Computational Methods For Knowledge Integration In The Analysis Of Large Scale Biological Networks

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Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology

Author : David A. Rosenblueth,
Publisher : Frontiers Media SA
ISBN 13 : 2889450422
Total Pages : 115 pages
Book Rating : 4.8/5 (894 download)

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Book Synopsis Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology by : David A. Rosenblueth,

Download or read book Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology written by David A. Rosenblueth, and published by Frontiers Media SA. This book was released on 2016-11-21 with total page 115 pages. Available in PDF, EPUB and Kindle. Book excerpt: The complexity of living organisms surpasses our unaided habilities of analysis. Hence, computational and mathematical methods are necessary for increasing our understanding of biological systems. At the same time, there has been a phenomenal recent progress allowing the application of novel formal methods to new domains. This progress has spurred a conspicuous optimism in computational biology. This optimism, in turn, has promoted a rapid increase in collaboration between specialists of biology with specialists of computer science. Through sheer complexity, however, many important biological problems are at present intractable, and it is not clear whether we will ever be able to solve such problems. We are in the process of learning what kind of model and what kind of analysis and synthesis techniques to use for a particular problem. Some existing formalisms have been readily used in biological problems, others have been adapted to biological needs, and still others have been especially developed for biological systems. This Research Topic has examples of cases (1) employing existing methods, (2) adapting methods to biology, and (3) developing new methods. We can also see discrete and Boolean models, and the use of both simulators and model checkers. Synthesis is exemplified by manual and by machine-learning methods. We hope that the articles collected in this Research Topic will stimulate new research.

Handbook of Research on Computational Methodologies in Gene Regulatory Networks

Author : Das, Sanjoy
Publisher : IGI Global
ISBN 13 : 1605666866
Total Pages : 740 pages
Book Rating : 4.6/5 (56 download)

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Book Synopsis Handbook of Research on Computational Methodologies in Gene Regulatory Networks by : Das, Sanjoy

Download or read book Handbook of Research on Computational Methodologies in Gene Regulatory Networks written by Das, Sanjoy and published by IGI Global. This book was released on 2009-10-31 with total page 740 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book focuses on methods widely used in modeling gene networks including structure discovery, learning, and optimization"--Provided by publisher.

Computational Methods for Microbiome Analysis

Author : Joao Carlos Setubal
Publisher : Frontiers Media SA
ISBN 13 : 2889664376
Total Pages : 170 pages
Book Rating : 4.8/5 (896 download)

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Book Synopsis Computational Methods for Microbiome Analysis by : Joao Carlos Setubal

Download or read book Computational Methods for Microbiome Analysis written by Joao Carlos Setubal and published by Frontiers Media SA. This book was released on 2021-02-02 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Systems Analytics and Integration of Big Omics Data

Author : Gary Hardiman
Publisher : MDPI
ISBN 13 : 3039287443
Total Pages : 202 pages
Book Rating : 4.0/5 (392 download)

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Book Synopsis Systems Analytics and Integration of Big Omics Data by : Gary Hardiman

Download or read book Systems Analytics and Integration of Big Omics Data written by Gary Hardiman and published by MDPI. This book was released on 2020-04-15 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: A “genotype" is essentially an organism's full hereditary information which is obtained from its parents. A "phenotype" is an organism's actual observed physical and behavioral properties. These may include traits such as morphology, size, height, eye color, metabolism, etc. One of the pressing challenges in computational and systems biology is genotype-to-phenotype prediction. This is challenging given the amount of data generated by modern Omics technologies. This “Big Data” is so large and complex that traditional data processing applications are not up to the task. Challenges arise in collection, analysis, mining, sharing, transfer, visualization, archiving, and integration of these data. In this Special Issue, there is a focus on the systems-level analysis of Omics data, recent developments in gene ontology annotation, and advances in biological pathways and network biology. The integration of Omics data with clinical and biomedical data using machine learning is explored. This Special Issue covers new methodologies in the context of gene–environment interactions, tissue-specific gene expression, and how external factors or host genetics impact the microbiome.

Biocomputing 2011 - Proceedings Of The Pacific Symposium

Author : Russ B Altman
Publisher : World Scientific
ISBN 13 : 9814462365
Total Pages : 500 pages
Book Rating : 4.8/5 (144 download)

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Book Synopsis Biocomputing 2011 - Proceedings Of The Pacific Symposium by : Russ B Altman

Download or read book Biocomputing 2011 - Proceedings Of The Pacific Symposium written by Russ B Altman and published by World Scientific. This book was released on 2010-11-29 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Pacific Symposium on Biocomputing (PSB) 2011 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2011 will be held on January 3 - 7, 2011 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2011 will bring together top researchers from the US, Asia Pacific, and around the world to exchange research results and address pertinent issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's “hot topics”. In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly evolving field.

Biocomputing 2011

Author : Russ B. Altman
Publisher : World Scientific
ISBN 13 : 9814335045
Total Pages : 386 pages
Book Rating : 4.8/5 (143 download)

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Book Synopsis Biocomputing 2011 by : Russ B. Altman

Download or read book Biocomputing 2011 written by Russ B. Altman and published by World Scientific. This book was released on 2010-09-01 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Pacific Symposium on Biocomputing (PSB) 2011 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2011 will be held on January 3 7, 2011 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference. PSB 2011 will bring together top researchers from the US, Asia Pacific, and around the world to exchange research results and address pertinent issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's "hot topics." In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly evolving field.

Genome Research

Author :
Publisher :
ISBN 13 :
Total Pages : 754 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Genome Research by :

Download or read book Genome Research written by and published by . This book was released on 2009 with total page 754 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Springer Handbook of Science and Technology Indicators

Author : Wolfgang Glänzel
Publisher : Springer Nature
ISBN 13 : 303002511X
Total Pages : 1126 pages
Book Rating : 4.0/5 (3 download)

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Book Synopsis Springer Handbook of Science and Technology Indicators by : Wolfgang Glänzel

Download or read book Springer Handbook of Science and Technology Indicators written by Wolfgang Glänzel and published by Springer Nature. This book was released on 2019-10-30 with total page 1126 pages. Available in PDF, EPUB and Kindle. Book excerpt: This handbook presents the state of the art of quantitative methods and models to understand and assess the science and technology system. Focusing on various aspects of the development and application of indicators derived from data on scholarly publications, patents and electronic communications, the individual chapters, written by leading experts, discuss theoretical and methodological issues, illustrate applications, highlight their policy context and relevance, and point to future research directions. A substantial portion of the book is dedicated to detailed descriptions and analyses of data sources, presenting both traditional and advanced approaches. It addresses the main bibliographic metrics and indexes, such as the journal impact factor and the h-index, as well as altmetric and webometric indicators and science mapping techniques on different levels of aggregation and in the context of their value for the assessment of research performance as well as their impact on research policy and society. It also presents and critically discusses various national research evaluation systems. Complementing the sections reflecting on the science system, the technology section includes multiple chapters that explain different aspects of patent statistics, patent classification and database search methods to retrieve patent-related information. In addition, it examines the relevance of trademarks and standards as additional technological indicators. The Springer Handbook of Science and Technology Indicators is an invaluable resource for practitioners, scientists and policy makers wanting a systematic and thorough analysis of the potential and limitations of the various approaches to assess research and research performance.

Contextualizing Systems Biology

Author : Martin Döring
Publisher : Springer
ISBN 13 : 3319171062
Total Pages : 325 pages
Book Rating : 4.3/5 (191 download)

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Book Synopsis Contextualizing Systems Biology by : Martin Döring

Download or read book Contextualizing Systems Biology written by Martin Döring and published by Springer. This book was released on 2015-12-18 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collective monograph aims at contributing to an improved understanding of the epistemic presumptions, sociocultural implications and historically backgrounds of the newly emerging and currently expanding approach of systems biology. In doing so, it offers empirically grounded, valuable and reflexive information about a paradigmatic shift in the biosciences for a wide range of scientists working in the interdisciplinary areas of systems biology, synthetic biology, molecular biology, biology, the philosophy of science, the sociology of science and scientific knowledge, science and technology studies, technology assessment and the like. The authors of this monograph share the theoretical methodological premise that science is a culturally and socially embedded practice which characterizes our culture as a scientific one and at the same time draws its innovative potential from its socio-cultural context. This dialectic relationship lies at the heart of the current development of systems biology which is conceived as a so-called successor of ‘-omics’ research and triggered by high-throughput information technologies. At the same time a need for a holistic conceptualization of complex biological processes emerges. The title Contextualizing Systems Biology suggests that this book analyzes the development and advent of systems biology from different theoretical and methodological perspectives. We investigate a variety of contexts ranging from the analysis of cognitive contexts (such as basic theoretical concepts) to regulative contexts (policies) to the concrete application of a systems biology in the socio-scientific context of a European research project. In empirically analyzing these different and interrelated layers and dimensions of systems biology, the scope of the book goes beyond present attempts to investigate the advent of new approaches in the biological sciences as it frames and assesses systems biology from an interdisciplinary and integrated perspective.

Computational Methods for Precision Oncology

Author : Alessandro Laganà
Publisher : Springer Nature
ISBN 13 : 303091836X
Total Pages : 341 pages
Book Rating : 4.0/5 (39 download)

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Book Synopsis Computational Methods for Precision Oncology by : Alessandro Laganà

Download or read book Computational Methods for Precision Oncology written by Alessandro Laganà and published by Springer Nature. This book was released on 2022-03-01 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: Precision medicine holds great promise for the treatment of cancer and represents a unique opportunity for accelerated development and application of novel and repurposed therapeutic approaches. Current studies and clinical trials demonstrate the benefits of genomic profiling for patients whose cancer is driven by specific, targetable alterations. However, precision oncologists continue to be challenged by the widespread heterogeneity of cancer genomes and drug responses in designing personalized treatments. Chapters provide a comprehensive overview of the computational approaches, methods, and tools that enable precision oncology, as well as related biological concepts. Covered topics include genome sequencing, the architecture of a precision oncology workflow, and introduces cutting-edge research topics in the field of precision oncology. This book is intended for computational biologists, bioinformaticians, biostatisticians and computational pathologists working in precision oncology and related fields, including cancer genomics, systems biology, and immuno-oncology.

Networks in Cell Biology

Author : Mark Buchanan
Publisher : Cambridge University Press
ISBN 13 : 0521882737
Total Pages : 282 pages
Book Rating : 4.5/5 (218 download)

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Book Synopsis Networks in Cell Biology by : Mark Buchanan

Download or read book Networks in Cell Biology written by Mark Buchanan and published by Cambridge University Press. This book was released on 2010-05-13 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: Key introductory text for graduate students and researchers in physics, biology and biochemistry.

Synthetic Biology

Author : Huimin Zhao
Publisher : Academic Press
ISBN 13 : 0123978203
Total Pages : 352 pages
Book Rating : 4.1/5 (239 download)

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Book Synopsis Synthetic Biology by : Huimin Zhao

Download or read book Synthetic Biology written by Huimin Zhao and published by Academic Press. This book was released on 2013-03-21 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic Biology provides a framework to examine key enabling components in the emerging area of synthetic biology. Chapters contributed by leaders in the field address tools and methodologies developed for engineering biological systems at many levels, including molecular, pathway, network, whole cell, and multi-cell levels. The book highlights exciting practical applications of synthetic biology such as microbial production of biofuels and drugs, artificial cells, synthetic viruses, and artificial photosynthesis. The roles of computers and computational design are discussed, as well as future prospects in the field, including cell-free synthetic biology and engineering synthetic ecosystems.Synthetic biology is the design and construction of new biological entities, such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components that can be modeled, understood, and tuned to meet specific performance criteria and the assembly of these smaller parts and devices into larger integrated systems that solve specific biotechnology problems. - Includes contributions from leaders in the field presents examples of ambitious synthetic biology efforts including creation of artificial cells from scratch, cell-free synthesis of chemicals, fuels, and proteins, engineering of artificial photosynthesis for biofuels production, and creation of unnatural living organisms - Describes the latest state-of-the-art tools developed for low-cost synthesis of ever-increasing sizes of DNA and efficient modification of proteins, pathways, and genomes - Highlights key technologies for analyzing biological systems at the genomic, proteomic, and metabolomic levels which are especially valuable in pathway, whole cell, and multi-cell applications - Details mathematical modeling tools and computational tools which can dramatically increase the speed of the design process as well as reduce the cost of development

Encyclopedia of Bioinformatics and Computational Biology

Author :
Publisher : Elsevier
ISBN 13 : 0128114320
Total Pages : 3421 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Encyclopedia of Bioinformatics and Computational Biology by :

Download or read book Encyclopedia of Bioinformatics and Computational Biology written by and published by Elsevier. This book was released on 2018-08-21 with total page 3421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

Computational Methods for Single-Cell Data Analysis

Author : Guo-Cheng Yuan
Publisher : Humana Press
ISBN 13 : 9781493990566
Total Pages : 271 pages
Book Rating : 4.9/5 (95 download)

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Book Synopsis Computational Methods for Single-Cell Data Analysis by : Guo-Cheng Yuan

Download or read book Computational Methods for Single-Cell Data Analysis written by Guo-Cheng Yuan and published by Humana Press. This book was released on 2019-02-14 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book provides state-of-art computational approaches to further explore the exciting opportunities presented by single-cell technologies. Chapters each detail a computational toolbox aimed to overcome a specific challenge in single-cell analysis, such as data normalization, rare cell-type identification, and spatial transcriptomics analysis, all with a focus on hands-on implementation of computational methods for analyzing experimental data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Methods for Single-Cell Data Analysis aims to cover a wide range of tasks and serves as a vital handbook for single-cell data analysis.

Biocomputing 2020 - Proceedings Of The Pacific Symposium

Author : Russ B Altman
Publisher : World Scientific
ISBN 13 : 9811215642
Total Pages : 764 pages
Book Rating : 4.8/5 (112 download)

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Book Synopsis Biocomputing 2020 - Proceedings Of The Pacific Symposium by : Russ B Altman

Download or read book Biocomputing 2020 - Proceedings Of The Pacific Symposium written by Russ B Altman and published by World Scientific. This book was released on 2019-11-28 with total page 764 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Pacific Symposium on Biocomputing (PSB) 2020 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2020 will be held on January 3 -7, 2020 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2020 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's 'hot topics.' In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.

Microarrays

Author : Jang B. Rampal
Publisher : Springer Science & Business Media
ISBN 13 : 1597453048
Total Pages : 927 pages
Book Rating : 4.5/5 (974 download)

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Book Synopsis Microarrays by : Jang B. Rampal

Download or read book Microarrays written by Jang B. Rampal and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 927 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second part in the two-volume work Microarrays details applications and data analysis. It includes insight into non-mammalian vertebrate systems, processes and protocols for high quality glass-based microarrays. Coverage includes applications in DNA, peptide, antibody and carbohydrate microarraying, oligonucleotide microarrays generated from hydrolysis PCR probe sequences, microarray platforms in clinical practice, and screening of cDNA libraries on glass slide microarrays. Authors in this volume also discuss protocols for predicting DNA duplex stability on oligonucleotide arrays and integrated analysis of microarray results.

2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008)

Author : Juan Manuel Corchado Rodríguez
Publisher : Springer Science & Business Media
ISBN 13 : 354085861X
Total Pages : 265 pages
Book Rating : 4.5/5 (48 download)

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Book Synopsis 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008) by : Juan Manuel Corchado Rodríguez

Download or read book 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008) written by Juan Manuel Corchado Rodríguez and published by Springer Science & Business Media. This book was released on 2008-09-16 with total page 265 pages. Available in PDF, EPUB and Kindle. Book excerpt: The success of Bioinformatics in recent years has been prompted by research in mole- lar biology and medicine in initiatives like the human genome project. The volume and diversification of data has increased so much that it is very hard if not impossible to analyze it by human experts. The analysis of this growing body of data, intensified by the development of a number of high-throughput experimental techniques that are generating the so called 'omics' data, has prompted for new computational methods. New global approaches, such as Systems Biology, have been emerging replacing the reductionist view that dominated biology research in the last decades, requiring the coordinated efforts of biological researchers with those related to data analysis, mathematical modelling and computer science. Computational methods have been helping in tasks related to knowledge discovery, modelling and optimization tasks. This workshop brings the opportunity to discuss applications of Bioinformatics and Computational Biology exploring the interactions between computer scientists, bio- gists and other scientific researchers. The IWPACBB technical program includes 29 papers (23 long papers and 6 short papers) selected from a submission pool of 51 papers, from 9 different countries. We thank the excellent work of the local organization members and also from the members of the Program Committee for their excellent reviewing work. October 2008 Juan M. Corchado Juan F. De Paz Miguel P. Rocha Florentino Fernández Riverola Organization