Metabolic Network Reconstruction And Modeling

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Metabolic Network Reconstruction and Modeling

Marco Fondi
Metabolic Network Reconstruction and Modeling Book PDF

Author : Marco Fondi
Publisher : Unknown
Page : 410 pages
File Size : 48,8 Mb
Release : 2018
Category : Cell metabolism
ISBN : 1493975285

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Metabolic Network Reconstruction and Modeling by Marco Fondi Pdf

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.

Current Challenges in Modeling Cellular Metabolism

Daniel Machado,Kai H. Zhuang,Nikolaus Sonnenschein,Markus J. Herrgård
Current Challenges in Modeling Cellular Metabolism Book PDF

Author : Daniel Machado,Kai H. Zhuang,Nikolaus Sonnenschein,Markus J. Herrgård
Publisher : Frontiers Media SA
Page : 117 pages
File Size : 44,5 Mb
Release : 2016-01-21
Category : Biology (General)
ISBN : 9782889197545

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Current Challenges in Modeling Cellular Metabolism by Daniel Machado,Kai H. Zhuang,Nikolaus Sonnenschein,Markus J. Herrgård Pdf

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.

The Chemistry of Microbiomes

National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Chemical Sciences and Technology,Chemical Sciences Roundtable
The Chemistry of Microbiomes Book PDF

Author : National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Chemical Sciences and Technology,Chemical Sciences Roundtable
Publisher : National Academies Press
Page : 133 pages
File Size : 43,5 Mb
Release : 2017-07-19
Category : Science
ISBN : 9780309458399

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The Chemistry of Microbiomes by National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Chemical Sciences and Technology,Chemical Sciences Roundtable Pdf

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.

Computational Systems Biology

Hong-Wu Ma,An-Ping Zeng
Computational Systems Biology Book PDF

Author : Hong-Wu Ma,An-Ping Zeng
Publisher : Elsevier Inc. Chapters
Page : 548 pages
File Size : 53,6 Mb
Release : 2013-11-26
Category : Medical
ISBN : 9780128070086

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Computational Systems Biology by Hong-Wu Ma,An-Ping Zeng Pdf

Understanding the complex interactions among cellular components (genes, proteins and metabolites) at a network level is a key issue in systems biology. In this chapter, we give an overview of metabolic network reconstruction from genome information and its structural analysis. First, two approaches for genome scale metabolic network reconstruction: high throughput reconstruction and high quality reconstruction, are discussed. Then the various means for mathematical representation of metabolic networks are explained, with particular emphasis on the problem arising from currency metabolites. Several topological features of metabolic network such as the power law connection degree distribution and the “bow-tie” global connectivity structure are explained in detail. In the last section, we discuss the different types of methods for network decomposition which can be used to identify somehow structurally and functionally independent modules in a complex network. This allows us to understand the functional organization of metabolic network from a modular perspective.

The Science and Applications of Synthetic and Systems Biology

Institute of Medicine,Board on Global Health,Forum on Microbial Threats
The Science and Applications of Synthetic and Systems Biology Book PDF

Author : Institute of Medicine,Board on Global Health,Forum on Microbial Threats
Publisher : National Academies Press
Page : 570 pages
File Size : 42,7 Mb
Release : 2011-12-30
Category : Science
ISBN : 9780309219396

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The Science and Applications of Synthetic and Systems Biology by Institute of Medicine,Board on Global Health,Forum on Microbial Threats Pdf

Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Systems Biology

Bernhard Palsson
Systems Biology Book PDF

Author : Bernhard Palsson
Publisher : Cambridge University Press
Page : 551 pages
File Size : 50,8 Mb
Release : 2015-01-26
Category : Medical
ISBN : 9781107038851

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Systems Biology by Bernhard Palsson Pdf

The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.

Encyclopedia of Systems Biology

Werner Dubitzky,Olaf Wolkenhauer,Hiroki Yokota,Kwang-Hyun Cho
Encyclopedia of Systems Biology Book PDF

Author : Werner Dubitzky,Olaf Wolkenhauer,Hiroki Yokota,Kwang-Hyun Cho
Publisher : Springer
Page : 0 pages
File Size : 42,7 Mb
Release : 2013-06-05
Category : Science
ISBN : 1441998624

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Encyclopedia of Systems Biology by Werner Dubitzky,Olaf Wolkenhauer,Hiroki Yokota,Kwang-Hyun Cho Pdf

Systems biology refers to the quantitative analysis of the dynamic interactions among several components of a biological system and aims to understand the behavior of the system as a whole. Systems biology involves the development and application of systems theory concepts for the study of complex biological systems through iteration over mathematical modeling, computational simulation and biological experimentation. Systems biology could be viewed as a tool to increase our understanding of biological systems, to develop more directed experiments, and to allow accurate predictions. The Encyclopedia of Systems Biology is conceived as a comprehensive reference work covering all aspects of systems biology, in particular the investigation of living matter involving a tight coupling of biological experimentation, mathematical modeling and computational analysis and simulation. The main goal of the Encyclopedia is to provide a complete reference of established knowledge in systems biology – a ‘one-stop shop’ for someone seeking information on key concepts of systems biology. As a result, the Encyclopedia comprises a broad range of topics relevant in the context of systems biology. The audience targeted by the Encyclopedia includes researchers, developers, teachers, students and practitioners who are interested or working in the field of systems biology. Keeping in mind the varying needs of the potential readership, we have structured and presented the content in a way that is accessible to readers from wide range of backgrounds. In contrast to encyclopedic online resources, which often rely on the general public to author their content, a key consideration in the development of the Encyclopedia of Systems Biology was to have subject matter experts define the concepts and subjects of systems biology.

Metabolic Pathway Engineering

Jean F. Challacombe
Metabolic Pathway Engineering Book PDF

Author : Jean F. Challacombe
Publisher : CRC Press
Page : 116 pages
File Size : 46,7 Mb
Release : 2021-07-14
Category : Medical
ISBN : 9781000260540

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Metabolic Pathway Engineering by Jean F. Challacombe Pdf

Metabolic systems engineering combines the tools and approaches of systems biology, synthetic biology, and evolutionary engineering. This book reviews studies on metabolism, from the earliest work of Lavoisier and Buchner to current cutting-edge research in metabolic systems engineering. This technology has been used in bioengineering applications to create high-performing microbes and plants that produce important chemicals, pharmaceuticals, crops, and other natural products. Current applications include optimizing metabolic pathways to enhance degradation of biomass for biofuel production and accelerated processing of environmental waste products and contaminants. The book includes examples to illustrate the applications of this technology in the optimization of metabolic pathways to create robust industrial strains as well as in the engineering of biological processes involving health and diseases of humans, animals, and plants. Written by a seasoned computational biologist with many years of experience in genomics, bioinformatics, and systems biology, this book will appeal to anyone interested in metabolic systems analysis and metabolic pathway engineering.

Optimization Methods in Metabolic Networks

Costas D. Maranas,Ali R. Zomorrodi
Optimization Methods in Metabolic Networks Book PDF

Author : Costas D. Maranas,Ali R. Zomorrodi
Publisher : John Wiley & Sons
Page : 288 pages
File Size : 46,9 Mb
Release : 2016-01-05
Category : Science
ISBN : 9781119189015

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Optimization Methods in Metabolic Networks by Costas D. Maranas,Ali R. Zomorrodi Pdf

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

Systems Biology

Bernhard Ø. Palsson
Systems Biology Book PDF

Author : Bernhard Ø. Palsson
Publisher : Cambridge University Press
Page : 287 pages
File Size : 45,5 Mb
Release : 2006-01-16
Category : Science
ISBN : 9781139448949

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Systems Biology by Bernhard Ø. Palsson Pdf

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.

Metabolic Network Analysis

T.P. Jayadev Reddy
Metabolic Network Analysis Book PDF

Author : T.P. Jayadev Reddy
Publisher : Daya Books
Page : 300 pages
File Size : 51,7 Mb
Release : 2007-03-02
Category : Medical
ISBN : 8176221694

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Metabolic Network Analysis by T.P. Jayadev Reddy Pdf

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.

Emerging Areas in Bioengineering

Ho Nam Chang
Emerging Areas in Bioengineering Book PDF

Author : Ho Nam Chang
Publisher : John Wiley & Sons
Page : 898 pages
File Size : 48,8 Mb
Release : 2018-03-12
Category : Science
ISBN : 9783527340880

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Emerging Areas in Bioengineering by Ho Nam Chang Pdf

With more than 40 contributions from expert authors, this is an extensive overview of all important research topics in the field of bioengineering, including metabolic engineering, biotransformations and biomedical applications. Alongside several chapters dealing with biotransformations and biocatalysis, a whole section is devoted to biofuels and the utilization of biomass. Current perspectives on synthetic biology and metabolic engineering approaches are presented, involving such example organisms as Escherichia coli and Corynebacterium glutamicum, while a further section covers topics in biomedical engineering including drug delivery systems and biopharmaceuticals. The book concludes with chapters on computer-aided bioprocess engineering and systems biology. This is a part of the Advanced Biotechnology book series, covering all pertinent aspects of the field with each volume prepared by eminent scientists who are experts on the topic in question. Invaluable reading for biotechnologists and bioengineers, as well as those working in the chemical and pharmaceutical industries. Advanced Biotechnology Biotechnology is a broad, interdisciplinary field of science, combining biological sciences and relevant engineering disciplines, that is becoming increasingly important as it benefits the environment and society as a whole. Recent years have seen substantial advances in all areas of biotechnology, resulting in the emergence of brand new fields. To reflect this progress, Sang-Yup Lee (KAIST, South Korea), Jens Nielsen (Chalmers University, Sweden), and Gregory Stephanopoulos (MIT, USA) have joined forces as the editors of a new Wiley-VCH book series. Advanced Biotechnology will cover all pertinent aspects of the field and each volume will be prepared by eminent scientists who are experts on the topic in question.

Yeasts in Biotechnology and Human Health

Isabel Sá-Correia
Yeasts in Biotechnology and Human Health Book PDF

Author : Isabel Sá-Correia
Publisher : Springer
Page : 242 pages
File Size : 43,7 Mb
Release : 2019-03-25
Category : Science
ISBN : 9783030130350

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Yeasts in Biotechnology and Human Health by Isabel Sá-Correia Pdf

This book discusses genome-based strategies to provide a holistic understanding of yeasts in Human Health and as model organisms in basic research or industrial production. Using numerous Saccharomyces cerevisiae strains and various non-conventional yeast species isolated from diverse origins, it describes essential biological processes, the biotechnological exploitation of yeast and pathogenesis control. It also demonstrates how functional and comparative genomics and the development of genome engineering tools are used in modern yeast research. The use of yeasts as experimental eukaryotic models increasingly gained prominence when several Nobel Prizes in Physiology/Medicine and Chemistry were awarded for innovative research, using yeast strains to elucidate molecular mechanisms in a wide range of human physiological processes and diseases, such as autophagy, cell cycle regulation and telomerase activity. This book offers useful insights for scientists in yeast research, clinical scientists working with yeast infectious models and for industrial researchers using applied microbiology.

Systems Biology

Isidore Rigoutsos,Gregory Stephanopoulos
Systems Biology Book PDF

Author : Isidore Rigoutsos,Gregory Stephanopoulos
Publisher : Oxford University Press
Page : 366 pages
File Size : 54,7 Mb
Release : 2006-09-14
Category : Science
ISBN : 9780190293758

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Systems Biology by Isidore Rigoutsos,Gregory Stephanopoulos Pdf

The advent of genome sequencing and associated technologies has transformed biologists' ability to measure important classes of molecules and their interactions. This expanded cellular view has opened the field to thousands of interactions that previously were outside the researchers' reach. The processing and interpretation of these new vast quantities of interconnected data call for sophisticated mathematical models and computational methods. Systems biology meets this need by combining genomic knowledge with theoretical, experimental and computational approaches from a number of traditional scientific disciplines to create a mechanistic explanation of cellular systems and processes. Systems Biology I: Genomics and Systems Biology II: Networks, Models, and Applications offer a much-needed study of genomic principles and their associated networks and models. Written for a wide audience, each volume presents a timely compendium of essential information that is necessary for a comprehensive study of the subject. The chapters in the two volumes reflect the hierarchical nature of systems biology. Chapter authors-world-recognized experts in their fields-provide authoritative discussions on a wide range of topics along this hierarchy. Volume I explores issues pertaining to genomics that range from prebiotic chemistry to noncoding RNAs. Volume II covers an equally wide spectrum, from mass spectrometry to embryonic stem cells. The two volumes are meant to provide a reliable reference for students and researchers alike.

Systems Biology

Jens Nielsen,Stefan Hohmann
Systems Biology Book PDF

Author : Jens Nielsen,Stefan Hohmann
Publisher : John Wiley & Sons
Page : 435 pages
File Size : 45,7 Mb
Release : 2017-05-30
Category : Computers
ISBN : 9783527335589

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Systems Biology by Jens Nielsen,Stefan Hohmann Pdf

Comprehensive coverage of the many different aspects of systems biology, resulting in an excellent overview of the experimental and computational approaches currently in use to study biological systems. Each chapter represents a valuable introduction to one specific branch of systems biology, while also including the current state of the art and pointers to future directions. Following different methods for the integrative analysis of omics data, the book goes on to describe techniques that allow for the direct quantification of carbon fluxes in large metabolic networks, including the use of 13C labelled substrates and genome-scale metabolic models. The latter is explained on the basis of the model organism Escherichia coli as well as the human metabolism. Subsequently, the authors deal with the application of such techniques to human health and cell factory engineering, with a focus on recent progress in building genome-scale models and regulatory networks. They highlight the importance of such information for specific biological processes, including the ageing of cells, the immune system and organogenesis. The book concludes with a summary of recent advances in genome editing, which have allowed for precise genetic modifications, even with the dynamic control of gene expression. This is part of the Advances Biotechnology series, covering all pertinent aspects of the field with each volume prepared by eminent scientists who are experts on the topic in question.