Computational Methods For High Throughput Genomics And Transcriptomics

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Computational Genomics with R

Author : Altuna Akalin
Publisher : CRC Press
ISBN 13 : 1498781861
Total Pages : 463 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Computational Genomics with R by : Altuna Akalin

Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Evolution of Translational Omics

Author : Institute of Medicine
Publisher : National Academies Press
ISBN 13 : 0309224187
Total Pages : 354 pages
Book Rating : 4.3/5 (92 download)

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Book Synopsis Evolution of Translational Omics by : Institute of Medicine

Download or read book Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.

Computational Methods for Single-Cell Data Analysis

Author : Guo-Cheng Yuan
Publisher : Humana Press
ISBN 13 : 9781493990566
Total Pages : 271 pages
Book Rating : 4.9/5 (95 download)

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Book Synopsis Computational Methods for Single-Cell Data Analysis by : Guo-Cheng Yuan

Download or read book Computational Methods for Single-Cell Data Analysis written by Guo-Cheng Yuan and published by Humana Press. This book was released on 2019-02-14 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book provides state-of-art computational approaches to further explore the exciting opportunities presented by single-cell technologies. Chapters each detail a computational toolbox aimed to overcome a specific challenge in single-cell analysis, such as data normalization, rare cell-type identification, and spatial transcriptomics analysis, all with a focus on hands-on implementation of computational methods for analyzing experimental data. 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. Authoritative and cutting-edge, Computational Methods for Single-Cell Data Analysis aims to cover a wide range of tasks and serves as a vital handbook for single-cell data analysis.

Transcriptomics and Gene Regulation

Author : Jiaqian Wu
Publisher : Springer
ISBN 13 : 9401774501
Total Pages : 190 pages
Book Rating : 4.4/5 (17 download)

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Book Synopsis Transcriptomics and Gene Regulation by : Jiaqian Wu

Download or read book Transcriptomics and Gene Regulation written by Jiaqian Wu and published by Springer. This book was released on 2015-11-17 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on modern computational and statistical tools for translational gene expression and regulation research to improve prognosis, diagnostics, prediction of severity, and therapies for human diseases. It introduces some of state of the art technologies as well as computational and statistical tools for translational bioinformatics in the areas of gene transcription and regulation, including the tools for next generation sequencing analyses, alternative spicing, the modeling of signaling pathways, network analyses in predicting disease genes, as well as protein and gene expression data integration in complex human diseases etc. The book is particularly useful for researchers and students in the field of molecular biology, clinical biology and bioinformatics, as well as physicians etc. Dr. Jiaqian Wu is assistant professor in the Vivian L. Smith Department of Neurosurgery and Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Centre, Houston, TX, USA.

Computing for Comparative Microbial Genomics

Author : David Wayne Ussery
Publisher : Springer Science & Business Media
ISBN 13 : 1848002548
Total Pages : 272 pages
Book Rating : 4.8/5 (48 download)

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Book Synopsis Computing for Comparative Microbial Genomics by : David Wayne Ussery

Download or read book Computing for Comparative Microbial Genomics written by David Wayne Ussery and published by Springer Science & Business Media. This book was released on 2009-02-26 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.

Gene Quantification

Author : Francois Ferre
Publisher : Springer Science & Business Media
ISBN 13 : 1461241642
Total Pages : 379 pages
Book Rating : 4.4/5 (612 download)

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Book Synopsis Gene Quantification by : Francois Ferre

Download or read book Gene Quantification written by Francois Ferre and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: Geneticists and molecular biologists have been interested in quantifying genes and their products for many years and for various reasons (Bishop, 1974). Early molecular methods were based on molecular hybridization, and were devised shortly after Marmur and Doty (1961) first showed that denaturation of the double helix could be reversed - that the process of molecular reassociation was exquisitely sequence dependent. Gillespie and Spiegelman (1965) developed a way of using the method to titrate the number of copies of a probe within a target sequence in which the target sequence was fixed to a membrane support prior to hybridization with the probe - typically a RNA. Thus, this was a precursor to many of the methods still in use, and indeed under development, today. Early examples of the application of these methods included the measurement of the copy numbers in gene families such as the ribosomal genes and the immunoglo bulin family. Amplification of genes in tumors and in response to drug treatment was discovered by this method. In the same period, methods were invented for estimating gene num bers based on the kinetics of the reassociation process - the so-called Cot analysis. This method, which exploits the dependence of the rate of reassociation on the concentration of the two strands, revealed the presence of repeated sequences in the DNA of higher eukaryotes (Britten and Kohne, 1968). An adaptation to RNA, Rot analysis (Melli and Bishop, 1969), was used to measure the abundance of RNAs in a mixed population.

Distributed, High-Performance and Grid Computing in Computational Biology

Author : Werner Dubitzky
Publisher : Springer Science & Business Media
ISBN 13 : 3540698418
Total Pages : 202 pages
Book Rating : 4.5/5 (46 download)

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Book Synopsis Distributed, High-Performance and Grid Computing in Computational Biology by : Werner Dubitzky

Download or read book Distributed, High-Performance and Grid Computing in Computational Biology written by Werner Dubitzky and published by Springer Science & Business Media. This book was released on 2007-01-03 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book constitutes the refereed proceedings of the International Workshop on Distributed, High-Performance and Grid Computing in Computational Biology, GCCB 2006, held in Eilat, Israel in January 2007 in conjunction with the 5th European Conference on Computational Biology, ECCB 2006. The 13 revised full papers presented were carefully reviewed and selected from many high quality submissions.

Population Genetics

Author :
Publisher : BoD – Books on Demand
ISBN 13 : 0850140579
Total Pages : 214 pages
Book Rating : 4.8/5 (51 download)

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Book Synopsis Population Genetics by :

Download or read book Population Genetics written by and published by BoD – Books on Demand. This book was released on 2024-04-18 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines the importance of DNA molecules as fundamental genomic elements in different types of organisms. In recent years, a wide range of tools and techniques have become available to investigate the versatility of genomic variabilities, exchanges, and differentiations. This book presents data and information from population genetics and evolutionary biology, making it a useful resource for scientists worldwide.

Encyclopedia of Bioinformatics and Computational Biology

Author :
Publisher : Elsevier
ISBN 13 : 0128114320
Total Pages : 3421 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Encyclopedia of Bioinformatics and Computational Biology by :

Download or read book Encyclopedia of Bioinformatics and Computational Biology written by and published by Elsevier. This book was released on 2018-08-21 with total page 3421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

Genomics, Proteomics, and Clinical Bacteriology

Author : Neil Woodford
Publisher : Springer Science & Business Media
ISBN 13 : 1592597637
Total Pages : 391 pages
Book Rating : 4.5/5 (925 download)

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Book Synopsis Genomics, Proteomics, and Clinical Bacteriology by : Neil Woodford

Download or read book Genomics, Proteomics, and Clinical Bacteriology written by Neil Woodford and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gazing into crystal balls is beyond the expertise of most scientists. Yet, as we look further into the 21st century, one does not have to be Nostradamus to predict that the current genomics and proteomics "revolution" will have an immense impact on medical bacteriology. This impact is already being re- ized in many academic departments, and although encroachment on routine diagnostic bacteriology, particularly in the hospital setting, is likely to occur at a slower pace, it remains nonetheless inevitable. Therefore, it is important that no one working in bacteriology should find themselves distanced from these fundamental developments. The involvement of all clinical bacteriologists is essential if the significant achievements of genome sequencing and analysis are to be turned into tangible advances, with resulting benefits for patient care and m- agement. It is our hope that Genomics, Proteomics, and Clinical Bacteriology: Methods and Reviews will play a part in bringing such a development to fruition. The advances in genomics and proteomics have already given us frequent opportunities to reassess our knowledge and understanding of established b- terial adversaries, and have provided us with the means to identify new foes. The new knowledge gained is enabling us to reconsider, for example, our c- cepts of bacterial pathogenicity, phylogeny and novel targets for antibacterial chemotherapy. These topics, and others, are considered in Genomics, Proteomics, and Clinical Bacteriology: Methods and Reviews.

Bioinformatics and Computational Biology Solutions Using R and Bioconductor

Author : Robert Gentleman
Publisher : Springer Science & Business Media
ISBN 13 : 0387293620
Total Pages : 478 pages
Book Rating : 4.3/5 (872 download)

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Book Synopsis Bioinformatics and Computational Biology Solutions Using R and Bioconductor by : Robert Gentleman

Download or read book Bioinformatics and Computational Biology Solutions Using R and Bioconductor written by Robert Gentleman and published by Springer Science & Business Media. This book was released on 2005-12-29 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: Full four-color book. Some of the editors created the Bioconductor project and Robert Gentleman is one of the two originators of R. All methods are illustrated with publicly available data, and a major section of the book is devoted to fully worked case studies. Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.

Advanced Data Mining Technologies in Bioinformatics

Author : Hui-Huang Hsu
Publisher : IGI Global
ISBN 13 : 1591408636
Total Pages : 343 pages
Book Rating : 4.5/5 (914 download)

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Book Synopsis Advanced Data Mining Technologies in Bioinformatics by : Hui-Huang Hsu

Download or read book Advanced Data Mining Technologies in Bioinformatics written by Hui-Huang Hsu and published by IGI Global. This book was released on 2006-01-01 with total page 343 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book covers research topics of data mining on bioinformatics presenting the basics and problems of bioinformatics and applications of data mining technologies pertaining to the field"--Provided by publisher.

Multidisciplinary Approaches to Theory in Medicine

Author : Ray Paton
Publisher : Elsevier
ISBN 13 : 0444518061
Total Pages : 570 pages
Book Rating : 4.4/5 (445 download)

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Book Synopsis Multidisciplinary Approaches to Theory in Medicine by : Ray Paton

Download or read book Multidisciplinary Approaches to Theory in Medicine written by Ray Paton and published by Elsevier. This book was released on 2006 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume will be a collection of chapters from authors with wide experience in their research field. The purpose is to produce a coherent book that reflects the common theme of theory in medical thinking and multidisciplinary research practice. In this context "theory" relates to frameworks of concepts, facts, models etc that help to inform practitioners (clinicians, scientists and engineers) both within their own fields and as they seek to share dialogue with colleagues from other fields. Multidisciplinary Approaches to Theory in Medicine will therefore be integrative across a broad spectrum of fields within medicine. To achieve this the chapters will be associated with others in a number of meaningful ways. Each chapter will share a number of points of contact that will include at least two of the following: Similar biomedical area (e.g., immunity, neuroscience, endocrinology, pathology, oncology, haematology, .) Similar multidisciplinary theoretical contexts (e.g., modelling, analysis, description, visualization, complex systems, .) Similar multidisciplinary medical issues and questions (e.g., clinical practice, decision making, informatics, .) Uniquely explores role of interdisciplinary exchange in the development and expansion of medical theory Timely and insightful essays on the growth and development of medical theories from some of the world's top clinicians and medical researchers, including Werner Arber, Frank Vertosick, and David Weatherall Assembles diverse perspectives on medicine and physiology from biology, statistics, ethics, computer science, philosophy, history Uniquely illuminates the social and historical processes through which theoretical research translates into clinical practice Reveals the growing role of technology, especially computational modelling, in changing the nature of Western medicine

Handbook of Personalized Medicine

Author : Ioannis S. Vizirianakis
Publisher : CRC Press
ISBN 13 : 9814411205
Total Pages : 1512 pages
Book Rating : 4.8/5 (144 download)

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Book Synopsis Handbook of Personalized Medicine by : Ioannis S. Vizirianakis

Download or read book Handbook of Personalized Medicine written by Ioannis S. Vizirianakis and published by CRC Press. This book was released on 2014-02-12 with total page 1512 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book compiles multidisciplinary efforts to conceptualize the environment in research and clinical setting that creates the fertile ground for the practical utility of personalized medicine decisions and also enables clinical pharmacogenomics for establishing pharmacotyping in drug prescription. Its covers innovative drug formulations and nanot

Systems Biology Approaches: Prevention, Diagnosis, and Understanding Mechanisms of Complex Diseases

Author : Sanket Joshi
Publisher : Springer Nature
ISBN 13 : 9819994624
Total Pages : 587 pages
Book Rating : 4.8/5 (199 download)

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

Download or read book Systems Biology Approaches: Prevention, Diagnosis, and Understanding Mechanisms of Complex Diseases written by Sanket Joshi and published by Springer Nature. This book was released on with total page 587 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Gene Network Inference

Author : Alberto Fuente
Publisher : Springer Science & Business Media
ISBN 13 : 3642451616
Total Pages : 135 pages
Book Rating : 4.6/5 (424 download)

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Book Synopsis Gene Network Inference by : Alberto Fuente

Download or read book Gene Network Inference written by Alberto Fuente and published by Springer Science & Business Media. This book was released on 2014-01-03 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents recent methods for Systems Genetics (SG) data analysis, applying them to a suite of simulated SG benchmark datasets. Each of the chapter authors received the same datasets to evaluate the performance of their method to better understand which algorithms are most useful for obtaining reliable models from SG datasets. The knowledge gained from this benchmarking study will ultimately allow these algorithms to be used with confidence for SG studies e.g. of complex human diseases or food crop improvement. The book is primarily intended for researchers with a background in the life sciences, not for computer scientists or statisticians.

Potato Improvement in the Post-Genomics Era

Author : Jagesh Tiwari
Publisher : CRC Press
ISBN 13 : 1000823539
Total Pages : 463 pages
Book Rating : 4.0/5 (8 download)

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Book Synopsis Potato Improvement in the Post-Genomics Era by : Jagesh Tiwari

Download or read book Potato Improvement in the Post-Genomics Era written by Jagesh Tiwari and published by CRC Press. This book was released on 2022-12-23 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book delves into post-genomics advances in potato improvement since the potato genome sequencing in 2011. It includes recent developments in the field of potato genetic resources, genes and SNP markers discovery, and the progress in next-generation breeding applying various omics technologies and modern sequencing tools. It covers cutting-edge technologies in potato - a global perspective, genome sequencing and resequencing of various cultivated and wild species, potato germplasm management and characterization, prebreeding genomics, genome mapping and gene cloning, markers discovery, marker-assisted selection, transgenics, microRNAs, transcriptomics, proteomics, metabolomics, phenomics, next-generation potato breeding technologies including genome editing and genomic selection and bioinformatics applications in the post-genomics era in potato. As genome editing and genomic selection have become emerging tools in crop improvement including potato, several research works have been demonstrated and applied world over. This book concentrates on genomics-aided characterization of germplasm and markers discovery to accelerate potato breeding. Further, various omics technologies strengthen our understanding on discovery of new genes/proteins/metabolites and key traits based on high-throughput phenotyping involved in various biotic and abiotic stresses in potato crop. The book is a useful source of information related to genomics-led research and development of this crop. It will serve as a valuable resource for potato researchers working in the area of molecular biology and would be beneficial for college students, PhD scholars, scientists, academicians, farmers and policy makers.