User Friendly Tools Applied To Genetics Or Systems Biology

Author : Helder Nakaya,Juilee Thakar,Vinicius Maracaja-Coutinho
Publisher : Frontiers Media SA
Page : 177 pages
File Size : 55,5 Mb
Release : 2020-12-01
Category : Science
ISBN : 9782889661336

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User-Friendly Tools Applied to Genetics or Systems Biology by Helder Nakaya,Juilee Thakar,Vinicius Maracaja-Coutinho Pdf

This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.

Author : David Edwards,Jason Stajich,David Hansen
Publisher : Springer Science & Business Media
Page : 450 pages
File Size : 47,9 Mb
Release : 2009-09-03
Category : Science
ISBN : 9780387927381

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Bioinformatics by David Edwards,Jason Stajich,David Hansen Pdf

Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory. The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding.

Author : Masao Nagasaki,Ayumu Saito,Atsushi Doi,Hiroshi Matsuno,Satoru Miyano
Publisher : Springer Science & Business Media
Page : 155 pages
File Size : 42,7 Mb
Release : 2009-04-21
Category : Science
ISBN : 9781848820234

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Foundations of Systems Biology by Masao Nagasaki,Ayumu Saito,Atsushi Doi,Hiroshi Matsuno,Satoru Miyano Pdf

Today, as hundreds of genomes have been sequenced and thousands of proteins and more than ten thousand metabolites have been identi?ed, navigating safely through this wealth of information without getting completely lost has become crucial for research in, and teaching of, molecular biology. Consequently, a considerable number of tools have been developed and put on the market in the last two decades that describe the multitude of potential/putative interactions between genes, proteins, metabolites, and other biologically relevant compounds in terms of metabolic, genetic, signaling, and other networks, their aim being to support all sorts of explorations through bio-data bases currently called Systems Biology. As a result, navigating safely through this wealth of information-processing tools has become equally crucial for successful work in molecular biology. To help perform such navigation tasks successfully, this book starts by providing an extremely useful overview of existing tools for ?nding (or designing) and inv- tigating metabolic, genetic, signaling, and other network databases, addressing also user-relevant practical questions like • Is the database viewable through a web browser? • Is there a licensing fee? • What is the data type (metabolic, gene regulatory, signaling, etc. )? • Is the database developed/maintained by a curator or a computer? • Is there any software for editing pathways? • Is it possible to simulate the pathway? It then goes on to introduce a speci?c such tool, that is, the fabulous “Cell - lustrator 3. 0” tool developed by the authors.

Author : Vijai Singh
Publisher : Academic Press
Page : 487 pages
File Size : 42,7 Mb
Release : 2022-01-12
Category : Science
ISBN : 9780323859868

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New Frontiers and Applications of Synthetic Biology by Vijai Singh Pdf

New Frontiers and Applications of Synthetic Biology presents a collection of chapters from eminent synthetic biologists across the globe who have established experience and expertise working with synthetic biology. This book offers several important areas of synthetic biology which allow us to read and understand easily. It covers the introduction of synthetic biology and design of promoter, new DNA synthesis and sequencing technology, genome assembly, minimal cells, small synthetic RNA, directed evolution, protein engineering, computational tools, de novo synthesis, phage engineering, a sensor for microorganisms, next-generation diagnostic tools, CRISPR-Cas systems, and more. This book is a good source for not only researchers in designing synthetic biology, but also for researchers, students, synthetic biologists, metabolic engineers, genome engineers, clinicians, industrialists, stakeholders and policymakers interested in harnessing the potential of synthetic biology in many areas. Offers basic understanding and knowledge in several aspects of synthetic biology Covers state-of-the-art tools and technologies of synthetic biology, including promoter design, DNA synthesis, DNA sequencing, genome design, directed evolution, protein engineering, computational tools, phage design, CRISPR-Cas systems, and more Discusses the applications of synthetic biology for smart drugs, vaccines, therapeutics, drug discovery, self-assembled materials, cell free systems, microfluidics, and more

Author : Daniel G. Gibson,Clyde A. Hutchison (III),Hamilton Othanel Smith,J. Craig Venter
Publisher : Perspectives Cshl
Page : 0 pages
File Size : 42,9 Mb
Release : 2017
Category : Science
ISBN : 1621821188

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Synthetic Biology by Daniel G. Gibson,Clyde A. Hutchison (III),Hamilton Othanel Smith,J. Craig Venter Pdf

Synthetic biology involves the rational design and construction of biological components and systemsfrom genetic elements and metabolic pathways to entirely new organisms. Progress in this field has been rapid, and it promises to significantly expand our capabilities in biotechnology, medicine, and agriculture. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology examines the tools and techniques employed by synthetic biologists, how these may be used to develop new drugs, diagnostic approaches, food sources, and clean energy, and what the field of synthetic biology has taught us about natural living systems. The contributors discuss advances in DNA synthesis and assembly, genome editing (e.g., CRISPR/Cas9), and artificial genetic systems. Progress in designing complex genetic switches and circuits, expanding the genetic code, modifying cellular organization, producing proteins using cell-free systems, and developing biodesign automation tools is also covered. The authors also explore ways to produce new organisms and products that have particular attributesfor example, microbial "molecular factories," synthetic organs and tissues, and plants with novel traits. This volume is an essential resource for molecular, cell, and systems biologists who seek to engineer living systems for human benefit.

Author : Jens Nielsen,Michael C. Jewett
Publisher : Springer Science & Business Media
Page : 284 pages
File Size : 50,9 Mb
Release : 2007-09-19
Category : Science
ISBN : 9783540747192

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Metabolomics by Jens Nielsen,Michael C. Jewett Pdf

Giving a fresh, substantial and in-depth overview of the topic, this book brings together the latest results in the field of metabolomics. It comprehensively presents the current state of the metabolomics field by underscoring experimental methods, analysis techniques, standardization practices, and advances in specific model systems. As a result, it helps to significantly broaden our perspective on the principles and strategies underpinning this emerging field.

Author : National Research Council,Division on Engineering and Physical Sciences,Computer Science and Telecommunications Board,Committee on Frontiers at the Interface of Computing and Biology
Publisher : National Academies Press
Page : 469 pages
File Size : 44,5 Mb
Release : 2006-01-01
Category : Science
ISBN : 9780309096126

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Catalyzing Inquiry at the Interface of Computing and Biology by National Research Council,Division on Engineering and Physical Sciences,Computer Science and Telecommunications Board,Committee on Frontiers at the Interface of Computing and Biology Pdf

Advances in computer science and technology and in biology over the last several years have opened up the possibility for computing to help answer fundamental questions in biology and for biology to help with new approaches to computing. Making the most of the research opportunities at the interface of computing and biology requires the active participation of people from both fields. While past attempts have been made in this direction, circumstances today appear to be much more favorable for progress. To help take advantage of these opportunities, this study was requested of the NRC by the National Science Foundation, the Department of Defense, the National Institutes of Health, and the Department of Energy. The report provides the basis for establishing cross-disciplinary collaboration between biology and computing including an analysis of potential impediments and strategies for overcoming them. The report also presents a wealth of examples that should encourage students in the biological sciences to look for ways to enable them to be more effective users of computing in their studies.

Author : Oded Maler,Ádám Halász,Thao Dang,Carla Piazza
Publisher : Springer
Page : 175 pages
File Size : 52,8 Mb
Release : 2015-12-24
Category : Computers
ISBN : 9783319276564

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Hybrid Systems Biology by Oded Maler,Ádám Halász,Thao Dang,Carla Piazza Pdf

This book constitutes the thoroughly refereed post-workshop proceedings of the Second International Workshop on Hybrid Systems Biology, HSB 2013, held as part of the ECAL 2013 event, in Taormina, Italy, in September 2013; and the Third International Workshop on Hybrid Systems Biology, HSB 2014, held as part of CAV 2014, in Vienna, Austria, in July 2014. This volume presents 8 full papers together with 2 invited tutorials/surveys from 21 submissions. The HSB 2013 workshop aims at collecting scientists working in the area of hybrid modeling applied to systems biology, in order to discuss about current achieved goals, current challenges and future possible developments. The scope of the HSB 2014 workshop is the general area of dynamical models in biology with an emphasis on hybrid approaches, which are not restricted to a narrow class of mathematical models, and which take advantage of techniques developed separately in different sub-fields. “br> /div

Author : Fabricio Alves Barbosa da Silva,Nicolas Carels,Floriano Paes Silva Junior
Publisher : Springer
Page : 259 pages
File Size : 43,7 Mb
Release : 2018-06-21
Category : Computers
ISBN : 9783319749747

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Theoretical and Applied Aspects of Systems Biology by Fabricio Alves Barbosa da Silva,Nicolas Carels,Floriano Paes Silva Junior Pdf

This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.

Author : Milan Češka,David Šafránek
Publisher : Springer
Page : 326 pages
File Size : 51,8 Mb
Release : 2018-08-27
Category : Computers
ISBN : 9783319994291

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Computational Methods in Systems Biology by Milan Češka,David Šafránek Pdf

This book constitutes the refereed proceedings of the 16th International Conference on Computational Methods in Systems Biology, CMSB 2018, held in BRNO, Czech Republic, in September 2018. The 15 full and 7 short papers presented together with 5 invited talks were carefully reviewed and selected from 46 submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology; parameter and model inference from experimental data; automated parameter and model synthesis; model integration and biological databases; multi-scale modeling and analysis methods; design, analysis, and verification methods for synthetic biology; methods for biomolecular computing and engineered molecular devices. Chapters 3, 9 and 10 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Author : Huimin Zhao
Publisher : Academic Press
Page : 352 pages
File Size : 41,6 Mb
Release : 2013-03-21
Category : Science
ISBN : 9780123978202

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Synthetic Biology by Huimin Zhao Pdf

Synthetic Biology provides a framework to examine key enabling components in the emerging area of synthetic biology. Chapters contributed by leaders in the field address tools and methodologies developed for engineering biological systems at many levels, including molecular, pathway, network, whole cell, and multi-cell levels. The book highlights exciting practical applications of synthetic biology such as microbial production of biofuels and drugs, artificial cells, synthetic viruses, and artificial photosynthesis. The roles of computers and computational design are discussed, as well as future prospects in the field, including cell-free synthetic biology and engineering synthetic ecosystems. Synthetic biology is the design and construction of new biological entities, such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components that can be modeled, understood, and tuned to meet specific performance criteria and the assembly of these smaller parts and devices into larger integrated systems that solve specific biotechnology problems. Includes contributions from leaders in the field presents examples of ambitious synthetic biology efforts including creation of artificial cells from scratch, cell-free synthesis of chemicals, fuels, and proteins, engineering of artificial photosynthesis for biofuels production, and creation of unnatural living organisms Describes the latest state-of-the-art tools developed for low-cost synthesis of ever-increasing sizes of DNA and efficient modification of proteins, pathways, and genomes Highlights key technologies for analyzing biological systems at the genomic, proteomic, and metabolomic levels which are especially valuable in pathway, whole cell, and multi-cell applications Details mathematical modeling tools and computational tools which can dramatically increase the speed of the design process as well as reduce the cost of development.

Author : Institute of Medicine,Board on Global Health,Forum on Microbial Threats
Publisher : National Academies Press
Page : 570 pages
File Size : 53,5 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.

Author : Edda Klipp,Ralf Herwig,Axel Kowald,Christoph Wierling,Hans Lehrach
Publisher : John Wiley & Sons
Page : 486 pages
File Size : 43,6 Mb
Release : 2008-07-15
Category : Medical
ISBN : 9783527604883

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Systems Biology in Practice by Edda Klipp,Ralf Herwig,Axel Kowald,Christoph Wierling,Hans Lehrach Pdf

Presenting the main concepts, this book leads students as well as advanced researchers from different disciplines to an understanding of current ideas in the complex field of comprehensive experimental investigation of biological objects, analysis of data, development of models, simulation, and hypothesis generation. It provides readers with guidance on how a specific complex biological question may be tackled: - How to formulate questions that can be answered - Which experiments to perform - Where to find information in databases and on the Internet - What kinds of models are appropriate - How to use simulation tools - What can be learned from the comparison of experimental data and modeling results - How to make testable predictions. The authors demonstrate how mathematical concepts can illuminate the principles underlying biology at a genetic, molecular, cellular and even organism level, and how to use mathematical tools for analysis and prediction.

Author : Z.-H. Liui,J.C. He
Publisher : Karger Medical and Scientific Publishers
Page : 277 pages
File Size : 46,6 Mb
Release : 2014-05-16
Category : Medical
ISBN : 9783318026511

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Podocytopathy by Z.-H. Liui,J.C. He Pdf

The podocyte is a key cell that forms the last barrier of the kidney filtration unit. One of the most exciting developments in the field of nephrology in the last decade has been the elucidation of its biology and its role in the pathophysiology of inherited and acquired glomerular disease, termed podocytopathy. In this publication, world-renowned experts summarize the most recent findings and advances in the field: they describe the unique biological features and injury mechanisms of the podocyte, novel techniques used in their study, and diagnosis and potential therapeutic approaches to glomerular diseases. Due to its broad scope, this publication is of great value not only for clinical nephrologists and researchers, but also for students, residents, fellows, and postdocs.

Author : Sanket Joshi
Publisher : Springer Nature
Page : 587 pages
File Size : 47,5 Mb
Release : 2024-06-02
Category : Electronic
ISBN : 9789819994625

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Systems Biology Approaches: Prevention, Diagnosis, and Understanding Mechanisms of Complex Diseases by Sanket Joshi Pdf