Download or read book Analysis of Large Scale Metabolic Networks written by Christoph Kaleta and published by . This book was released on 2010 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Statistics for High Dimensional Data written by Peter Bühlmann and published by Springer Science & Business Media. This book was released on 2011-06-08 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern statistics deals with large and complex data sets, and consequently with models containing a large number of parameters. This book presents a detailed account of recently developed approaches, including the Lasso and versions of it for various models, boosting methods, undirected graphical modeling, and procedures controlling false positive selections. A special characteristic of the book is that it contains comprehensive mathematical theory on high-dimensional statistics combined with methodology, algorithms and illustrations with real data examples. This in-depth approach highlights the methods’ great potential and practical applicability in a variety of settings. As such, it is a valuable resource for researchers, graduate students and experts in statistics, applied mathematics and computer science.
Download or read book Correlation based network analysis of cancer metabolism written by Emily G. Armitage and published by Springer. This book was released on 2014-05-12 with total page 67 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the rise of systems biology as an approach in biochemistry research, using high throughput techniques such as mass spectrometry to generate metabolic profiles of cancer metabolism is becoming increasingly popular. There are examples of cancer metabolic profiling studies in the academic literature; however they are often only in journals specific to the metabolomics community. This book will be particularly useful for post-graduate students and post-doctoral researchers using this pioneering technique of network-based correlation analysis. The approach can be adapted to the analysis of any large scale metabolic profiling experiment to answer a range of biological questions in a range of species or for a range of diseases.
Download or read book Towards a New View on Metabolic Networks written by René Rex and published by . This book was released on 2013 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Plant Metabolomics written by Kazuki Saito and published by Springer Science & Business Media. This book was released on 2006-06-29 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics – which deals with all metabolites of an organism – is a rapidly-emerging sector of post-genome research fields. It plays significant roles in a variety of fields from medicine to agriculture and holds a fundamental position in functional genomics studies and their application in plant biotechnology. This volume comprehensively covers plant metabolomics for the first time. The chapters offer cutting-edge information on analytical technology, bioinformatics and applications. They were all written by leading researchers who have been directly involved in plant metabolomics research throughout the world. Up-to-date information and future developments are described, thereby producing a volume which is a landmark of plant metabolomics research and a beneficial guideline to graduate students and researchers in academia, industry, and technology transfer organizations in all plant science fields.
Download or read book Large Scale Networks in Engineering and Life Sciences written by Peter Benner and published by Springer. This book was released on 2014-10-21 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: This edited volume provides insights into and tools for the modeling, analysis, optimization, and control of large-scale networks in the life sciences and in engineering. Large-scale systems are often the result of networked interactions between a large number of subsystems, and their analysis and control are becoming increasingly important. The chapters of this book present the basic concepts and theoretical foundations of network theory and discuss its applications in different scientific areas such as biochemical reactions, chemical production processes, systems biology, electrical circuits, and mobile agents. The aim is to identify common concepts, to understand the underlying mathematical ideas, and to inspire discussions across the borders of the various disciplines. The book originates from the interdisciplinary summer school “Large Scale Networks in Engineering and Life Sciences” hosted by the International Max Planck Research School Magdeburg, September 26-30, 2011, and will therefore be of interest to mathematicians, engineers, physicists, biologists, chemists, and anyone involved in the network sciences. In particular, due to their introductory nature the chapters can serve individually or as a whole as the basis of graduate courses and seminars, future summer schools, or as reference material for practitioners in the network sciences.
Download or read book Electron Microscopy of Plant Cells written by C Hawes and published by Academic Press. This book was released on 2012-12-02 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Electron Microscopy of Plant Cells serves as manual or reference of major modern techniques used to prepare plant material for transmission and scanning electron microscopy. There have been other books that generally discuss electron microscope methodology. This book focuses on problem areas encountered through the presence of tough cell walls and large central vacuole. It details preparative techniques for botanical specimens. Each of the nine chapters of this book covers the basic principles, useful applications, and reliable procedures used on the method of electron microscopy. Other topics discussed in each chapter include the general preparation and straining of thin sections, quantitative morphological analysis, and enzyme cytochemistry. This book also explains the immunogold labelling, rapid-freezing methods, and ambient- and low-temperature scanning electron microscopy among others. This book will be invaluable to general scientists, biologists, botanists, and students specializing in plant anatomy.
Download or read book Systems Biology written by Bernhard Ø. Palsson and published by Cambridge University Press. This book was released on 2006-01-16 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome sequences are now available that enable us to determine the biological components that make up a cell or an organism. The discipline of systems biology examines how these components interact and form networks, and how the networks generate whole cell functions corresponding to observable phenotypes. This textbook, devoted to systems biology, describes how to model networks, how to determine their properties, and how to relate these to phenotypic functions. The prerequisites are some knowledge of linear algebra and biochemistry. Though the links between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, in an associated website Palsson provides problem sets, projects and Powerpoint slides, and keeps the presentation in the book concrete with illustrative material and experimental results.
Download or read book Large Scale Structure And Dynamics Of Complex Networks From Information Technology To Finance And Natural Science written by Alessandro Vespignani and published by World Scientific. This book was released on 2007-06-28 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the culmination of three years of research effort on a multidisciplinary project in which physicists, mathematicians, computer scientists and social scientists worked together to arrive at a unifying picture of complex networks. The contributed chapters form a reference for the various problems in data analysis visualization and modeling of complex networks.
Download or read book The Chemistry of Microbiomes written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2017-07-19 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication. The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystemsâ€"earth, marine, and humanâ€"and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.
Download or read book Metabolic Engineering written by Sang Yup Lee and published by John Wiley & Sons. This book was released on 2021-06-02 with total page 1075 pages. Available in PDF, EPUB and Kindle. Book excerpt: Learn more about foundational and advanced topics in metabolic engineering in this comprehensive resource edited by leaders in the field Metabolic Engineering: Concepts and Applications delivers a one-stop resource for readers seeking a complete description of the concepts, models, and applications of metabolic engineering. This guide offers practical insights into the metabolic engineering of major cell lines, including E. Coli, Bacillus and Yarrowia Lipolytica, and organisms, including human, animal, and plant). The distinguished editors also offer readers resources on microbiome engineering and the use of metabolic engineering in bioremediation. Written in two parts, Metabolic Engineering begins with the essential models and strategies of the field, like Flux Balance Analysis, Quantitative Flux Analysis, and Proteome Constrained Models. It also provides an overview of topics like Pathway Design, Metabolomics, and Genome Editing of Bacteria and Eukarya. The second part contains insightful descriptions of the practical applications of metabolic engineering, including specific examples that shed light on the topics within. In addition to subjects like the metabolic engineering of animals, humans, and plants, you’ll learn more about: Metabolic engineering concepts and a historical perspective on their development The different modes of analysis, including flux balance analysis and quantitative flux analysis An illuminating and complete discussion of the thermodynamics of metabolic pathways The Genome architecture of E. coli, as well as genome editing of both bacteria and eukarya An in-depth treatment of the application of metabolic engineering techniques to organisms including corynebacterial, bacillus, and pseudomonas, and more Perfect for students of biotechnology, bioengineers, and biotechnologists, Metabolic Engineering: Concepts and Applications also has a place on the bookshelves of research institutes, biotechnological institutes and industry labs, and university libraries. It's comprehensive treatment of all relevant metabolic engineering concepts, models, and applications will be of use to practicing biotechnologists and bioengineers who wish to solidify their understanding of the field.
Download or read book Systems Biology written by Bernhard Palsson and published by Cambridge University Press. This book was released on 2015-01-26 with total page 551 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.
Download or read book Plant Metabolic Networks written by Jörg Schwender and published by Springer Science & Business Media. This book was released on 2009-06-12 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plants are the basis for human nutrition and of increasing interest for the chemical industry as a source of chemical feed stocks. Fuels derived from plant biomass will increasingly replace fossil fuels in the future. In order to increase crop productivity, design new plant products, and create new energy crops, there is need for methods of qualitative and quantitative analysis of metabolism which are able to guide the rational re-design of metabolic networks. In this book, recent advances in qualitative and quantitative analysis of metabolism are summarized to give an overview of the current state of knowledge. Principles of the analysis of network structure, flux analysis, and kinetic modeling are described. Analytical methods necessary to produce the data needed for metabolic flux analysis and for kinetic modeling are described. The analysis of larger metabolic networks is only possible by using computer assistance. Therefore each chapter of the book shall also describe software available for this purpose.
Download or read book Knowledge based Scaling for Biological Models written by Anna Zhukova and published by . This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome-scale metabolic models describe the relationships between thousands of reactions and biochemical molecules, and are used to improve our understanding of organism's metabolism. They found applications in pharmaceutical, chemical and bioremediation industries.The complexity of metabolic models hampers many tasks that are important during the process of model inference, such as model comparison, analysis, curation and refinement by human experts. The abundance of details in large-scale networks can mask errors and important organism-specific adaptations. It is therefore important to find the right levels of abstraction that are comfortable for human experts. These abstract levels should highlight the essential model structure and the divergences from it, such as alternative paths or missing reactions, while hiding inessential details.To address this issue, we defined a knowledge-based generalization that allows for production of higher-level abstract views of metabolic network models. We developed a theoretical method that groups similar metabolites and reactions based on the network structure and the knowledge extracted from metabolite ontologies, and then compresses the network based on this grouping. We implemented our method as a python library, that is available for download from metamogen.gforge.inria.fr.To validate our method we applied it to 1 286 metabolic models from the Path2Model project, and showed that it helps to detect organism-, and domain-specific adaptations, as well as to compare models.Based on discussions with users about their ways of navigation in metabolic networks, we defined a 3-level representation of metabolic networks: the full-model level, the generalized level, the compartment level. We combined our model generalization method with the zooming user interface (ZUI) paradigm and developed Mimoza, a user-centric tool for zoomable navigation and knowledgebased exploration of metabolic networks that produces this 3-level representation. Mimoza is available both as an on-line tool and for download atmimoza.bordeaux.inria.fr.
Download or read book Metabolic Network Analysis written by T.P. Jayadev Reddy and published by Daya Books. This book was released on 2007-03-02 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolism Is A Set Of Chemical Reactions, Used By Living Organisms To Process Chemical Compounds In Order To Take Energy, Extract Building Blocks And Eliminate Toxic Compounds. It Comprises The Network Of Interactions That Provide Energy And Building Blocks For Cells And Organisms, A Network Sustaining The Living And Allowing It To Grow And Reproduce. Understanding The Nature And Functions Of Metabolic Networks Is Imperative To Biology, Toxicology And Medicine. With The Sequencing Of Complete Genomes, It Is Now Possible To Reconstruct The Network Of Biochemical Reactions In Many Organisms, From Bacteria To Human. This Book Examines How Biological Components Interact And Form Metabolic Networks, And How These Networks Generate Cell Functions Corresponding To Observable Phenotypes. It Describes How To Model Metabolic Networks, How To Determine Their Properties, And How To Relate These To Phenotypic Functions. It Will Be A Highly Beneficial Reference Tool For Researchers And Scholars In All Areas Of Life Sciences. Contents Chapter 1: Biology Of Cellular Networks; Chapter 2: Characteristics Of Metabolic Networks; Chapter 3: Signalling Pathways; Chapter 4: Networks In Genomics And Proteomics; Chapter 5: Modelling Of Biological Network; Chapter 6: Pathway Analysis In Metabolic Networks; Chapter 7: Topological Features Of Metabolic Networks; Chapter 8: Structure Of Expanding Metabolic Networks; Chapter 9: Modularity In Metabolic Networks; Chapter 10: Connectivity In Metabolic Networks; Chapter 11: Metabolic Network Interactions; Chapter 12: Microbial Metabolic Networks; Chapter 13: Protein Interaction Networks; Chapter 14: Implications Of Human Metabolome; Chapter 15: Metabolic Network Prediction; Chapter 16: Algebraic Comparison Of Metabolic Networks; Chapter 17: Regulation Of Metabolic Pathways.
Download or read book Systems Biology Informatics for the Development and Use of Genome scale Metabolic Models written by Neil Swainston and published by . This book was released on 2012 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology attempts to understand biological systems through the generation of predictive models that allow the behaviour of the system to be simulated in silico. Metabolic systems biology has in recent years focused upon the reconstruction and constraint-based analysis of genome-scale metabolic networks, which provide computational and mathematical representations of the known metabolic capabilities of a given organism. This thesis initially concerns itself with the development of such metabolic networks, first considering the community-driven development of consensus networks of the metabolic functions of Saccharomyces cerevisiae. This is followed by a consideration of automated approaches to network reconstruction that can be applied to facilitate what has, until recently, been an arduous manual process. The use of such large-scale networks in the generation of dynamic kinetic models is then considered. The development of such models is dependent upon the availability of experimentally determined parameters, from omics approaches such as transcriptomics, proteomics and metabolomics, and from kinetic assays. A discussion of the challenges faced with developing informatics infrastructure to support the acquisition, analysis and dissemination of quantitative proteomics and enzyme kinetics data follows, along with the introduction of novel software approaches to address these issues. The requirement for integrating experimental data with kinetic models is considered, along with approaches to construct, parameterise and simulate kinetic models from the network reconstructions and experimental data discussed previously. Finally, future requirements for metabolic systems biology informatics are considered, in the context of experimental data management, modelling infrastructure, and data integration required to bridge the gap between experimental and modelling approaches.
Download or read book Integrating Omics Data written by George Tseng and published by Cambridge University Press. This book was released on 2015-09-23 with total page 497 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tutorial chapters by leaders in the field introduce state-of-the-art methods to handle information integration problems of omics data.
