Computational Genomics

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Introduction To Computational Genomics

Author : Nello Cristianini
ISBN : 9781139460156
Genre : Computers
File Size : 46.14 MB
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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.
Category: Computers

Applied Computational Genomics

Author : Yin Yao Shugart
ISBN : 9789400755581
Genre : Medical
File Size : 58.3 MB
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"Applied Computational Genomics" focuses on an in-depth review of statistical development and application in the area of human genomics including candidate gene mapping, linkage analysis, population-based, genome-wide association, exon sequencing and whole genome sequencing analysis. The authors are extremely experienced in the area of statistical genomics and will give a detailed introduction of the evolution in the field and critical evaluations of the advantages and disadvantages of the statistical models proposed. They will also share their views on a future shift toward translational biology. The book will be of value to human geneticists, medical doctors, health educators, policy makers, and graduate students majoring in biology, biostatistics, and bioinformatics. Dr. Yin Yao Shugart is investigator in the Intramural Research Program at the National Institute of Mental Health, Bethesda, Maryland USA. ​
Category: Medical

Computational Genomics

Author : Richard P. Grant
ISBN : 1904933017
Genre : Science
File Size : 84.61 MB
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"Suitable for bioscientists who are just getting to grips with computational biology the book also offers enough detail to act as a guide for experienced bioinformaticians at the cutting edge of the technology. The book is also useful as a teaching reference."--BOOK JACKET.
Category: Science

Computational Genetics And Genomics

Author : Gary Peltz
ISBN : 9781592599301
Genre : Medical
File Size : 78.85 MB
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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.
Category: Medical

Computational Genomics With R

Author : Altuna Akalin
ISBN : 1498781853
Genre :
File Size : 48.59 MB
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Computational Genomics with R provides a starting point for beginners of genomic data analysis and also guides the 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. It 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. 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: - get the basics of R and dive right into specialized uses of R for computational genomics such as using Bioconductor packages. - be familiar with statistics, supervised and unsupervised learning techniques which are important in data modeling and exploratory analysis of high-dimensional data - understand genomic intervals and operations on them, which are used for tasks such as aligned read counting and genomic feature annotation - learn about the basics of processing and quality checking high-throughput sequencing data - be able to do sequence analysis, such as calculating GC content for parts of a genome or find transcription factor binding sites - learn about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization - be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq - learn basic techniques to integrate and interpret multi-omics datasets
Category:

Computational Genome Analysis

Author : Richard C. Deonier
ISBN : 0387987851
Genre : Computers
File Size : 47.15 MB
Format : PDF
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This book presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. The book features a free download of the R software statistics package and the text provides great crossover material that is interesting and accessible to students in biology, mathematics, statistics and computer science. More than 100 illustrations and diagrams reinforce concepts and present key results from the primary literature. Exercises are given at the end of chapters.
Category: Computers

Frontiers In Computational Genomics

Author : Michael Y. Galperin
ISBN : 0954246446
Genre : Science
File Size : 64.38 MB
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Bioinformatics is a new and fast expanding area of biology encompassing the organization, analysis and interpretation of the huge amount of data emerging from sequencing and genome projects. Major new programs, software and internet facilities have evolved recently that enable bioinformatic analysis at the whole genome level and more novel technologies are currently being developed. Written by experts in the field, this concise yet informative volume covers all aspects of bioinformatics pertaining to genomic studies. It is an essential book for anyone involved in genomic science or bioinformatics.
Category: Science

Bioinformatics And Computational Genomics

Author : Lee Kozar
ISBN : 1405124377
Genre : Science
File Size : 76.20 MB
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As the bioinformatics course has begun to evolve it has become clear that students need a cohesive picture of what bioinformatics is, what methods it employs, how genomes are analyzed and also a solid understanding of its biological, mathematical and statistical underpinnings. This text covers a complete range of the key topics and provides a useful learning and teaching format complete with coverage of free software and exercises.
Category: Science

Ethics Computing And Genomics

Author : Herman T. Tavani
ISBN : 0763736201
Genre : Computers
File Size : 60.35 MB
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Comprised of eighteen chapters contributed by experts in the fields of biology, computer science, information technology, law, and philosophy, Ethics, Computing, and Genomics provides instructors with a flexible resource for undergraduate and graduate courses in an exciting new field of applied ethics: computational genomics. The chapters are organized in a way that takes the reader from a discussion of conceptual frameworks and methodological perspectives, including ethical theory, to an in-depth analysis of controversial issues involving privacy and confidentiality, information consent, and intellectual property. The volume concludes with some predictions about the future of computational genomics, including the role that nanotechnology will likely play as biotechnologies and information technologies continue to converge.
Category: Computers

Computational Genetics

Author : Rajiv Tyagi
ISBN : 818356464X
Genre : Medical genetics
File Size : 59.30 MB
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Category: Medical genetics

Applied Computational Genomics

Author : Yin Yao
ISBN : 9789811310713
Genre : Medical
File Size : 87.90 MB
Format : PDF, Kindle
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The volume provides a review of statistical development and application in the area of human genomics, including candidate gene mapping, linkage analysis, population-based genome-wide association, exon sequencing, and whole genome sequencing analysis. The authors are extremely experienced in the field of statistical genomics and will give a detailed introduction to the evolution of the field, as well as critical comments on the advantages and disadvantages of the proposed statistical models. The future directions of translational biology will also be described.
Category: Medical

Computational Genomic Signatures

Author : Ozkan Ufuk Nalbantoglu
ISBN : 9781608451456
Genre : Computers
File Size : 28.18 MB
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This text introduces the general concept of computational genomic signatures, and it reviews some of the DNA sequence models which can be used as computational genomic signatures. The text takes the position that a practical computational genomic signature consists of both a model and a measure for computing the distance or similarity between models. Therefore, a discussion of sequence similarity/distance measurement in the context of computational genomic signatures is presented.
Category: Computers

Current Topics In Computational Molecular Biology

Author : Tao Jiang
ISBN : 0262100924
Genre : Science
File Size : 76.52 MB
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A survey of current topics in computational molecular biology. Computational molecular biology, or bioinformatics, draws on the disciplines of biology, mathematics, statistics, physics, chemistry, computer science, and engineering. It provides the computational support for functional genomics, which links the behavior of cells, organisms, and populations to the information encoded in the genomes, as well as for structural genomics. At the heart of all large-scale and high-throughput biotechnologies, it has a growing impact on health and medicine. This survey of computational molecular biology covers traditional topics such as protein structure modeling and sequence alignment, and more recent ones such as expression data analysis and comparative genomics. It combines algorithmic, statistical, database, and AI-based methods for studying biological problems. The book also contains an introductory chapter, as well as one on general statistical modeling and computational techniques in molecular biology. Each chapter presents a self-contained review of a specific subject. Not for sale in China, including Hong Kong.
Category: Science

Computational Analysis Of The Mammalian Cis Regulatory Landscape

Author :
ISBN : STANFORD:jh459nm5080
Genre :
File Size : 89.44 MB
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Improvements in DNA sequencing technologies have made it possible to determine the genetic makeup of many organisms. Computational analyses of the massive amounts of sequence data available have produced many insights into evolutionary and developmental biology. For example, comparison of the full genome sequences of human and mouse discovered that the majority of functional sequence in the human genome does not code for protein. Much of this functional non-coding sequence appears to act in a regulatory role, dictating the precise tissues and developmental time points in which each protein should be produced. This dissertation describes three major contributions to the computational analysis of regulatory elements. First, I describe the Genomic Regions Enrichment of Annotations Tool (GREAT), a novel statistical method and associated web-based tool developed to infer the biological functions of regulatory elements based on the functions of their putative target genes. I demonstrate its marked improvement over current methods at interpreting functional enrichment signals for a variety of regulatory element types. Next, I discuss a computational methodology developed to identify medium- to large-scale (10-100,000 nucleotide) genomic deletions from whole genome sequences of multiple mammals. Using this methodology, I quantify the dispensability of highly conserved non-coding elements (CNEs) as their likelihood to be deleted in a subset of species. Despite their genomic prevalence and apparent redundancy in function, CNEs are very rarely lost in extant species. Even more surprisingly, there is a very weak relationship between dispensability and nucleotide conservation level. Sequences under purifying selection at moderate levels of nucleotide conservation are lost at a rate similar to those at perfect sequence conservation. Instead, evolutionary resistance to loss is more strongly correlated with depth of sequence homology, as ancient enhancers are more resistant to deletion than ones that arose more recently in evolution. Finally, I present the discovery and analysis of human-specific genomic deletions. By comparing the genome sequences of five species including human and our nearest ape relative, the chimpanzee, I identified 583 regions present in non-human species that contain highly-conserved sequence but are surprisingly deleted in humans. Statistical analyses indicate that these deletions occur preferentially near steroid hormone receptor genes and brain-expressed genes that are known to inhibit proliferation. Experimental results provide particular examples that may have contributed to unique human traits: the loss of an AR enhancer is correlated with the human loss of penile spines and sensory vibrissae, and the loss of a GADD45G enhancer is correlated with the human expansion of the cerebral cortex.
Category:

Sequence Evolution Function

Author : Eugene Koonin
ISBN : 1402072740
Genre : Science
File Size : 68.82 MB
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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.
Category: Science

Computational And Statistical Approaches To Genomics

Author : Wei Zhang
ISBN : 0387262881
Genre : Science
File Size : 60.43 MB
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The second edition of this book adds eight new contributors to reflect a modern cutting edge approach to genomics. It contains the newest research results on genomic analysis and modeling using state-of-the-art methods from engineering, statistics, and genomics. These tools and models are then applied to real biological and clinical problems. The book’s original seventeen chapters are also updated to provide new initiatives and directions.
Category: Science