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From Knowledge Networks To Biological Models
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Book Synopsis From Knowledge Networks to Biological Models by : Anton Yuryev
Download or read book From Knowledge Networks to Biological Models written by Anton Yuryev and published by Bentham Science Publishers. This book was released on 2012 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most findings about molecular interactions and cellular regulatory events are published in peer-reviewed scientific literature in the form of scientific jargon. the computerized text-mining algorithms are used to convert free grammar of human language into a set of formalized relationships between biological concepts in order to use this wealth of information. the compendium of such interactions extracted from an entire set of biomedical literature is a called knowledge network. Knowledge networks are the first step in the process of digitizing molecular biological knowledge. the next step is building molecular models depicting principal molecular events that govern various biological processes. Data mining in knowledge networks is the essence of building new biological models. the purpose is to elucidate major pathways of information flow through a molecular physical interaction network that happens during a disease, a cell process or an experiment. Such models contain key proteins involved in the process and can be used for prioritizing disease targets, for understanding of drug action and prevention of drug-induced toxicities, for analysis of patient predispositions and design of personalized therapies, for design of diagnostic biomarkers and analysis of patient molecular data. This e-book contains detailed examples illustrating the path to the digital biology and computerized drug development for personalized medicine. It provides conceptual principals for building biological models and for applying the models to make predictions relevant for drug development and translational medicine. The e-book will also be useful for researchers who use high-throughput technologies for molecular profiling of disease and drug action. It provides examples for analysis of gene expression microarrays to infer biological models, to find biomarkers for drug response and for applications of high-throughput molecular profiling technologies for personalized medicine. Scientists in academia, in pharmaceutical industry as well as graduate students will benefit from reading this book. the illustrations from the book can also be readily used in taught courses for molecular biology and pharmacology.
Book Synopsis Toward Precision Medicine by : National Research Council
Download or read book Toward Precision Medicine written by National Research Council and published by National Academies Press. This book was released on 2012-01-16 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: Motivated by the explosion of molecular data on humans-particularly data associated with individual patients-and the sense that there are large, as-yet-untapped opportunities to use this data to improve health outcomes, Toward Precision Medicine explores the feasibility and need for "a new taxonomy of human disease based on molecular biology" and develops a potential framework for creating one. The book says that a new data network that integrates emerging research on the molecular makeup of diseases with clinical data on individual patients could drive the development of a more accurate classification of diseases and ultimately enhance diagnosis and treatment. The "new taxonomy" that emerges would define diseases by their underlying molecular causes and other factors in addition to their traditional physical signs and symptoms. The book adds that the new data network could also improve biomedical research by enabling scientists to access patients' information during treatment while still protecting their rights. This would allow the marriage of molecular research and clinical data at the point of care, as opposed to research information continuing to reside primarily in academia. Toward Precision Medicine notes that moving toward individualized medicine requires that researchers and health care providers have access to very large sets of health- and disease-related data linked to individual patients. These data are also critical for developing the information commons, the knowledge network of disease, and ultimately the new taxonomy.
Book Synopsis Biological Modeling and Simulation by : Russell Schwartz
Download or read book Biological Modeling and Simulation written by Russell Schwartz and published by MIT Press. This book was released on 2008-07-25 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.
Book Synopsis Knowledge Networks and Markets in the Life Sciences by : OECD
Download or read book Knowledge Networks and Markets in the Life Sciences written by OECD and published by OECD Publishing. This book was released on 2012-05-18 with total page 131 pages. Available in PDF, EPUB and Kindle. Book excerpt: This report considers the development of Knowledge Networks and Markets and examines the impact of current initiatives and the possible options for governments, working with the private sector, to improve innovation efficiency and effectiveness.
Book Synopsis Algorithms for Computational Biology by : María Botón-Fernández
Download or read book Algorithms for Computational Biology written by María Botón-Fernández and published by Springer. This book was released on 2016-06-11 with total page 187 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the Third InternationalConference on Algorithms for Computational Biology, AlCoB 2016, held inTrujillo, Spain, in June 2016. The 13 full papers presented in this volume were carefully reviewed andselected from 23 submissions. They are organized in the following topical sections: biological networks and modelling; biological structure processing; phylogenetics; and sequence analysis and rearrangement. In addition one invited talk is included.
Book Synopsis Network-based Mathematical Modeling in Cell and Developmental Biology by : Susan Mertins
Download or read book Network-based Mathematical Modeling in Cell and Developmental Biology written by Susan Mertins and published by Frontiers Media SA. This book was released on 2024-08-22 with total page 137 pages. Available in PDF, EPUB and Kindle. Book excerpt: The vast amount of knowledge in Cell Signaling gathered through reductionist efforts and omics technology is poised to approach a Systems Biology understanding of precise representations of cell structure and function and predictions at multi-scale levels despite the complexity. Super-resolution microscopy and single cell analysis are also providing opportunities to explore both spatial and temporal landscapes. Notably, many basic biological processes have been studied capturing mechanistic detail with the goal to understand cellular proliferation and differentiation, gene regulation, morphogenesis, metabolism, and cell-cell communication. Similarly, at the intracellular level, addressing functions such as self-assembly, phase separation, and transport is leading to insights not readily understood as linear pathways. Therefore, network-based mathematical modeling, delineating dynamic biochemical reactions through ordinary and partial differential equations, promises to discover emergent biological properties not heretofore expected.
Book Synopsis Logical Modeling of Biological Systems by : Luis Fariñas del Cerro
Download or read book Logical Modeling of Biological Systems written by Luis Fariñas del Cerro and published by John Wiley & Sons. This book was released on 2014-08-08 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology is the systematic study of the interactions between the components of a biological system and studies how these interactions give rise to the function and behavior of the living system. Through this, a life process is to be understood as a whole system rather than the collection of the parts considered separately. Systems Biology is therefore more than just an emerging field: it represents a new way of thinking about biology with a dramatic impact on the way that research is performed. The logical approach provides an intuitive method to provide explanations based on an expressive relational language. This book covers various aspects of logical modeling of biological systems, bringing together 10 recent logic-based approaches to Systems Biology by leading scientists. The chapters cover the biological fields of gene regulatory networks, signaling networks, metabolic pathways, molecular interaction and network dynamics, and show logical methods for these domains based on propositional and first-order logic, logic programming, answer set programming, temporal logic, Boolean networks, Petri nets, process hitting, and abductive and inductive logic programming. It provides an excellent guide for all scientists, biologists, bioinformaticians, and engineers, who are interested in logic-based modeling of biological systems, and the authors hope that new scientists will be encouraged to join this exciting scientific endeavor.
Book Synopsis Logical Modeling of Cellular Processes: From Software Development to Network Dynamics by : Matteo Barberis
Download or read book Logical Modeling of Cellular Processes: From Software Development to Network Dynamics written by Matteo Barberis and published by Frontiers Media SA. This book was released on 2019-08-16 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical models have become invaluable tools for understanding the intricate dynamic behavior of complex biochemical and biological systems. Among computational strategies, logical modeling has been recently gaining interest as an alternative approach to address network dynamics. Due to its advantages, including scalability and independence of kinetic parameters, the logical modeling framework is becoming increasingly popular to study the dynamics of highly interconnected systems, such as cell cycle progression, T cell differentiation and gene regulation. Novel tools and standards have been developed to increase the interoperability of logical models, which can now be employ to respond a variety of biological questions. This Research Topic brings together the most recent and cutting-edge approaches in the area of logical modeling including, among others, novel biological applications, software development and model analysis techniques.
Book Synopsis Complex Networks by : Guido Caldarelli
Download or read book Complex Networks written by Guido Caldarelli and published by EOLSS Publications. This book was released on 2010-11-30 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of complex network exploded since the 1990s, the number of publications in a variety of different areas has grown exponentially and practically, and every discipline started to recognize the presence of these mathematical structures in its area of research. Actually almost any system from the nowadays traditional example of the Internet to complex patterns of metabolic reactions can be analyzed through the graph theory. In its simplest and non rigorous definition a graph is a mathematical object consisting of a set of elements (vertices) and a series of links between these vertices (edges). This is of course a very general description, and as any mathematical abstraction, the idea is to discard many of the particular properties of the phenomenon studied. Nevertheless, this modeling is remarkably accurate for a variety of situations. Vertices can be persons related by friendship or acquaintances relations. Vertices can be proteins connected with one another if they interact in the cell. Networks have always existed in Nature of course, but it is fair to say that given the present technological explosion, they became more and more important. Starting from the Internet the web of connections between computers we started to link and share our documents through web applications and we start to get connected with a number of persons larger than usual. It is this revolution in our daily habit that made natural thinking of networks in science and research. Once this has been realized it became natural to see the cell as a network of molecular events from chemical reactions to gene expressions. The point is to establish if this new perspective can help researchers in finding new results and by understanding the development of these phenomena and possibly control their evolution. We believe that this is the case and in the following we shall provide the evidence of that. Together with applications there are of course true scientific questions attached to network theory. Consider the various ways in which the edges are distributed among the vertices: even by keeping the number of edges and vertices constant we have many different patterns possible. Interestingly some features used to describe these shapes are not related to the particular example considered, but instead they are universal. That is to say they can be found in almost any network around. In this book, we introduce the subject of complex networks and we present the structure of the associated topics that range from social science to biology and finance. We start by considering the mathematical foundations of networks and we then move to an overview of the various applications
Book Synopsis Integration of Omics Approaches and Systems Biology for Clinical Applications by : Antonia Vlahou
Download or read book Integration of Omics Approaches and Systems Biology for Clinical Applications written by Antonia Vlahou and published by John Wiley & Sons. This book was released on 2018-01-24 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduces readers to the state of the art of omics platforms and all aspects of omics approaches for clinical applications This book presents different high throughput omics platforms used to analyze tissue, plasma, and urine. The reader is introduced to state of the art analytical approaches (sample preparation and instrumentation) related to proteomics, peptidomics, transcriptomics, and metabolomics. In addition, the book highlights innovative approaches using bioinformatics, urine miRNAs, and MALDI tissue imaging in the context of clinical applications. Particular emphasis is put on integration of data generated from these different platforms in order to uncover the molecular landscape of diseases. The relevance of each approach to the clinical setting is explained and future applications for patient monitoring or treatment are discussed. Integration of omics Approaches and Systems Biology for Clinical Applications presents an overview of state of the art omics techniques. These methods are employed in order to obtain the comprehensive molecular profile of biological specimens. In addition, computational tools are used for organizing and integrating these multi-source data towards developing molecular models that reflect the pathophysiology of diseases. Investigation of chronic kidney disease (CKD) and bladder cancer are used as test cases. These represent multi-factorial, highly heterogeneous diseases, and are among the most significant health issues in developed countries with a rapidly aging population. The book presents novel insights on CKD and bladder cancer obtained by omics data integration as an example of the application of systems biology in the clinical setting. Describes a range of state of the art omics analytical platforms Covers all aspects of the systems biology approach—from sample preparation to data integration and bioinformatics analysis Contains specific examples of omics methods applied in the investigation of human diseases (Chronic Kidney Disease, Bladder Cancer) Integration of omics Approaches and Systems Biology for Clinical Applications will appeal to a wide spectrum of scientists including biologists, biotechnologists, biochemists, biophysicists, and bioinformaticians working on the different molecular platforms. It is also an excellent text for students interested in these fields.
Book Synopsis Systems Biology and Livestock Science by : Marinus te Pas
Download or read book Systems Biology and Livestock Science written by Marinus te Pas and published by John Wiley & Sons. This book was released on 2011-09-23 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology is an interdisciplinary approach to the study of life made possible through the explosion of molecular data made available through the genome revolution and the simultaneous development of computational technologies that allow us to interpret these large data sets. Systems Biology has changed the way biological science views and studies life and has been implemented in research efforts across the biological sciences. Systems Biology and Livestock Science will be the first book to review the latest advances using this research methodology in efforts to improve the efficiency, health, and quality of livestock production. Systems Biology and Livestock Science opens with useful introductory chapters explaining key systems biology principles. The chapters then progress to look at specific advances in fields across livestock science. Coverage includes, but is not limited to, chapters on systems biology approaches to animal nutrition, reproduction, health and disease, and animal physiology. Written by leading researchers in the field, Systems Biology and Livestock Science, will be an invaluable resource to researchers, professionals, and advance students working in this rapidly developing discipline.
Book Synopsis Knowledge Networks by : Denise Bedford
Download or read book Knowledge Networks written by Denise Bedford and published by Emerald Group Publishing. This book was released on 2021-10-26 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: Knowledge Networks describes the role of networks in the knowledge economy, explains network structures and behaviors, walks the reader through the design and setup of knowledge network analyses, and offers a step by step methodology for conducting a knowledge network analysis.
Book Synopsis Advances in Systems Biology by : Igor I. Goryanin
Download or read book Advances in Systems Biology written by Igor I. Goryanin and published by Springer Science & Business Media. This book was released on 2011-12-08 with total page 679 pages. Available in PDF, EPUB and Kindle. Book excerpt: The International Society for Systems Biology (ISSB) is a society aimed at advancing world-wide systems biology research by providing a forum for scientific discussions and various academic services. The ISSB helps coordinate researchers to form alliances for meeting the unique needs of multidisciplinary and international systems biology research. The annual International Conference on Systems Biology (ICSB) serves as the main meeting for the society and is one of the largest academic and commercial gatherings under the broad heading of ‘Systems Biology’.
Book Synopsis Integrative Computational Systems Biology Approaches in Immunology and Medicine by : Lars Kaderali
Download or read book Integrative Computational Systems Biology Approaches in Immunology and Medicine written by Lars Kaderali and published by Frontiers Media SA. This book was released on 2019-04-09 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics by : Christine Sinoquet
Download or read book Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics written by Christine Sinoquet and published by Oxford University Press, USA. This book was released on 2014 with total page 483 pages. Available in PDF, EPUB and Kindle. Book excerpt: At the crossroads between statistics and machine learning, probabilistic graphical models (PGMs) provide a powerful formal framework to model complex data. An expanding volume of biological data of various types, the so-called 'omics', is in need of accurate and efficient methods for modelling and PGMs are expected to have a prominent role to play.
Book Synopsis Nanotoxicology by : Hemant Kumar Daima
Download or read book Nanotoxicology written by Hemant Kumar Daima and published by CRC Press. This book was released on 2021-07-15 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of nanomedicine has risen quickly due to the increasing number of designer-made nanomaterials. These nanomaterials have the potential to manage diseases and change the way medicine is currently studied. However, the increased practice of using nanomaterials has shed light on how many concepts of nanomedicine and nanotoxicity have been overlooked. Nanotoxicology: Toxicity Evaluation of Nanomedicine Applications addresses the existing gaps between nanomedicine and nanotoxicity. This book also brings together up-to-date knowledge on advances toward safe-by-design nanomaterials and existing toxicity challenges. This book delivers a comprehensive coverage in the field with fundamental understanding, serving as a platform to convey essential concepts of nanotoxicology and how these concepts can be employed to develop advanced nanomaterials for a range of biomedical applications. This book is an effort to answer some of the thoughtful nanotoxicological complications and their auspicious probable solutions with new approaches and careful toxicity assessment. Key Features: Reveals novel nanoscale approaches, toxicity assessment, and biomedical applications Includes importance of nanotoxicity concepts in developing smart nanomaterials Highlights unique contributions and "A to Z" aspects on the state-of-the-art from global leaders Offers a complete package to learn fundamentals with recommendations on nanomaterials toxicity and safe-by-design nanomedicines Nanotoxicology: Toxicity Evaluation of Nanomedicine Applications illuminates the high potential of many innovative nanomaterials, ultimately demonstrating them to be promising substitutes for available therapies that can be effectively used in fighting a myriad of biomedical complications. Further, this book reports legal, ethical, safety, and regulatory issues associated with nanomaterials, which have often been neglected, if not overlooked in literature and limiting clinical translation at nanoscale level. It will equip readers with cutting-edge knowledge of promising developments in nanomedicine and nanotoxicology, along with potential future prospects.
Book Synopsis Analysis of Biological Networks by : Björn H. Junker
Download or read book Analysis of Biological Networks written by Björn H. Junker and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to biological networks and methods for their analysis Analysis of Biological Networks is the first book of its kind to provide readers with a comprehensive introduction to the structural analysis of biological networks at the interface of biology and computer science. The book begins with a brief overview of biological networks and graph theory/graph algorithms and goes on to explore: global network properties, network centralities, network motifs, network clustering, Petri nets, signal transduction and gene regulation networks, protein interaction networks, metabolic networks, phylogenetic networks, ecological networks, and correlation networks. Analysis of Biological Networks is a self-contained introduction to this important research topic, assumes no expert knowledge in computer science or biology, and is accessible to professionals and students alike. Each chapter concludes with a summary of main points and with exercises for readers to test their understanding of the material presented. Additionally, an FTP site with links to author-provided data for the book is available for deeper study. This book is suitable as a resource for researchers in computer science, biology, bioinformatics, advanced biochemistry, and the life sciences, and also serves as an ideal reference text for graduate-level courses in bioinformatics and biological research.
