On The Systems Characterization Of Metabolic Networks
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On The Systems Characterization Of Metabolic Networks
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Author : Neema Jamshidi
language : en
Publisher:
Release Date : 2009
On The Systems Characterization Of Metabolic Networks written by Neema Jamshidi and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009 with categories.
Significant progress has been made in the development of genome-scale models of metabolism in the past 15 years. The majority of the efforts have focused on the analysis of the right null space. While the steady state solution space is very important since homeostatic mechanisms are continuously trying to push the system back to a steady state, there are three other subspaces which also have significance. This dissertation approaches metabolic networks with the goal of investigating all four fundamental subspaces of linear systems, particularly the row and column spaces, which determine the dynamic capabilities of networks. First, the key matrices are defined and their general properties and characteristics are identified. The subspaces are analyzed for a simple metabolic network. Next the right null space is explored in a targeted manner using real networks, the cardiomyocyte mitochondria and a genome-scale model of Mycobacterium tuberculosis, focusing on perfectly correlated reaction sets and the biologically interesting implications they may hold. This is followed by the development of analytical methods to define the time scale hierarchy in the column space of the human red cell, human folate metabolism, and yeast glycolysis. These studies are further pursued by investigating various decompositions of the stoichiometric and gradient matrices that are determined by the underlying physico-chemical characteristics. These investigations lead to the identification of key properties of metabolic networks, such as the duality between fluxes and concentrations in dynamic networks. Having established how to decompose these networks, a middle-out integration approach is described for building or reconstructing kinetic networks using '-omic' data streams that are increasingly available. This approach is applied to construct a dynamic model of human red cell metabolism with and without mechanistic integration of allosteric regulatory functions of enzymes, dynamic models of E. coli, as well as a general hepatocyte mitochondria model which can be used for application of these methods, when the appropriate data becomes available. Simulations with the regulated erythrocyte model highlight the importance of active versus inactive states of enzymes and how the binding state of the enzyme exerts control of the flux through competing pathways. The subsequent chapter investigates perturbational analyses and how they can inform functional states and identify pathophysiological conditions. This dissertation culminates in a description of a conceptually new approach to modeling, 'delta' networks, that relaxes data requirements and is focused on identifying the functional differences between different data sets in an effort to understand as much of the four subspaces as possible, not just the right null space. The studies carried out in this dissertation also further support the use of models as data interrogation tools; for data integration, analysis, as well as for the evaluation of data consistency. The developments and advancements made herein take steps towards achieving genome-scale dynamic regulated networks of metabolism, which can in principle be applied to any biological network.
Fundamentals Of Systems Analysis And Modeling Of Biosystems And Metabolism
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Author : Kazuyuki Shimizu
language : en
Publisher: Bentham Science Publishers
Release Date : 2015-06-04
Fundamentals Of Systems Analysis And Modeling Of Biosystems And Metabolism written by Kazuyuki Shimizu and has been published by Bentham Science Publishers this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-06-04 with Science categories.
An understanding of biological systems at cellular and molecular levels helps researchers to model cellular behavior in different experimental conditions. This, in turn, can lead to insights about the influence of cell culture environment and the effect of knockout gene research when studying mutations that affect specific metabolic pathways. A systems biology approach, therefore, allows researchers to simulate experimental observations in order to predict outcomes at the cellular level. Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism presents the basic concepts required for a systems biology approach towards cellular modeling. The book is intended as a primer for systems biology and biomedical engineering graduates and researchers. The text introduces readers to concepts related to cellular metabolism and its regulation, (enzymatic regulation and transcriptional regulation) which are also incorporated into a main metabolic model of a cell. The book also has chapters dedicated to identifying and incorporating steady-state and dynamic characteristics when considering a biological model for a computer simulation. Readers will be able to (1) understand the basis of systems analysis towards creating appropriate biological models and simulations, (2) develop useful kinetic models based on cellular transport phenomena and metabolic regulation, (3) understand how to simulate a cell growth phenotype, and analyze it with experimental data.
On Systems Biology And The Pathway Analysis Of Metabolic Networks
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Author : Christophe Heinz Schilling
language : en
Publisher:
Release Date : 2000
On Systems Biology And The Pathway Analysis Of Metabolic Networks written by Christophe Heinz Schilling and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2000 with categories.
Applications And Theory Of Petri Nets 2004
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Author : Jordi Cortadella
language : en
Publisher: Springer Science & Business Media
Release Date : 2004-06-15
Applications And Theory Of Petri Nets 2004 written by Jordi Cortadella and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004-06-15 with Business & Economics categories.
This book constitutes the refereed proceedings of the 25th International Conference on Applications and Theory of Petri Nets, ICATPN 2004, held in Bologna, Italy in June 2004. The 19 revised full regular papers and 5 revised tool presentation papers presented together with 6 invited papers were carefully reviewed and selected from 62 submissions. All current issues on research and development in the area of Petri nets are addressed, in particular concurrent systems design and analysis, modular systems development, formal specification, model validation, model checking, workflow management, flow charts, networking, formal methods in software engineering, etc.
Reprogramming Microbial Metabolic Pathways
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Author : Xiaoyuan Wang
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-10-19
Reprogramming Microbial Metabolic Pathways written by Xiaoyuan Wang and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-10-19 with Medical categories.
Metabolic engineering has been developed over the past 20 years to become an important tool for the rational engineering of industrial microorganisms. This book has a particular interest in the methods and applications of metabolic engineering to improve the production and yield of a variety of different metabolites. The overall goal is to achieve a better understanding of the metabolism in different microorganisms, and provide a rational basis to reprogram microorganisms for improved biochemical production.
Systems Medicine
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Author :
language : en
Publisher: Academic Press
Release Date : 2020-08-24
Systems Medicine written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-08-24 with Science categories.
Technological advances in generated molecular and cell biological data are transforming biomedical research. Sequencing, multi-omics and imaging technologies are likely to have deep impact on the future of medical practice. In parallel to technological developments, methodologies to gather, integrate, visualize and analyze heterogeneous and large-scale data sets are needed to develop new approaches for diagnosis, prognosis and therapy. Systems Medicine: Integrative, Qualitative and Computational Approaches is an innovative, interdisciplinary and integrative approach that extends the concept of systems biology and the unprecedented insights that computational methods and mathematical modeling offer of the interactions and network behavior of complex biological systems, to novel clinically relevant applications for the design of more successful prognostic, diagnostic and therapeutic approaches. This 3 volume work features 132 entries from renowned experts in the fields and covers the tools, methods, algorithms and data analysis workflows used for integrating and analyzing multi-dimensional data routinely generated in clinical settings with the aim of providing medical practitioners with robust clinical decision support systems. Importantly the work delves into the applications of systems medicine in areas such as tumor systems biology, metabolic and cardiovascular diseases as well as immunology and infectious diseases amongst others. This is a fundamental resource for biomedical students and researchers as well as medical practitioners who need to need to adopt advances in computational tools and methods into the clinical practice. Encyclopedic coverage: ‘one-stop’ resource for access to information written by world-leading scholars in the field of Systems Biology and Systems Medicine, with easy cross-referencing of related articles to promote understanding and further research Authoritative: the whole work is authored and edited by recognized experts in the field, with a range of different expertise, ensuring a high quality standard Digitally innovative: Hyperlinked references and further readings, cross-references and diagrams/images will allow readers to easily navigate a wealth of information
Signals And Systems Analysis In Biomedical Engineering
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Author : Robert B. Northrop
language : en
Publisher: CRC Press
Release Date : 2016-04-19
Signals And Systems Analysis In Biomedical Engineering written by Robert B. Northrop and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-19 with Medical categories.
The first edition of this text, based on the author's 30 years of teaching and research on neurosensory systems, helped biomedical engineering students and professionals strengthen their skills in the common network of applied mathematics that ties together the diverse disciplines that comprise this field. Updated and revised to include new materia
Mathematical Modeling In Systems Biology
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Author : Brian P. Ingalls
language : en
Publisher: MIT Press
Release Date : 2022-06-07
Mathematical Modeling In Systems Biology written by Brian P. Ingalls and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-06-07 with Science categories.
An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.
Guide To Yeast Genetics Functional Genomics Proteomics And Other Systems Analysis
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Author :
language : en
Publisher: Academic Press
Release Date : 2010-02-27
Guide To Yeast Genetics Functional Genomics Proteomics And Other Systems Analysis written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-02-27 with Science categories.
This fully updated edition of the bestselling three-part Methods in Enzymology series, Guide to Yeast Genetics and Molecular Cell Biology is specifically designed to meet the needs of graduate students, postdoctoral students, and researchers by providing all the up-to-date methods necessary to study genes in yeast. Procedures are included that enable newcomers to set up a yeast laboratory and to master basic manipulations. This volume serves as an essential reference for any beginning or experienced researcher in the field. - Provides up-to-date methods necessary to study genes in yeast - Includes proceedures that enable newcomers to set up a yeast laboratory and to master basic manipulations - Serves as an essential reference for any beginning or experienced researcher in the field
Comprehensive Analysis Of Parasite Biology
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Author : Sylke Müller
language : en
Publisher: John Wiley & Sons
Release Date : 2016-07-11
Comprehensive Analysis Of Parasite Biology written by Sylke Müller and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-07-11 with Medical categories.
Dieses Buch, geschrieben von Fachexperten auf dem Gebiet, fasst den aktuellen Stand der Wissenschaft im Hinblick auf phänotypische und zielorientierte Ansätze der Entwicklung von Arzneistoffen gegen pathogene Protozoen zusammen. Der Schwerpunkt liegt dabei vor allem auf virtuellen Substanzen und dem Hochdurchsatz-Screening, auf Naturprodukten, dem computergestützten Design von Arzneistoffen, dem strukturgestützten Design von Arzneistoffen, der Identifizierung von Wirkmechanismen und dem Pathway-Modelling. Weiterhin werden moderne "omik"-Technologien sowie enzymatische Drug Targets erörtert. Mathematische, auf der Systembiologie basierende Ansätze werden als neue Methoden für die Auflösung komplexer Mechanismen, die Pathogene überleben lassen, und für die Target-Identifizierung vorgestellt. Präsentiert werden darüber hinaus neu entwickelte Wirkstoffe, die über bestimmte Pathways Parasiten abtöten und als Leitsubstanzen für weitere Arzneimittelentwicklungen dienen.