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 462 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.
Download or read book Introduction to Computational Genomics written by Nello Cristianini and published by Cambridge University Press. This book was released on 2006-12-14 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: Where did SARS come from? Have we inherited genes from Neanderthals? How do plants use their internal clock? The genomic revolution in biology enables us to answer such questions. But the revolution would have been impossible without the support of powerful computational and statistical methods that enable us to exploit genomic data. Many universities are introducing courses to train the next generation of bioinformaticians: biologists fluent in mathematics and computer science, and data analysts familiar with biology. This readable and entertaining book, based on successful taught courses, provides a roadmap to navigate entry to this field. It guides the reader through key achievements of bioinformatics, using a hands-on approach. Statistical sequence analysis, sequence alignment, hidden Markov models, gene and motif finding and more, are introduced in a rigorous yet accessible way. A companion website provides the reader with Matlab-related software tools for reproducing the steps demonstrated in the book.
Download or read book Computational Modeling of Genetic and Biochemical Networks written by James M. Bower and published by MIT Press. This book was released on 2001 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: How new modeling techniques can be used to explore functionally relevant molecular and cellular relationships.
Download or read book Computational Genetics written by Rajiv Tyagi and published by Discovery Publishing House. This book was released on 2009 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Introduction to Computational Biology written by Michael S. Waterman and published by CRC Press. This book was released on 2018-05-02 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology is in the midst of a era yielding many significant discoveries and promising many more. Unique to this era is the exponential growth in the size of information-packed databases. Inspired by a pressing need to analyze that data, Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences. This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps. It examines problems associated with reading DNA sequences and comparing sequences to finding common patterns. The author then considers that statistics of pattern counts in sequences, RNA secondary structure, and the inference of evolutionary history of related sequences. Introduction to Computational Biology exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology.
Download or read book Sequence Evolution Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.
Download or read book Bioinformatics and Computational Biology written by Basant K. Tiwary and published by Springer Nature. This book was released on 2021-11-23 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook introduces fundamental concepts of bioinformatics and computational biology to the students and researchers in biology, medicine, veterinary science, agriculture, and bioengineering . The respective chapters provide detailed information on biological databases, sequence alignment, molecular evolution, next-generation sequencing, systems biology, and statistical computing using R. The book also presents a case-based discussion on clinical, veterinary, agricultural bioinformatics, and computational bioengineering for application-based learning in the respective fields. Further, it offers readers guidance on reconstructing and analysing biological networks and highlights computational methods used in systems medicine and genome-wide association mapping of diseases. Given its scope, this textbook offers an essential introductory book on bioinformatics and computational biology for undergraduate and graduate students in the life sciences, botany, zoology, physiology, biotechnology, bioinformatics, and genomic science as well as systems biology, bioengineering and the agricultural, and veterinary sciences.
Download or read book Introduction to Computational Biology written by Bernhard Haubold and published by Springer Science & Business Media. This book was released on 2006-08-09 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written with the advanced undergraduate in mind, this book introduces into the field of Bioinformatics. The authors explain the computational and conceptional background to the analysis of large-scale sequence data. Many of the corresponding analysis methods are rooted in evolutionary thinking, which serves as a common thread throughout the book. The focus is on methods of comparative genomics and subjects covered include: alignments, gene finding, phylogeny, and the analysis of single nucleotide polymorphisms (SNPs). The volume contains exercises, questions & answers to selected problems.
Download or read book Computational Genetics and Genomics written by Gary Peltz and published by Springer Science & Business Media. This book was released on 2007-11-05 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ultimately, the quality of the tools available for genetic analysis and experimental disease models will be assessed on the basis of whether they provide new information that generates novel treatments for human disease. In addition, the time frame in which genetic discoveries impact clinical practice is also an important dimension of how society assesses the results of the significant public financial investment in genetic research. Because of the investment and the increased expectation that new tre- ments will be found for common diseases, allowing decades to pass before basic discoveries are made and translated into new therapies is no longer acceptable. Computational Genetics and Genomics: Tools for Understanding Disease provides an overview and assessment of currently available and developing tools for genetic analysis. It is hoped that these new tools can be used to identify the genetic basis for susceptibility to disease. Although this very broad topic is addressed in many other books and journal articles, Computational Genetics and Genomics: Tools for Understanding Disease focuses on methods used for analyzing mouse genetic models of biomedically - portant traits. This volume aims to demonstrate that commonly used inbred mouse strains can be used to model virtually all human disea- related traits. Importantly, recently developed computational tools will enable the genetic basis for differences in disease-related traits to be rapidly identified using these inbred mouse strains. On average, a decade is required to carry out the development process required to demonstrate that a new disease treatment is beneficial.
Download or read book Combinatorics of Genome Rearrangements written by Guillaume Fertin and published by MIT Press. This book was released on 2009 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive survey of a rapidly expanding field of combinatorial optimization, mathematically oriented but offering biological explanations when required. From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs dramatically, and the mutations that affect this organization are known as genome rearrangements. Combinatorial methods are used to reconstruct putative rearrangement scenarios in order to explain the evolutionary history of a set of species, often formalizing the evolutionary events that can explain the multiple combinations of observed genomes as combinatorial optimization problems. This book offers the first comprehensive survey of this rapidly expanding application of combinatorial optimization. It can be used as a reference for experienced researchers or as an introductory text for a broader audience. Genome rearrangement problems have proved so interesting from a combinatorial point of view that the field now belongs as much to mathematics as to biology. This book takes a mathematically oriented approach, but provides biological background when necessary. It presents a series of models, beginning with the simplest (which is progressively extended by dropping restrictions), each constructing a genome rearrangement problem. The book also discusses an important generalization of the basic problem known as the median problem, surveys attempts to reconstruct the relationships between genomes with phylogenetic trees, and offers a collection of summaries and appendixes with useful additional information.
Download or read book Statistical Modeling and Machine Learning for Molecular Biology written by Alan Moses and published by CRC Press. This book was released on 2017-01-06 with total page 281 pages. Available in PDF, EPUB and Kindle. Book excerpt: • Assumes no background in statistics or computers • Covers most major types of molecular biological data • Covers the statistical and machine learning concepts of most practical utility (P-values, clustering, regression, regularization and classification) • Intended for graduate students beginning careers in molecular biology, systems biology, bioengineering and genetics
Download or read book Computational Molecular Evolution written by Ziheng Yang and published by Oxford University Press, USA. This book was released on 2006-10-05 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.
Download or read book Computational Exome and Genome Analysis written by Peter N. Robinson and published by CRC Press. This book was released on 2017-09-13 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.
Download or read book Frontiers in Computational and Systems Biology written by Jianfeng Feng and published by Springer Science & Business Media. This book was released on 2010-06-14 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological and biomedical studies have entered a new era over the past two decades thanks to the wide use of mathematical models and computational approaches. A booming of computational biology, which sheerly was a theoretician’s fantasy twenty years ago, has become a reality. Obsession with computational biology and theoretical approaches is evidenced in articles hailing the arrival of what are va- ously called quantitative biology, bioinformatics, theoretical biology, and systems biology. New technologies and data resources in genetics, such as the International HapMap project, enable large-scale studies, such as genome-wide association st- ies, which could potentially identify most common genetic variants as well as rare variants of the human DNA that may alter individual’s susceptibility to disease and the response to medical treatment. Meanwhile the multi-electrode recording from behaving animals makes it feasible to control the animal mental activity, which could potentially lead to the development of useful brain–machine interfaces. - bracing the sheer volume of genetic, genomic, and other type of data, an essential approach is, ?rst of all, to avoid drowning the true signal in the data. It has been witnessed that theoretical approach to biology has emerged as a powerful and st- ulating research paradigm in biological studies, which in turn leads to a new - search paradigm in mathematics, physics, and computer science and moves forward with the interplays among experimental studies and outcomes, simulation studies, and theoretical investigations.
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.
Download or read book Introduction to Computational Genomics written by Nello Cristianini and published by Cambridge University Press. This book was released on 2006-12-14 with total page 7 pages. Available in PDF, EPUB and Kindle. Book excerpt: Where did SARS come from? Have we inherited genes from Neanderthals? How do plants use their internal clock? The genomic revolution in biology enables us to answer such questions. But the revolution would have been impossible without the support of powerful computational and statistical methods that enable us to exploit genomic data. Many universities are introducing courses to train the next generation of bioinformaticians: biologists fluent in mathematics and computer science, and data analysts familiar with biology. This readable and entertaining book, based on successful taught courses, provides a roadmap to navigate entry to this field. It guides the reader through key achievements of bioinformatics, using a hands-on approach. Statistical sequence analysis, sequence alignment, hidden Markov models, gene and motif finding and more, are introduced in a rigorous yet accessible way. A companion website provides the reader with Matlab-related software tools for reproducing the steps demonstrated in the book.
Download or read book Computational Biology written by Röbbe Wünschiers and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: -Teaches the reader how to use Unix, which is the key to basic computing and allows the most flexibility for bioinformatics applications -Written specifically with the needs of molecular biologists in mind -Easy to follow, written for beginners with no computational knowledge -Includes examples from biological data analysis -Can be use either for self-teaching or in courses
