Release : 2015-08-11
Category : Computers
ISBN : 9780128026465

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Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology by Hamid R Arabnia,Quoc Nam Tran Pdf

Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology discusses the latest developments in all aspects of computational biology, bioinformatics, and systems biology and the application of data-analytics and algorithms, mathematical modeling, and simu- lation techniques. • Discusses the development and application of data-analytical and theoretical methods, mathematical modeling, and computational simulation techniques to the study of biological and behavioral systems, including applications in cancer research, computational intelligence and drug design, high-performance computing, and biology, as well as cloud and grid computing for the storage and access of big data sets. • Presents a systematic approach for storing, retrieving, organizing, and analyzing biological data using software tools with applications to general principles of DNA/RNA structure, bioinformatics and applications, genomes, protein structure, and modeling and classification, as well as microarray analysis. • Provides a systems biology perspective, including general guidelines and techniques for obtaining, integrating, and analyzing complex data sets from multiple experimental sources using computational tools and software. Topics covered include phenomics, genomics, epigenomics/epigenetics, metabolomics, cell cycle and checkpoint control, and systems biology and vaccination research. • Explains how to effectively harness the power of Big Data tools when data sets are so large and complex that it is difficult to process them using conventional database management systems or traditional data processing applications. Discusses the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological and behavioral systems. Presents a systematic approach for storing, retrieving, organizing and analyzing biological data using software tools with applications. Provides a systems biology perspective including general guidelines and techniques for obtaining, integrating and analyzing complex data sets from multiple experimental sources using computational tools and software.

Author : Inna Kuperstein,Emmanuel Barillot
Publisher : CRC Press
Page : 167 pages
File Size : 42,7 Mb
Release : 2019-09-09
Category : Computers
ISBN : 9781000682922

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Computational Systems Biology Approaches in Cancer Research by Inna Kuperstein,Emmanuel Barillot Pdf

Praise for Computational Systems BiologyApproaches in Cancer Research: "Complex concepts are written clearly and with informative illustrations and useful links. The book is enjoyable to read yet provides sufficient depth to serve as a valuable resource for both students and faculty." — Trey Ideker, Professor of Medicine, UC Xan Diego, School of Medicine "This volume is attractive because it addresses important and timely topics for research and teaching on computational methods in cancer research. It covers a broad variety of approaches, exposes recent innovations in computational methods, and provides acces to source code and to dedicated interactive web sites." — Yves Moreau, Department of Electrical Engineering, SysBioSys Centre for Computational Systems Biology, University of Leuven With the availability of massive amounts of data in biology, the need for advanced computational tools and techniques is becoming increasingly important and key in understanding biology in disease and healthy states. This book focuses on computational systems biology approaches, with a particular lens on tackling one of the most challenging diseases - cancer. The book provides an important reference and teaching material in the field of computational biology in general and cancer systems biology in particular. The book presents a list of modern approaches in systems biology with application to cancer research and beyond. It is structured in a didactic form such that the idea of each approach can easily be grasped from the short text and self-explanatory figures. The coverage of topics is diverse: from pathway resources, through methods for data analysis and single data analysis to drug response predictors, classifiers and image analysis using machine learning and artificial intelligence approaches. Features Up to date using a wide range of approaches Applicationexample in each chapter Online resources with useful applications’

Author : Karthik Raman
Publisher : CRC Press
Page : 359 pages
File Size : 43,8 Mb
Release : 2021-05-30
Category : Computers
ISBN : 9780429944529

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An Introduction to Computational Systems Biology by Karthik Raman Pdf

Emphasises a hands-on approach to modelling Strong emphasis on coding and software tools for systems biology Covers the entire spectrum of modelling, from static networks, to dynamic models Thoughtful exercises to test and enable student understanding of concepts Current chapters on exciting new developments like whole-cell modelling and community modelling

Author : Kayvan Najarian,Siamak Najarian,Shahriar Gharibzadeh,Christopher N. Eichelberger
Publisher : CRC Press
Page : 190 pages
File Size : 42,5 Mb
Release : 2009-04-13
Category : Medical
ISBN : 9781439882948

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Systems Biology and Bioinformatics by Kayvan Najarian,Siamak Najarian,Shahriar Gharibzadeh,Christopher N. Eichelberger Pdf

The availability of molecular imaging and measurement systems enables today's biologists to swiftly monitor thousands of genes involved in a host of diseases, a critical factor in specialized drug development. Systems Biology and Bioinformatics: A Computational Approach provides students with a comprehensive collection of the computational methods

Author : Sonia Cortassa,Miguel A. Aon
Publisher : Springer Nature
Page : 494 pages
File Size : 49,6 Mb
Release : 2022-05-23
Category : Science
ISBN : 9781071618318

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Computational Systems Biology in Medicine and Biotechnology by Sonia Cortassa,Miguel A. Aon Pdf

This volume addresses the latest state-of-the-art systems biology-oriented approaches that--driven by big data and bioinformatics--are utilized by Computational Systems Biology, an interdisciplinary field that bridges experimental tools with computational tools to tackle complex questions at the frontiers of knowledge in medicine and biotechnology. The chapters in this book are organized into six parts: systems biology of the genome, epigenome, and redox proteome; metabolic networks; aging and longevity; systems biology of diseases; spatiotemporal patterns of rhythms, morphogenesis, and complex dynamics; and genome scale metabolic modeling in biotechnology. In every chapter, readers will find varied methodological approaches applied at different levels, from molecular, cellular, organ to organisms, genome to phenome, and health and disease. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics; criteria utilized for applying specific methodologies; lists of the necessary materials, reagents, software, databases, algorithms, mathematical models, and dedicated analytical procedures; step-by-step, readily reproducible laboratory, bioinformatics, and computational protocols all delivered in didactic and clear style and abundantly illustrated with express case studies and tutorials; and tips on troubleshooting and advice for achieving reproducibility while avoiding mistakes and misinterpretations. The overarching goal driving this volume is to excite the expert and stimulate the newcomer to the field of Computational Systems Biology. Cutting-edge and authoritative, Computational Systems Biology in Medicine and Biotechnology: Methods and Protocols is a valuable resource for pre- and post-graduate students in medicine and biotechnology, and in diverse areas ranging from microbiology to cellular and organismal biology, as well as computational and experimental biologists, and researchers interested in utilizing comprehensive systems biology oriented methods.

Author : Frederick Marcus
Publisher : Springer Science & Business Media
Page : 296 pages
File Size : 55,5 Mb
Release : 2008-07-22
Category : Science
ISBN : 9783540783534

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Bioinformatics and Systems Biology by Frederick Marcus Pdf

Collaborative research in bioinformatics and systems biology is a key element of modern biology and health research. This book highlights and provides access to many of the methods, environments, results and resources involved, including integral laboratory data generation and experimentation and clinical activities. Collaborative projects embody a research paradigm that connects many of the top scientists, institutions, their resources and research worldwide, resulting in first-class contributions to bioinformatics and systems biology. Central themes include describing processes and results in collaborative research projects using computational biology and providing a guide for researchers to access them. The book is also a practical guide on how science is managed. It shows how collaborative researchers are putting results together in a way accessible to the entire biomedical community.

Author : Saeid Kadkhodaei,Farahnaz Sadat Golestan Hashemi,Morvarid Akhavan Rezaei,Sahar Abbasiliasi,Joo Shun Tan,Hamid Rajabi Memari,Faruku Bande,Ali Baradaran,Mahdi Moradpour,Arbakariya B, Ariff
Publisher : Springer
Page : 121 pages
File Size : 42,6 Mb
Release : 2018-05-16
Category : Science
ISBN : 9783319903910

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Cis/Transgene Optimization by Saeid Kadkhodaei,Farahnaz Sadat Golestan Hashemi,Morvarid Akhavan Rezaei,Sahar Abbasiliasi,Joo Shun Tan,Hamid Rajabi Memari,Faruku Bande,Ali Baradaran,Mahdi Moradpour,Arbakariya B, Ariff Pdf

This book is a practical review which focuses on computational analysis and on in silico approaches towards the systematic discovery of various key functional gene expression elements in microalgae as a model. So far, in this regard very little information is available. Efficient stepwise procedures for analysing the matrix attachment regions (MARs) are outlined, as well as for translation initiation sites (TIS), signal peptide (SP) sequences, gene optimization and transformation systems. These outlines can be efficiently deployed as practical models for the systematic discovery of key expression elements and for the optimization of cis/transgenes in other micro/organisms. The first chapter is an introduction on the key gene expression elements analysed in this book, including scaffold/matrix attachment regions, translation initiation sites, signal peptides as well as gene optimization. Chapter 2 focuses on systematic strategies and computational approaches toward in silico analysis of each factor. The analyses outcomes is assessed individually in chapter 3 followed by developing the specific conceptual models for each element in Chapter 4. The concluding remarks are discussed in Chapter 5. This work is of interest to computational and experimental biologists interested in transcriptional regulation analysis as well as to researchers and scientists who wish to consider the use of bioinformatics and computational biology in design, analysis, or regulatory reviews of key gene expression elements for the production of recombinant proteins experiments.

Author : Huma M. Lodhi,Stephen H. Muggleton
Publisher : John Wiley & Sons
Page : 435 pages
File Size : 46,8 Mb
Release : 2010-03-25
Category : Computers
ISBN : 9780470556740

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Elements of Computational Systems Biology by Huma M. Lodhi,Stephen H. Muggleton Pdf

Groundbreaking, long-ranging research in this emergent field that enables solutions to complex biological problems Computational systems biology is an emerging discipline that is evolving quickly due to recent advances in biology such as genome sequencing, high-throughput technologies, and the recent development of sophisticated computational methodologies. Elements of Computational Systems Biology is a comprehensive reference covering the computational frameworks and techniques needed to help research scientists and professionals in computer science, biology, chemistry, pharmaceutical science, and physics solve complex biological problems. Written by leading experts in the field, this practical resource gives detailed descriptions of core subjects, including biological network modeling, analysis, and inference; presents a measured introduction to foundational topics like genomics; and describes state-of-the-art software tools for systems biology. Offers a coordinated integrated systems view of defining and applying computational and mathematical tools and methods to solving problems in systems biology Chapters provide a multidisciplinary approach and range from analysis, modeling, prediction, reasoning, inference, and exploration of biological systems to the implications of computational systems biology on drug design and medicine Helps reduce the gap between mathematics and biology by presenting chapters on mathematical models of biological systems Establishes solutions in computer science, biology, chemistry, and physics by presenting an in-depth description of computational methodologies for systems biology Elements of Computational Systems Biology is intended for academic/industry researchers and scientists in computer science, biology, mathematics, chemistry, physics, biotechnology, and pharmaceutical science. It is also accessible to undergraduate and graduate students in machine learning, data mining, bioinformatics, computational biology, and systems biology courses.

Author : Xiaobo Zhou,Stephen T. C. Wong
Publisher : World Scientific
Page : 398 pages
File Size : 51,5 Mb
Release : 2008
Category : Science
ISBN : 9789812707048

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Computational Systems Bioinformatics by Xiaobo Zhou,Stephen T. C. Wong Pdf

Computational systems biology is a new and rapidly developing field of research, concerned with understanding the structure and processes of biological systems at the molecular, cellular, tissue, and organ levels through computational modeling as well as novel information theoretic data and image analysis methods. By focusing on either information processing of biological data or on modeling physical and chemical processes of biosystems, and in combination with the recent breakthrough in deciphering the human genome, computational systems biology is guaranteed to play a central role in disease prediction and preventive medicine, gene technology and pharmaceuticals, and other biotechnology fields. This book begins by introducing the basic mathematical, statistical, and data mining principles of computational systems biology, and then presents bioinformatics technology in microarray and sequence analysis step-by-step. Offering an insightful look into the effectiveness of the systems approach in computational biology, it focuses on recurrent themes in bioinformatics, biomedical applications, and future directions for research.

Author : Emmanuel Barillot,Laurence Calzone,Philippe Hupe,Jean-Philippe Vert,Andrei Zinovyev
Publisher : CRC Press
Page : 463 pages
File Size : 53,7 Mb
Release : 2012-08-25
Category : Science
ISBN : 9781439831441

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Computational Systems Biology of Cancer by Emmanuel Barillot,Laurence Calzone,Philippe Hupe,Jean-Philippe Vert,Andrei Zinovyev Pdf

The future of cancer research and the development of new therapeutic strategies rely on our ability to convert biological and clinical questions into mathematical models—integrating our knowledge of tumour progression mechanisms with the tsunami of information brought by high-throughput technologies such as microarrays and next-generation sequencing. Offering promising insights on how to defeat cancer, the emerging field of systems biology captures the complexity of biological phenomena using mathematical and computational tools. Novel Approaches to Fighting Cancer Drawn from the authors’ decade-long work in the cancer computational systems biology laboratory at Institut Curie (Paris, France), Computational Systems Biology of Cancer explains how to apply computational systems biology approaches to cancer research. The authors provide proven techniques and tools for cancer bioinformatics and systems biology research. Effectively Use Algorithmic Methods and Bioinformatics Tools in Real Biological Applications Suitable for readers in both the computational and life sciences, this self-contained guide assumes very limited background in biology, mathematics, and computer science. It explores how computational systems biology can help fight cancer in three essential aspects: Categorising tumours Finding new targets Designing improved and tailored therapeutic strategies Each chapter introduces a problem, presents applicable concepts and state-of-the-art methods, describes existing tools, illustrates applications using real cases, lists publically available data and software, and includes references to further reading. Some chapters also contain exercises. Figures from the text and scripts/data for reproducing a breast cancer data analysis are available at www.cancer-systems-biology.net.

Author : Wong Stephen Tin Chi,Zhou Xiaobo
Publisher : World Scientific Publishing Company
Page : 400 pages
File Size : 48,9 Mb
Release : 2008-01-02
Category : Science
ISBN : 9789813106994

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Computational Systems Bioinformatics - Methods And Biomedical Applications by Wong Stephen Tin Chi,Zhou Xiaobo Pdf

Computational systems biology is a new and rapidly developing field of research, concerned with understanding the structure and processes of biological systems at the molecular, cellular, tissue, and organ levels through computational modeling as well as novel information theoretic data and image analysis methods. By focusing on either information processing of biological data or on modeling physical and chemical processes of biosystems, and in combination with the recent breakthrough in deciphering the human genome, computational systems biology is guaranteed to play a central role in disease prediction and preventive medicine, gene technology and pharmaceuticals, and other biotechnology fields.This book begins by introducing the basic mathematical, statistical, and data mining principles of computational systems biology, and then presents bioinformatics technology in microarray and sequence analysis step-by-step. Offering an insightful look into the effectiveness of the systems approach in computational biology, it focuses on recurrent themes in bioinformatics, biomedical applications, and future directions for research.

Author : Andres Kriete,Roland Eils
Publisher : Academic Press
Page : 548 pages
File Size : 50,6 Mb
Release : 2013-11-26
Category : Computers
ISBN : 9780124059382

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Computational Systems Biology by Andres Kriete,Roland Eils Pdf

This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.