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Author: Altuna Akalin
Publisher: CRC Press
ISBN: 1498781861
Category : Mathematics
Languages : en
Pages : 463
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Book Description
Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.
Author: Altuna Akalin
Publisher: CRC Press
ISBN: 1498781861
Category : Mathematics
Languages : en
Pages : 463
Get Book Here
Book Description
Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.
Author: Nava Segev
Publisher: Springer Science & Business Media
ISBN: 038793877X
Category : Science
Languages : en
Pages : 459
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Book Description
This book covers the past, present and future of the intra-cellular trafficking field, which has made a quantum leap in the last few decades. It details how the field has developed and evolved as well as examines future directions.
Author:
Publisher:
ISBN: 9780815332183
Category : Cells
Languages : en
Pages : 0
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Book Description
Author: Charles J. Epstein
Publisher: Oxford University Press, USA
ISBN: 019514502X
Category : Medical
Languages : en
Pages : 1110
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Book Description
In this book, the clinical chapters are organized into sections by defined developmental pathways or gene families, and each section is preceded by a general overview. For each disorder the authors cover the disease-causing genes, the role of these genes in development as elucidated in model organisms, the human mutations that have been identified, and the developmental pathogenesis of the condition. Clinical descriptions, along with discussions of therapy and counseling, are provided. This book will be an invaluable resource for physicians, dentists, and other health professionals and for basic scientists interested in developmental processes and genetic perturbations that affect them.
Author: Kenneth Berendzen
Publisher: Bentham Science Publishers
ISBN: 1608054926
Category : Science
Languages : en
Pages : 225
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Book Description
A major goal of integrative research is understanding regulatory networks to such an extent as to allow researchers to model developmental and stress responses. Regulatory networks of living systems include complex and vast interactions between proteins, metabolites, RNA, various signaling molecules and DNA. One aspect of systems biology is understanding the dynamics of protein-DNA interactions affecting gene expression that are caused by transcription factors (TFs) and chromatin remodeling factors. This e-book provides a resource for summarizing current knowledge eukaryotic transcription and explores cis-elements and methods for their analysis, prediction and discovery. The book also presents an overview of exploring gene regulatory networks, chromatin, and miRNAs. Information about state-of-the-art techniques for the determination of TF - cis-element interactions in vivo and in silico give cutting edge insights on how genomic-scale research is being approached. The Analysis of Regulatory DNA provides readers with both the necessary background knowledge and provocative, up-to-date insights aimed at sparking new and vibrant experimental designs for understanding and predicting cis-elements in the eukaryotic genome.
Author: Ekaterina Shelest
Publisher: Frontiers Media SA
ISBN: 2889199673
Category : Biotechnology
Languages : en
Pages : 191
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Book Description
Transcription regulation is a complex process that can be considered and investigated from different perspectives. Traditionally and due to technical reasons (including the evolution of our understanding of the underlying processes) the main focus of the research was made on the regulation of expression through transcription factors (TFs), the proteins directly binding to DNA. On the other hand, intensive research is going on in the field of chromatin structure, remodeling and its involvement in the regulation. Whatever direction we select, we can speak about several levels of regulation. For instance, concentrating on TFs, we should consider multiple regulatory layers, starting with signaling pathways and ending up with the TF binding sites in the promoters and other regulatory regions. However, it is obvious that the TF regulation, also including the upstream processes, represents a modest portion of all processes leading to gene expression. For more comprehensive description of the gene regulation, we need a systematic and holistic view, which brings us to the importance of systems biology approaches. Advances in methodology, especially in high-throughput methods, result in an ever-growing mass of data, which in many cases is still waiting for appropriate consideration. Moreover, the accumulation of data is going faster than the development of algorithms for their systematic evaluation. Data and methods integration is indispensable for the acquiring a systematic as well as a systemic view. In addition to the huge amount of molecular or genetic components of a biological system, the even larger number of their interactions constitutes the enormous complexity of processes occurring in a living cell (organ, organism). In systems biology, these interactions are represented by networks. Transcriptional or, more generally, gene regulatory networks are being generated from experimental ChIPseq data, by reverse engineering from transcriptomics data, or from computational predictions of transcription factor (TF) – target gene relations. While transcriptional networks are now available for many biological systems, mathematical models to simulate their dynamic behavior have been successfully developed for metabolic and, to some extent, for signaling networks, but relatively rarely for gene regulatory networks. Systems biology approaches provide new perspectives that raise new questions. Some of them address methodological problems, others arise from the newly obtained understanding of the data. These open questions and problems are also a subject of this Research Topic.
Author: Juliusz Ashot Kozak
Publisher: CRC Press
ISBN: 149875273X
Category : Science
Languages : en
Pages : 343
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Book Description
Calcium Entry Channels in Non-Excitable Cells focuses on methods of investigating the structure and function of non-voltage gated calcium channels. Each chapter presents important discoveries in calcium entry pathways, specifically dealing with the molecular identification of store-operated calcium channels which were reviewed by earlier volumes in the Methods in Signal Transduction series. Crystallographic and pharmacological approaches to the study of calcium channels of epithelial cells are also discussed. Calcium ion is a messenger in most cell types. Whereas voltage gated calcium channels have been studied extensively, the non-voltage gated calcium entry channel genes have only been identified relatively recently. The book will fill this important niche.
Author: Sang Yeol Lee
Publisher: Frontiers Media SA
ISBN: 2889634914
Category :
Languages : en
Pages : 336
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Book Description
Plant responses to environmental stress are governed by complex molecular and biochemical signal transduction processes, which act in coordination to determine tolerance or sensitivity at the whole plant level. Upon exposure to abiotic stress, plants express a sophisticated coordinated response to reprogram interconnected defense networks and metabolic pathways, by alterations in the transcription, translation, and post-translational modification of defense-related genes and proteins. Traditionally, physiological and phenotypic responses were the major ones to be collected in plant stress biology. However, modern studies include the identification of key genes that influence stress tolerance and plant growth under the imposing stress and the verification of gene functions using knock out mutants or overexpression lines. In addition, genomics has become a necessary tool for the understanding of plant stress responses at the whole genome levels. The identification of stress-tolerant plant resources and the investigation of the functional role of the genetic variants is also a valuable tool in this research field. Recently, the advent of CRISPR/Cas genome editing technology, enables these variations to be introduced in crops for improved stress tolerance traits. Through the understanding of the molecular mechanisms involved in plant signaling in response to abiotic stress and crop performance characters under stress conditions, we hope to open new ways for the breeding of superior crops.
Author: Kerstin Kaufmann
Publisher: Springer Nature
ISBN: 1071633546
Category :
Languages : en
Pages : 380
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Book Description
Author: Yunbo Luo
Publisher: John Wiley & Sons
ISBN: 139418767X
Category : Science
Languages : en
Pages : 244
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Book Description
Understand the critical factors in fruit development with this up-to-date guide Fruit is an essential part of the human diet, and fruit production has never been more central to global human nutrition and public health. Fruit ripening is a vital stage in the emergence of nutrient-rich food, and modifications to the fruit development process can impact flavor, texture, nutritional value, and more. The process of ripening is controlled by nearly sixty transcription factors (TFs), a proper understanding of which is therefore crucial to regulating fruit quality and competing in the global food marketplace. Transcriptional Regulation of Flesh Fruit Development and Ripening is a comprehensive introduction to recent developments in the study of fruit ripening, focusing especially on these transcription factors. It details the major families of transcription factors and their properties, as well as providing methods for screening and identifying transcription factors to aid in genetic modification of fruit. The result is a thorough, accessible reference to a critical set of factors in fruit development. Transcriptional Regulation of Flesh Fruit Development and Ripening readers will also find: Detailed regulation of transcription factor families including MADS-box, NAC, ethylene response factor, and more Discussion of both climacteric and non-climacteric fruits throughout Analysis of how multiple TFs interact to influence fruit ripening Transcriptional Regulation of Flesh Fruit Development and Ripening is a must-have volume for food scientists, horticultural researchers, agriculturalists, and graduate students working in these or related fields.
