Download or read book ANALYSIS OF STOICHIOMETRY IN METABOLIC NETWORKS CELL METABOLISM LINEAR OPTIMIZATION written by JOANNE MARY SAVINELL and published by . This book was released on 1991 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: the metabolic capabilities of the cell, interpreting flux measurements, improving experimental design, and studying metabolic design.
Download or read book Optimization Methods in Metabolic Networks written by Costas D. Maranas and published by John Wiley & Sons. This book was released on 2016-02-23 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides a tutorial on the computational tools that use mathematical optimization concepts and representations for the curation, analysis and redesign of metabolic networks Organizes, for the first time, the fundamentals of mathematical optimization in the context of metabolic network analysis Reviews the fundamentals of different classes of optimization problems including LP, MILP, MLP and MINLP Explains the most efficient ways of formulating a biological problem using mathematical optimization Reviews a variety of relevant problems in metabolic network curation, analysis and redesign with an emphasis on details of optimization formulations Provides a detailed treatment of bilevel optimization techniques for computational strain design and other relevant problems
Download or read book Metabolic Pathway Analysis Via Integer Linear Programming written by Francisco J. Planes and published by . This book was released on 2008 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The understanding of cellular metabolism has been an intriguing challenge in classical cellular biology for decades. Essentially, cellular metabolism can be viewed as a complex system of enzyme-catalysed biochemical reactions that produces the energy and material necessary for the maintenance of life. In modern biochemistry, it is well-known that these reactions group into metabolic pathways so as to accomplish a particular function in the cell. The identification of these metabolic pathways is a key step to fully understanding the metabolic capabilities of a given organism. Typically, metabolic pathways have been elucidated via experimentation on different organisms. However, experimental findings are generally limited and fail to provide a complete description of all pathways. For this reason it is important to have mathematical models that allow us to identify and analyze metabolic pathways in a computational fashion. This is precisely the main theme of this thesis. We firstly describe, review and discuss existent mathematical/computational approaches to metabolic pathways, namely stoichiometric and path finding approaches. Then, we present our initial mathematical model named the Beasley-Planes (BP) model, which significantly improves on previous stoichiometric approaches. We also illustrate a successful application of the BP model to optimally disrupt metabolic pathways. The main drawback of the BP model is that it needs as input extra pathway knowledge. This is especially inappropriate if we wish to detect unknown metabolic pathways. As opposed to the BP model and stoichoimetric approaches, this issue is not found in path finding approaches. For this reason a novel path finding approach is built and examined in detail. This analysis serves us as inspiration to build the Improved Beasley-Planes (IBP) model. The IBP model incorporates elements of both stoichometric and path finding approaches. Though somewhat less accurate than the BP model, the IBP model solves the issue of extra pathway knowledge. Our research clearly demonstrates that there is a significant chance of developing a mathematical optimisation model that underlies many/all metabolic pathways.
Download or read book Systemic Analysis of the Stoichiometric Matrix and Kinetic Characterization of Metabolic Networks written by Iman Famili and published by . This book was released on 2004 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Analysis of Biochemical Systems written by Eberhard O. Voit and published by Cambridge University Press. This book was released on 2000-09-04 with total page 556 pages. Available in PDF, EPUB and Kindle. Book excerpt: Teaches the use of modern computational methods for the analysis of biomedical systems using case studies and accompanying software.
Download or read book Pathway Analysis and Optimization in Metabolic Engineering written by Néstor V. Torres and published by Cambridge University Press. This book was released on 2002-12-19 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: Facility in the targeted manipulation of the genetic and metabolic composition of organisms, combined with unprecedented computational power, is forging a niche for a new subspecialty of biotechnology called metabolic engineering. First published in 2002, this book introduces researchers and advanced students in biology and engineering to methods of optimizing biochemical systems of biotechnological relevance. It examines the development of strategies for manipulating metabolic pathways, demonstrates the need for effective systems models, and discusses their design and analysis, while placing special emphasis on optimization. The authors propose power-law models and methods of biochemical systems theory toward these ends. All concepts are derived from first principles, and the text is richly illustrated with numerous graphs and examples throughout. Special features include: nontechnical and technical introductions to models of biochemical systems; a review of basic methods of model design and analysis; concepts of optimization; and detailed case studies.
Download or read book Metabolic Networks Elementary Flux Modes and Polyhedral Cones written by Isaac Klapper and published by SIAM. This book was released on 2021-06-15 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a mathematical analysis of the relationship between the cell biology idea of metabolic networks and the mathematical idea of polyhedral cones. Such cones can be used to describe the set of steady state admissible fluxes through metabolic networks, and consequently they have become important constructs in the field of microbiology. Fundamental objects called elementary flux modes (EFMs) can be described mathematically via convex cone concepts; the fundamental algorithm of this relationship is the Double Description method. While this method has an extended history in the field of computational geometry, this monograph addresses its relatively recent use in the context of cellular metabolism, providing an easy-to-read introduction to a central topic of mathematical systems biology. Metabolic Networks, Elementary Flux Modes, and Polyhedral Cones addresses important topics in the mathematical description of metabolic activity that have not previously appeared in unified form and presents a careful study of the Double Description method in the context of metabolic analysis. It makes mathematical aspects of the material readily accessible to bioengineers and system biologists, and biological aspects readily accessible to mathematicians. This book is intended for readers from both mathematical and biological backgrounds, including mathematicians, engineers, and biologists interested in cell metabolism. It will also be helpful to mathematicians interested in applying computational geometry methods in computational biology as well as for systems biologists and modelers interested in the mathematical and algorithmic foundations of metabolic pathway analysis.
Download or read book Metabolic Engineering written by Sang Yup Lee and published by CRC Press. This book was released on 2020-10-29 with total page 453 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique reference/text presents the basic theory and practical applications of metabolic engineering (ME). It offers systematic analysis of complex metabolic pathways and ways of employing recombinant DNA techniques to alter cell behavior, metabolic patterns, and product formation. Treating ME as a distinct subfield of genetic engineering, the book demonstrates new means of enabling cells to produce valuable proteins, polypeptides, and primary and secondary metabolites. Written by more than 35 leading international experts in the field, this book discusses metabolic engineering in plant and mammalian cells, bacteria, and yeasts and assesses metabolic engineering applications in agriculture, pharmaceuticals, and environmental systems. It illuminates the potential of the "cell factory" model for production of chemicals and therapeutics and examines methods for developing new antiviral and antibacterial molecules and effective gene and somatic-cell therapies. Metabolic Engineering also addresses the use of metabolic flux analysis, metabolic control analysis, and online metabolic flux analysis.
Download or read book On Systems Biology and the Pathway Analysis of Metabolic Networks written by Christophe Heinz Schilling and published by . This book was released on 2000 with total page 674 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Modelling Metabolism with Mathematica written by Peter Mulquiney and published by CRC Press. This book was released on 2003-05-14 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the advent of sophisticated general programming environments like Mathematica, the task of developing new models of metabolism and visualizing their responses has become accessible to students of biochemistry and the life sciences in general. Modelling Metabolism with Mathematica presents the approaches, methods, tools, and algorithms for mode
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2008 with total page 946 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Handbook of Industrial Cell Culture written by Victor A. Vinci and published by Springer Science & Business Media. This book was released on 2002-12-06 with total page 533 pages. Available in PDF, EPUB and Kindle. Book excerpt: A diverse team of researchers, technologists, and engineers describe, in simple and practical language, the major current and evolving technologies for improving the biocatalytic capabilities of mammalian, microbial, and plant cells. The authors present state-of-the-art techniques, proven methods, and strategies for industrial screening, cultivation, and scale-up of these cells, and describe their biotech and industrial uses. Special emphasis is given to the solving critical issues encountered during the discovery of new drugs, process development, and the manufacture of new and existing compounds. Other topics include recombinant protein expression, bioinformatics, high throughput screening, analytical tools in biotechnology, DNA shuffling, and genomics discovery.
Download or read book Introduction To Metabolic And Cellular Engineering An Second Edition written by Sonia Del Carmen Cortassa and published by World Scientific. This book was released on 2011-12-28 with total page 447 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolic and Cellular Engineering (MCE) is more than an exciting scientific enterprise. It has become the cornerstone for coping with the challenges ahead of mankind. Continuous developments, new concepts, and technological innovations will enable us to deal with emerging challenges, and solve problems once thought impossible ten years ago. Challenges in MCE are broad- from unraveling fundamental aspects of cellular function to meeting unsatiated energy and food demands that are rising in parallel with population growth.In charting the progress of MCE during the last decade, we could not help but feel in awe of the enormous strides of progress made from the nascent Metabolic Engineering to the Systems Bioengineering of today. The burgeoning availability of genomic sequences from diverse species has been spectacular. It has become the engine that drives the genetic means for the modification of existing organisms and the generation of synthetic, man-made ones. From the initial attempts at purposeful genetic modification of a cell for the production of valuable compounds, we have now moved on to changing microbes genetically or metabolically.The arsenal of experimental and theoretical tools available for Metabolic and Cellular Engineering has expanded enormously, driven by the re-emergence of Physiology as Systems Biology. The revival of the concept of networks fueled by new developments has become central to Systems Biology. Networks represent an integrative vision of how processes of disparate nature relate to each other, and as such is becoming a key analytical and conceptual tool for MCE. This book reflects and addresses all these ongoing changes while providing the essential conceptual and analytical tools needed to understand and work in the MCE research field.
Download or read book An Introduction to Metabolic and Cellular Engineering written by Sonia Cortassa and published by World Scientific. This book was released on 2002 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolic and cellular engineering is a powerful alliance of two technologies: genetics-molecular biology and fermentation technology.
Download or read book Metabolic Network Reconstruction and Modeling written by Marco Fondi and published by Humana Press. This book was released on 2018-08-30 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume looks at the latest methodologies used to study cellular metabolism with in silico approaches. The chapters in this book are divided into 3 parts: part I discusses tools and methods used for metabolic reconstructions and basic constraint-based metabolic modeling (CBMM); Part II explores protocols for the generation of experimental data for metabolic reconstruction and modeling, including transcriptomics, proteomics, and mutant generations; and Part III cover advanced techniques for quantitative modeling of cellular metabolism, including dynamic Flux Balance Analysis and multi-objective optimization. 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. Cutting-edge and thorough, Metabolic Network Reconstruction and Modeling: Methods and Protocols is a valuable resource for qualified investigators studying cellular metabolism, and novice researchers who want to start working with CBMM.
Download or read book Current Challenges in Modeling Cellular Metabolism written by Daniel Machado and published by Frontiers Media SA. This book was released on 2016-01-21 with total page 117 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical and computational models play an essential role in understanding the cellular metabolism. They are used as platforms to integrate current knowledge on a biological system and to systematically test and predict the effect of manipulations to such systems. The recent advances in genome sequencing techniques have facilitated the reconstruction of genome-scale metabolic networks for a wide variety of organisms from microbes to human cells. These models have been successfully used in multiple biotechnological applications. Despite these advancements, modeling cellular metabolism still presents many challenges. The aim of this Research Topic is not only to expose and consolidate the state-of-the-art in metabolic modeling approaches, but also to push this frontier beyond the current edge through the introduction of innovative solutions. The articles presented in this e-book address some of the main challenges in the field, including the integration of different modeling formalisms, the integration of heterogeneous data sources into metabolic models, explicit representation of other biological processes during phenotype simulation, and standardization efforts in the representation of metabolic models and simulation results.
Download or read book A Network Based Approach to Cell Metabolism written by Oriol Güell and published by Springer. This book was released on 2017-08-16 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis uses a systems-level approach to study the cellular metabolism, unveiling new mechanisms and responses that were impossible to reach with traditional reductionists procedures. The results reported here have a potential application in areas like metabolic engineering and disease treatment. They could also be used in determining the accuracy of the gene essentiality of new genome-scale reconstructions. Different methods and techniques, within the contexts of Systems Biology and the field known as Complex Networks Analysis have been applied in this work to show different features of the robustness of metabolic networks. The specific issues addressed here range from pure topological aspec ts of the networks themselves to the balance of biochemical fluxes.
