Bioinformatics Algorithms

An Active Learning Approach

Author: Phillip Compeau,Pavel Pevzner

Publisher: N.A

ISBN: 9780990374602

Category: Bioinformatics

Page: 392

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Bioinformatics Algorithms: an Active Learning Approach is one of the first textbooks to emerge from the recent Massive Open Online Course (MOOC) revolution. A light-hearted and analogy-filled companion to the authors' acclaimed MOOC on Coursera, this book presents students with a dynamic approach to learning bioinformatics. It strikes a unique balance between practical challenges in modern biology and fundamental algorithmic ideas, thus capturing the interest of students of both biology and computer science. Each chapter begins with a central biological question, such as "Are There Fragile Regions in the Human Genome?" or "Which DNA Patterns Play the Role of Molecular Clocks?" and then steadily develops the algorithmic sophistication required to answer this question. Hundreds of exercises are incorporated directly into the text as soon as they are needed; readers can test their knowledge through automated coding challenges on the Rosalind Bioinformatics Textbook Track. A website augments the textbook by providing additional educational materials, including video lectures and PowerPoint slides.--Book website.

Bioinformatics for Biologists

Author: Pavel Pevzner,Ron Shamir

Publisher: Cambridge University Press

ISBN: 1139501615

Category: Science

Page: N.A

View: 9210

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The computational education of biologists is changing to prepare students for facing the complex datasets of today's life science research. In this concise textbook, the authors' fresh pedagogical approaches lead biology students from first principles towards computational thinking. A team of renowned bioinformaticians take innovative routes to introduce computational ideas in the context of real biological problems. Intuitive explanations promote deep understanding, using little mathematical formalism. Self-contained chapters show how computational procedures are developed and applied to central topics in bioinformatics and genomics, such as the genetic basis of disease, genome evolution or the tree of life concept. Using bioinformatic resources requires a basic understanding of what bioinformatics is and what it can do. Rather than just presenting tools, the authors - each a leading scientist - engage the students' problem-solving skills, preparing them to meet the computational challenges of their life science careers.

Genome-Scale Algorithm Design

Biological Sequence Analysis in the Era of High-Throughput Sequencing

Author: Veli Mäkinen,Djamal Belazzougui,Fabio Cunial,Alexandru I. Tomescu

Publisher: Cambridge University Press

ISBN: 1316342948

Category: Science

Page: N.A

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High-throughput sequencing has revolutionised the field of biological sequence analysis. Its application has enabled researchers to address important biological questions, often for the first time. This book provides an integrated presentation of the fundamental algorithms and data structures that power modern sequence analysis workflows. The topics covered range from the foundations of biological sequence analysis (alignments and hidden Markov models), to classical index structures (k-mer indexes, suffix arrays and suffix trees), Burrows–Wheeler indexes, graph algorithms and a number of advanced omics applications. The chapters feature numerous examples, algorithm visualisations, exercises and problems, each chosen to reflect the steps of large-scale sequencing projects, including read alignment, variant calling, haplotyping, fragment assembly, alignment-free genome comparison, transcript prediction and analysis of metagenomic samples. Each biological problem is accompanied by precise formulations, providing graduate students and researchers in bioinformatics and computer science with a powerful toolkit for the emerging applications of high-throughput sequencing.

An Introduction to Bioinformatics Algorithms

Author: Neil C. Jones,Pavel A. Pevzner,Pavel Pevzner

Publisher: MIT Press

ISBN: 9780262101066

Category: Computers

Page: 435

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Algorithms and Complexity. Molecular Biology Primer. Exhaustive Search. Greedy Algorithms. Dynamic Programming Algorithms. Divide-and-Conquer Algorithms. Graph Algorithms. Combinatorial Pattern Matching. Clustering and Trees. Hidden Markov Models. Randomized Algorithms.

Bioinformatics

The Machine Learning Approach

Author: Pierre Baldi,Søren Brunak,Professor Pierre Baldi,Francis Bach

Publisher: MIT Press

ISBN: 9780262025065

Category: Computers

Page: 452

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Pierre Baldi and Soren Brunak present the key machine learning approaches and apply them to the computational problems encountered in the analysis of biological data. The book is aimed at two types of researchers and students. First are the biologists and biochemists who need to understand new data-driven algorithms, such as neural networks and hidden Markov models, in the context of biological sequences and their molecular structure and function. Second are those with a primary background in physics, mathematics, statistics, or computer science who need to know more about specific applications in molecular biology.

Introduction to Information Retrieval

Author: Christopher D. Manning,Prabhakar Raghavan,Hinrich Schütze

Publisher: Cambridge University Press

ISBN: 1139472100

Category: Computers

Page: N.A

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Class-tested and coherent, this textbook teaches classical and web information retrieval, including web search and the related areas of text classification and text clustering from basic concepts. It gives an up-to-date treatment of all aspects of the design and implementation of systems for gathering, indexing, and searching documents; methods for evaluating systems; and an introduction to the use of machine learning methods on text collections. All the important ideas are explained using examples and figures, making it perfect for introductory courses in information retrieval for advanced undergraduates and graduate students in computer science. Based on feedback from extensive classroom experience, the book has been carefully structured in order to make teaching more natural and effective. Slides and additional exercises (with solutions for lecturers) are also available through the book's supporting website to help course instructors prepare their lectures.

The Elements of Statistical Learning

Data Mining, Inference, and Prediction

Author: Trevor Hastie,Robert Tibshirani,Jerome Friedman

Publisher: Springer Science & Business Media

ISBN: 0387216065

Category: Mathematics

Page: 536

View: 9016

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During the past decade there has been an explosion in computation and information technology. With it have come vast amounts of data in a variety of fields such as medicine, biology, finance, and marketing. The challenge of understanding these data has led to the development of new tools in the field of statistics, and spawned new areas such as data mining, machine learning, and bioinformatics. Many of these tools have common underpinnings but are often expressed with different terminology. This book describes the important ideas in these areas in a common conceptual framework. While the approach is statistical, the emphasis is on concepts rather than mathematics. Many examples are given, with a liberal use of color graphics. It should be a valuable resource for statisticians and anyone interested in data mining in science or industry. The book’s coverage is broad, from supervised learning (prediction) to unsupervised learning. The many topics include neural networks, support vector machines, classification trees and boosting---the first comprehensive treatment of this topic in any book. This major new edition features many topics not covered in the original, including graphical models, random forests, ensemble methods, least angle regression & path algorithms for the lasso, non-negative matrix factorization, and spectral clustering. There is also a chapter on methods for “wide” data (p bigger than n), including multiple testing and false discovery rates. Trevor Hastie, Robert Tibshirani, and Jerome Friedman are professors of statistics at Stanford University. They are prominent researchers in this area: Hastie and Tibshirani developed generalized additive models and wrote a popular book of that title. Hastie co-developed much of the statistical modeling software and environment in R/S-PLUS and invented principal curves and surfaces. Tibshirani proposed the lasso and is co-author of the very successful An Introduction to the Bootstrap. Friedman is the co-inventor of many data-mining tools including CART, MARS, projection pursuit and gradient boosting.

Data Mining: Concepts and Techniques

Author: Jiawei Han,Jian Pei,Micheline Kamber

Publisher: Elsevier

ISBN: 9780123814807

Category: Computers

Page: 744

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Data Mining: Concepts and Techniques provides the concepts and techniques in processing gathered data or information, which will be used in various applications. Specifically, it explains data mining and the tools used in discovering knowledge from the collected data. This book is referred as the knowledge discovery from data (KDD). It focuses on the feasibility, usefulness, effectiveness, and scalability of techniques of large data sets. After describing data mining, this edition explains the methods of knowing, preprocessing, processing, and warehousing data. It then presents information about data warehouses, online analytical processing (OLAP), and data cube technology. Then, the methods involved in mining frequent patterns, associations, and correlations for large data sets are described. The book details the methods for data classification and introduces the concepts and methods for data clustering. The remaining chapters discuss the outlier detection and the trends, applications, and research frontiers in data mining. This book is intended for Computer Science students, application developers, business professionals, and researchers who seek information on data mining. Presents dozens of algorithms and implementation examples, all in pseudo-code and suitable for use in real-world, large-scale data mining projects Addresses advanced topics such as mining object-relational databases, spatial databases, multimedia databases, time-series databases, text databases, the World Wide Web, and applications in several fields Provides a comprehensive, practical look at the concepts and techniques you need to get the most out of your data

Algorithms for Next-Generation Sequencing Data

Techniques, Approaches, and Applications

Author: Mourad Elloumi

Publisher: Springer

ISBN: 3319598260

Category: Computers

Page: 355

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The 14 contributed chapters in this book survey the most recent developments in high-performance algorithms for NGS data, offering fundamental insights and technical information specifically on indexing, compression and storage; error correction; alignment; and assembly. The book will be of value to researchers, practitioners and students engaged with bioinformatics, computer science, mathematics, statistics and life sciences.

Registries for Evaluating Patient Outcomes

A User’s Guide

Author: Agency for Healthcare Research and Quality/AHRQ

Publisher: Government Printing Office

ISBN: 1587634333

Category: Medical

Page: 356

View: 8611

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This User’s Guide is intended to support the design, implementation, analysis, interpretation, and quality evaluation of registries created to increase understanding of patient outcomes. For the purposes of this guide, a patient registry is an organized system that uses observational study methods to collect uniform data (clinical and other) to evaluate specified outcomes for a population defined by a particular disease, condition, or exposure, and that serves one or more predetermined scientific, clinical, or policy purposes. A registry database is a file (or files) derived from the registry. Although registries can serve many purposes, this guide focuses on registries created for one or more of the following purposes: to describe the natural history of disease, to determine clinical effectiveness or cost-effectiveness of health care products and services, to measure or monitor safety and harm, and/or to measure quality of care. Registries are classified according to how their populations are defined. For example, product registries include patients who have been exposed to biopharmaceutical products or medical devices. Health services registries consist of patients who have had a common procedure, clinical encounter, or hospitalization. Disease or condition registries are defined by patients having the same diagnosis, such as cystic fibrosis or heart failure. The User’s Guide was created by researchers affiliated with AHRQ’s Effective Health Care Program, particularly those who participated in AHRQ’s DEcIDE (Developing Evidence to Inform Decisions About Effectiveness) program. Chapters were subject to multiple internal and external independent reviews.

Introduction to Mathematical Methods in Bioinformatics

Author: Alexander Isaev

Publisher: Springer Science & Business Media

ISBN: 9783540219736

Category: Science

Page: 294

View: 8704

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This book looks at the mathematical foundations of the models currently in use. All existing books on bioinformatics are software-orientated and they concentrate on computer implementations of mathematical models of biology. This book is unique in the sense that it looks at the mathematical foundations of the models, which are crucial for correct interpretation of the outputs of the models.

Probabilistic Methods for Bioinformatics

with an Introduction to Bayesian Networks

Author: Richard E. Neapolitan

Publisher: Morgan Kaufmann

ISBN: 9780080919362

Category: Computers

Page: 424

View: 6267

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The Bayesian network is one of the most important architectures for representing and reasoning with multivariate probability distributions. When used in conjunction with specialized informatics, possibilities of real-world applications are achieved. Probabilistic Methods for BioInformatics explains the application of probability and statistics, in particular Bayesian networks, to genetics. This book provides background material on probability, statistics, and genetics, and then moves on to discuss Bayesian networks and applications to bioinformatics. Rather than getting bogged down in proofs and algorithms, probabilistic methods used for biological information and Bayesian networks are explained in an accessible way using applications and case studies. The many useful applications of Bayesian networks that have been developed in the past 10 years are discussed. Forming a review of all the significant work in the field that will arguably become the most prevalent method in biological data analysis. Unique coverage of probabilistic reasoning methods applied to bioinformatics data--those methods that are likely to become the standard analysis tools for bioinformatics. Shares insights about when and why probabilistic methods can and cannot be used effectively; Complete review of Bayesian networks and probabilistic methods with a practical approach.

Essential Bioinformatics

Author: Jin Xiong

Publisher: Cambridge University Press

ISBN: 113945062X

Category: Science

Page: N.A

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Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.

Bioinformatics Algorithms

Techniques and Applications

Author: Ion Mandoiu,Alexander Zelikovsky

Publisher: John Wiley & Sons

ISBN: 9780470253427

Category: Computers

Page: 483

View: 8404

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Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers: General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding Microarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression data Algorithmic issues arising in the analysis of genetic variation across human population, including computational inference of haplotypes from genotype data and disease association search in case/control epidemiologic studies Algorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactions Each chapter begins with a self-contained introduction to a computational problem; continues with a brief review of the existing literature on the subject and an in-depth description of recent algorithmic and methodological developments; and concludes with a brief experimental study and a discussion of open research challenges. This clear and approachable presentation makes the book appropriate for researchers, practitioners, and graduate students alike.

Computational Molecular Biology

An Algorithmic Approach

Author: Pavel Pevzner

Publisher: MIT Press

ISBN: 9780262161978

Category: Computers

Page: 314

View: 2536

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Computational gene hunting. Restriction mapping. Map assembly. Sequencing. DNA arrays. Sequence comparision. Multiple alignment. Finding signals in DNA. Gene prediction. Genome rearrangements. Computational proteomics. Problems .All you need to know about molecular biology. Bibliography. Index.

Data Mining

Practical Machine Learning Tools and Techniques

Author: Ian H. Witten,Eibe Frank,Mark A. Hall,Christopher J. Pal

Publisher: Morgan Kaufmann

ISBN: 0128043571

Category: Computers

Page: 654

View: 7441

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Data Mining: Practical Machine Learning Tools and Techniques, Fourth Edition, offers a thorough grounding in machine learning concepts, along with practical advice on applying these tools and techniques in real-world data mining situations. This highly anticipated fourth edition of the most acclaimed work on data mining and machine learning teaches readers everything they need to know to get going, from preparing inputs, interpreting outputs, evaluating results, to the algorithmic methods at the heart of successful data mining approaches. Extensive updates reflect the technical changes and modernizations that have taken place in the field since the last edition, including substantial new chapters on probabilistic methods and on deep learning. Accompanying the book is a new version of the popular WEKA machine learning software from the University of Waikato. Authors Witten, Frank, Hall, and Pal include today's techniques coupled with the methods at the leading edge of contemporary research. Please visit the book companion website at http://www.cs.waikato.ac.nz/ml/weka/book.html It contains Powerpoint slides for Chapters 1-12. This is a very comprehensive teaching resource, with many PPT slides covering each chapter of the book Online Appendix on the Weka workbench; again a very comprehensive learning aid for the open source software that goes with the book Table of contents, highlighting the many new sections in the 4th edition, along with reviews of the 1st edition, errata, etc. Provides a thorough grounding in machine learning concepts, as well as practical advice on applying the tools and techniques to data mining projects Presents concrete tips and techniques for performance improvement that work by transforming the input or output in machine learning methods Includes a downloadable WEKA software toolkit, a comprehensive collection of machine learning algorithms for data mining tasks-in an easy-to-use interactive interface Includes open-access online courses that introduce practical applications of the material in the book

An Introduction to Conditional Random Fields

Author: Charles Sutton,Andrew McCallum

Publisher: Now Pub

ISBN: 9781601985729

Category: Computers

Page: 120

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An Introduction to Conditional Random Fields provides a comprehensive tutorial aimed at application-oriented practitioners seeking to apply CRFs. The monograph does not assume previous knowledge of graphical modeling, and so is intended to be useful to practitioners in a wide variety of fields.

Sequence — Evolution — Function

Computational Approaches in Comparative Genomics

Author: Eugene Koonin,Michael Y. Galperin

Publisher: Springer Science & Business Media

ISBN: 1475737831

Category: Science

Page: 462

View: 5154

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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.

Encyclopedia of Data Warehousing and Mining

Author: John Wang

Publisher: IGI Global

ISBN: 9781591405573

Category: Computers

Page: 1248

View: 7058

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- Numerous contributions from international scholars providing comprehensive coverage of theory and concepts of DMW - Examples of best practices and case studies in data mining and warehousing - A renowned, extremely knowledgeable, and demanding editorial advisory board - A compendium of terms, definitions and explanations of concepts, processes and acronyms provided by international experts - Organized by titles and indexed by authors and topics, making it a convenient method of reference for readers - Cross referencing of key terms, figures and information related to DMW - With the purchase of a print copy, your library will have access to the electronic edition of this encyclopedia, free of charge for the life of the edition.

Independent Component Analysis

Author: Aapo Hyvärinen,Juha Karhunen,Erkki Oja

Publisher: Wiley-Interscience

ISBN: 9780471405405

Category: Science

Page: 504

View: 1037

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A comprehensive introduction to ICA for students and practitioners Independent Component Analysis (ICA) is one of the most exciting new topics in fields such as neural networks, advanced statistics, and signal processing. This is the first book to provide a comprehensive introduction to this new technique complete with the fundamental mathematical background needed to understand and utilize it. It offers a general overview of the basics of ICA, important solutions and algorithms, and in-depth coverage of new applications in image processing, telecommunications, audio signal processing, and more. Independent Component Analysis is divided into four sections that cover: * General mathematical concepts utilized in the book * The basic ICA model and its solution * Various extensions of the basic ICA model * Real-world applications for ICA models Authors Hyvarinen, Karhunen, and Oja are well known for their contributions to the development of ICA and here cover all the relevant theory, new algorithms, and applications in various fields. Researchers, students, and practitioners from a variety of disciplines will find this accessible volume both helpful and informative.