Book Description
Advances in computers and biotechnology have had a profound impact on biomedical research, and as a result complex data sets can now be generated to address extremely complex biological questions. Correspondingly, advances in the statistical methods necessary to analyze such data are following closely behind the advances in data generation methods. The statistical methods required by bioinformatics present many new and difficult problems for the research community.
This book provides an introduction to some of these new methods. The main biological topics treated include sequence analysis, BLAST, microarray analysis, gene finding, and the analysis of evolutionary processes. The main statistical techniques covered include hypothesis testing and estimation, Poisson processes, Markov models and Hidden Markov models, and multiple testing methods.
The second edition features new chapters on microarray analysis and on statistical inference, including a discussion of ANOVA, and discussions of the statistical theory of motifs and methods based on the hypergeometric distribution. Much material has been clarified and reorganized.
The book is written so as to appeal to biologists and computer scientists who wish to know more about the statistical methods of the field, as well as to trained statisticians who wish to become involved with bioinformatics. The earlier chapters introduce the concepts of probability and statistics at an elementary level, but with an emphasis on material relevant to later chapters and often not covered in standard introductory texts. Later chapters should be immediately accessible to the trained statistician. Sufficient mathematical background consists of introductory courses in calculus and linear algebra. The basic biological concepts that are used are explained, or can be understood from the context, and standard mathematical concepts are summarized in an Appendix. Problems are provided at the end of each chapter allowing the reader to develop aspects of the theory outlined in the main text.
Warren J. Ewens holds the Christopher H. Brown Distinguished Professorship at the University of Pennsylvania. He is the author of two books, Population Genetics and Mathematical Population Genetics. He is a senior editor of Annals of Human Genetics and has served on the editorial boards of Theoretical Population Biology, GENETICS, Proceedings of the Royal Society B and SIAM Journal in Mathematical Biology. He is a fellow of the Royal Society and the Australian Academy of Science.
Gregory R. Grant is a senior bioinformatics researcher in the University of Pennsylvania Computational Biology and Informatics Laboratory. He obtained his Ph.D. in number theory from the University of Maryland in 1995 and his Masters in Computer Science from the University of Pennsylvania in 1999.
Comments on the First Edition. "This book would be an ideal text for a postgraduate course…[and] is equally well suited to individual study…. I would recommend the book highly" (Biometrics). "Ewens and Grant have given us a very welcome introduction to what is behind those pretty [graphical user] interfaces" (Naturwissenschaften.). "The authors do an excellent job of presenting the essence of the material without getting bogged down in mathematical details" (Journal. American Staistical. Association). "The authors have restructured classical material to a great extent and the new organization of the different topics is one of the outstanding services of the book" (Metrika).
Customer Reviews:
Most Elegant Account of Bioinformatics.......2004-11-27
I was impressed with the 1st edition of this book for its most comprehensive and elegant of statistical techniques in bioinformatics. The book is slightly below the level of the now classic M S Waterman (1995)book:Introduction to Computational Biology: Maps, Sequences and Genomes. But this book is more update in some areas and has much more background materials on probability and statistics, which should provide a solid basis for understanding bioinformatics. Its pedagorical sense is unparalleled. It would make a very good choice for a stat/math oriented introduction to bioinformatics (as opposed to algorithimc/database oriented approach in cs).
Book Description
This is the first comprehensive introduction to Support Vector Machines (SVMs), a new generation learning system based on recent advances in statistical learning theory. Students will find the book both stimulating and accessible, while practitioners will be guided smoothly through the material required for a good grasp of the theory and its applications. The concepts are introduced gradually in accessible and self-contained stages, while the presentation is rigorous and thorough. Pointers to relevant literature and web sites containing software make it an ideal starting point for further study.
Customer Reviews:
More for mathematicians than computer scientist.......2006-09-20
This book introduces the concepts of kernel-based methods and focuses specifically on Support Vector Machines (SVM). It is hard to read and a good background in mathematic is clearly needed. The book has a strong emphasis on SVM starting from the very first line of text. Concepts are well explained, although equations are not clear. The notation doesn't facilitate the reading at all. The book covers linear as well as kernel learning. The kernel trick is well described. It is easy to understand ideas behind SVM while reading the corresponding chapter. Finally a small chapter on SVM applications is proposed. Unfortunately, it only contains typical SVM applications (i.e. standard problems).
I think this book is good if you:
* Have a strong mathematical background
* Work in the specific domain of SVM (or kernel-based methods in general)
* Want to write a research paper about SVM and need the correct notations
However, this book is NOT intended for people who:
* Don't like to read theorems, corollaries and remarks
* Are not interested in reading hundreds of proofs
This is my personal opinion as a computer scientist: this book is definitely written for mathematicians.
A little dry........2006-01-09
The book is a little dry at times. Also, I didn't get a very clear idea of how to select kernel functions, which seems pretty important.
Not even close to an intro..........2004-03-21
Oh Puhleeeezzzzz... How is your vector math??? Remember your linear algebra well? Do you have a background in SVM's? Intuitively able to suck out of thin air the meaning of the Gamma co-efficient as applied to svm's?? You've read all the background papers and remember your formal logic???? No?? too bad..your out of luck..
This book is more aptly titled an Introduction to the Formalisms of SVM's. If your a software engineer trying to implement one of these, forget it.. Be nice if they put that quadratic algorthim psuedocode into something more readable than greek symbology..
If you are trying to build one of these engines, then this book is of absolutely no help, unless you have a background in machine learning and have read all the papers on SVM's. If you can decompose the math into code in your head, then you might find it entertaining... What I don't get is how all the rest of these reviewers can give such "glowing praise" for this book and have it be so completely worthless as an introduction... makes me think some of these are shills..
Bottom line is, if your trying to code a svm, this book will not help. If your trying to understand how to implement a svm, this book will not help. If you are trying to understand how an svm works, this book will not help. If you want to know the mathematical basis for SVM's and like that presentation.. this is the book for you..
Excellent book.......2003-11-19
I just happened to read the reviews on the book on Support vector machines by Nello Cristianini and John Shawe-Taylor. Could not resist adding my own comments about the book. Excellent book. I plan to use the book for the course on "Fundamentals of computer aided engineering" that I teach at the Swiss Federal Institute of Technology, Lausanne (EPFL).
This is it !.......2001-08-31
The book is just great. The appendix on algorithms could have more explanations. Also the application section is a short. It would have been more usuful to take one of these applicaitons and describe it in details. But all in all, the book is excellent.
Average customer rating:
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Bioinformatics for Glycobiology and Glycomics: An Introduction
Manufacturer: John Wiley & Sons
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ASIN: 0470016671 |
Book Description
This book is the first dedicated to the bioinformatics of carbohydrates and glycoproteins. It provides a state-of-the-art overview and demonstrates the value of bioinformatics for glycobiology, not simply as a review of databases and tools but rather as an introduction to a new branch of glycobiology.
Efficient bioinformatics descriptions and tools can considerably enhance the efficiency of glycomics research, in terms of data quality, analysis and experimental costs. This book illustrates ways to use bioinformatics to enhance glycomics data mining and improve glycomics analysis.
Book Description
On 26 June 2000, the completion of the draft sequence of the Human Genome saw the sciences of biology and medicine change forever. It promised new insights into our genetic make-up, how our genes shape who we are, and how we function, and new possibilities for an improved quality of life, exploiting new knowledge to design novel, more effective drugs. At the heart of this breakthrough lies a scientific discipline which is now one of the most important information gathering, data-mining, and knowledge-building tools in current research and healthcare development: bioinformatics. Written by a pioneer of the use of bioinformatics in research, Introduction to Bioinformatics 2/e introduces the student to the power of bioinformatics as a set of scientific tools. The book explains how to access the data archives of genomes and proteins, and the kind of questions these data and tools can answer - how to make inferences from the data archives, to make connections among them, and to derive useful and interesting predictions. Retaining and enhancing the rich pedagogy and lucid presentation of the first edition, the book is accompanied by a fully integrated Online Resource Centre, encouraging students to explore the computational tools of bioinformatics in a relevant and stimulating way. Online Resource Centre - Figures from the book available to download, to facilitate lecture slide preparation - Web link library of all URLs cited in the book, and hyperlinks to a wide range of further reading articles, to give students ready access to these resources - Links to PDB structures of all proteins cited in the book, to enable students to investigate the 3D structures of proteins in a visual, interactive way - Data from the book in computer-readable form, which is available for instant use to facilitate hands-on learning by the student - Guidance to help students answer problems from the text, to support and encourage self-learning
Book Description
This introductory text offers a clear exposition of the algorithmic principles driving advances in bioinformatics. Accessible to students in both biology and computer science, it strikes a unique balance between rigorous mathematics and practical techniques, emphasizing the ideas underlying algorithms rather than offering a collection of apparently unrelated problems.
The book introduces biological and algorithmic ideas together, linking issues in computer science to biology and thus capturing the interest of students in both subjects. It demonstrates that relatively few design techniques can be used to solve a large number of practical problems in biology, and presents this material intuitively.
An Introduction to Bioinformatics Algorithms is one of the first books on bioinformatics that can be used by students at an undergraduate level. It includes a dual table of contents, organized by algorithmic idea and biological idea; discussions of biologically relevant problems, including a detailed problem formulation and one or more solutions for each; and brief biographical sketches of leading figures in the field. These interesting vignettes offer students a glimpse of the inspirations and motivations for real work in bioinformatics, making the concepts presented in the text more concrete and the techniques more approachable.
PowerPoint presentations, practical bioinformatics problems, sample code, diagrams, demonstrations, and other materials can be found at the Author's website.
Customer Reviews:
Uma excelente introdução à bioinformática.......2007-08-04
Este livro é excelente por várias razões. Entre elas posso citar o fato de estar totalmente voltado ao aprendizado por exemplos, sempre de forma a relacionar um problema computacional com um problema em bioinformática. É um livro muito abrangente, cobre muito bem os tópicos relacionados a alinhamentos e comparações de sequências. Seu capítulo sobre Algoritmos com Grafos é o meu preferido. O autor consegue passar as noções fundamentais com muita simplicidade, de forma que qualquer pessoa possa aprender num ritmo bem rápido.
Excellent algorithms exercise & bioinformatics intro.......2005-09-25
This is the first book that I've read regarding bioinformatics, so Im updating this as my class moves along. You better have a grasp of basic data structures prior to beginning this book and background with a programming language as there is very little hand-holding in this text. A bio background makes it all more interesting but certainly is not critical. There are no sample code or sources printed with the book nor is there an included CD nor answers to exercises. There is an associated web site where some ideas may be had and errata found/reported, but its not very active that I have seen. The pseudo code in the book is very python-like so easy to make use of. I personally transfer the book's concepts to C/C++ (habit) without much problem, except sometimes my results differ from the book. Apparently these are book bugs, so be sure to check the web site out if unexpected things pop up.
Presently my class is in chapter 8 (of 12) and looking back I would like to caution that some data processing algorithms will drive a computer's CPU quite hard so be aware of battery-munching & heat. My only bones with this book so far are the alphabet soup of variables and lack of answers to exercises. It would be nice if variable definitions were refreshed at the beginning of pseudo code samples.
I like this book as an algorithms text over traditional texts because the applications are much more fascinating. Imagine searching for something and you don't know where that something is. On top of that add not even knowing exactly what it is you are looking for. And when you do find it, its not even in the data searched! This may sound unlikely or even impossible, but it is neither. Rather, its very cool.
4-stars
Should really be called Intro Data Structures and Algorithms.......2005-07-08
I knew most of the stuff before I opened the first page. It's basically teaching data structures 101 using a few watered down bioinformatic problems for motivation. The lack of applied problems involving real data was most disappointing. It does have a lot of the type questions that some nerd (me one day :P) might ask you on a job interview. The questions are also a good way to kill time if you have nothing better to do. I give the book credit for stressing dynamic programming. I believe that this is one of the most important concepts in problem solving.
3 stars because I think it is a fairly good introduction for fledgling computer scientists BUT not a good reference for comptuer scientists trying to apply their skills to solve bioinformatic problems.
A very good introduction!.......2004-12-13
This book gives a broad overview of algorithmic methods used in bioinformatics. It is well writen and the mathematics needed to understand is undergraduate level. Reading this book makes appetite to apply these methods to problems or to dig deeper in the corresponding method.
Overall, a very good book, and due to its introductory level, one can recommend to all people interested in bioinformatics from all disciplines.
The First Undergraduate Text.......2004-12-07
Bioinformatics is probably the fastest growing field in both biology and computer science. The problems have come from the computer science department and the biology department having such fundamentally different goals. The computer scientists see the computer as an end in itself with no real thought on trying to do something useful with it. The biologists see the computer as just another tool in their laboratory. And the biological problems are huge, massive computers like the new Cray's and large Linux clusters are being devoted to biological applications.
This book is intended to fit into the chasm between biology and computer science. It discusses computer the algorithmic principles in terms of practical techniques that make sense to the undergraduate biologist. The book is well suited for a first class for the budding bioinformaticist.
Each main chapter in the book first introduces an algorithm, then it discusses the biologically relevant problems that this algorithm addresses, it includes a detailed problem and one or more solutions. Finally the chapter concludes with brief biographical sketches of leading figures in the field.
This is the first book of its type, and it's likely to remain a classic in the field through many editions and many years.
Book Description
Computational Genome Analysis: An Introduction 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 is appropriate for a one-semester course for advanced undergraduate or beginning graduate students, and it can also introduce computational biology to computer scientists, mathematicians, or biologists who are extending their interests into this exciting field.
This book features:
Topics organized around biological problems, such as sequence alignment and assembly, DNA signals, analysis of gene expression, and human genetic variation
Presentation of fundamentals of probability, statistics, and algorithms
Implementation of computational methods with numerous examples based upon the R statistics package
Extensive descriptions and explanations to complement the analytical development
More than 100 illustrations and diagrams (some in color) to reinforce concepts and present key results from the primary literature
Exercises at the end of chapters
Michael S. Waterman is a University Professor, a USC Associates Chair in Natural Sciences, and Professor of Biological Sciences, Computer Science, and Mathematics at the University of Southern California. A member of the National Academy of Sciences and the American Academy of Arts and Sciences, Professor Waterman is Founding Editor and Co-Editor in Chief of the Journal of Computational Biology. His research has focused on computational analysis of molecular sequence data. His best-known work is the co-development of the local alignment Smith-Waterman algorithm, which has become the foundational tool for database search methods. His interests have also encompassed physical mapping, as exemplified by the Lander-Waterman formulas, and genome sequence assembly using an Eulerian path method.
Simon Tavaré holds the George and Louise Kawamoto Chair in Biological Sciences and is a Professor of Biological Sciences, Mathematics, and Preventive Medicine at the University of Southern California. Professor Tavaré's research lies at the interface between statistics and biology, specifically focusing on problems arising in molecular biology, human genetics, population genetics, molecular evolution, and bioinformatics. His statistical interests focus on stochastic computation. Among the applications are linkage disequilibrium mapping, stem cell evolution, and inference in the fossil record. Dr. Tavaré is also a professor in the Department of Oncology at the University of Cambridge, England, where his group concentrates on cancer genomics.
Richard C. Deonier is Professor Emeritus in the Molecular and Computational Biology Section of the Department of Biological Sciences at the University of Southern California. Originally trained as a physical biochemist, His major research has been in areas of molecular genetics, with particular interests in physical methods for gene mapping, bacterial transposable elements, and conjugative plasmids. During 30 years of active teaching, he has taught chemistry, biology, and computational biology at both the undergraduate and graduate levels.
Customer Reviews:
"Computational genome analysis: An Introduction" Deonier R., Tavare S., Waterman M. Springer-Verlag New York, Inc., Secaucus, NJ.......2006-07-08
This textbook was based on the authors' instructional experiences in undergraduate Computational Biology courses for Bachelor seniors, first-year Master's, and Ph.D. students at the University of Southern California. Readers could also include investigators in medical schools, computer scientists, biologists, applied mathematicians, biochemists, and persons working in the biotechnology industry.
This text is based on the classic man-machine-work model in which a human performs laboratory-level work while also interacting with a digital computer. The complete inventory of all DNA that determines the identity of an organism is known as the genome. The computer or 'machine' utilizes the R language and produces statistical solutions dealing with genomes. The objects analyzed fall into these categories: the basic unit of life or the cell; the chemical energy stored in ATP (Adenosine triphosphate), the genetic information encoded by DNA (Deoxyribonucleic Acid) , and that information transcribed into RNA (Ribonucleic Acid). Since all life on the planet is based on cells, except for viruses, one can see why this volume is an important contribution to the scientific knowledge base particularly with reference to the evolution of species.
The R language developed at Bell Laboratories is used throughout the text. R is a probability statistics environment available for free download and can be used with Windows, Macintosh, and Linux operating systems. It functions very much like the S-PLUS statistics package. Since the reader would need to know how to actually implement the concepts in computational biology to fully understand them, the authors include examples of computations using R. This volume is described as a "roll up your sleeves and get dirty" introduction to the computational side of genomics and bioinformatics. It is intended to provide a foundation for an intelligent application of the available computational tools and for intellectual growth as new experimental approaches lead to new computational tools.
One must accept the fact that analyzing cells, DNA, and RNA is based on probability statistics. The text utilizes 1% algebra, 1 % integral calculus and 98% probability statistics --- the 98% being processed in R language. It isn't intended to describe the laboratory processes and protocols used to manipulate the samples but it does directly connect the computer solutions to the laboratory or work activity. Each chapter ends with a number of problems; while this is typical of the classical textbook, it would have been helpful if a teacher's answer book had been appended.
The Chapter headings are: Biology in a Nutshell; Words, Word Distributions and Occurences; Physical Mapping of DNA; Genome Rearrangements; Sequence Alignment; Rapid Alignment Methods: FASTA and BLAST; DNA Sequence Assembly; Signals in DNA; Similarity, Distance, and Clustering; Measuring Expression of Genome Information; Inferring the Past: Phylogenetic Trees; Genetic Variation in Populations; Comparative Geonomics; Glossary; A Brief Introduction to R; Internet Bioinformatics Resources; Miscellaneous Data.
Leonard C. Silvern
Systems Engineering Laboratories
Clarkdale, AZ
Book Description
This guide to the contemporary toolbox of methods for data analysis will serve graduate students and researchers across the biological sciences. Modern computational tools, such as Maximum Likelihood, Monte Carlo and Bayesian methods, mean that data analysis no longer depends on elaborate assumptions designed to make analytical approaches tractable. These new 'computer-intensive' methods are currently not consistently available in statistical software packages and often require more detailed instructions. The purpose of this book therefore is to introduce some of the most common of these methods by providing a relatively simple description of the techniques. Examples of their application are provided throughout, using real data taken from a wide range of biological research. A series of software instructions for the statistical software package S-PLUS are provided along with problems and solutions for each chapter.
Average customer rating:
- Worst bioinformatics book I have read
|
Bioinformatics Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice
Michael Moorhouse , and
Paul Barry
Manufacturer: Wiley
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An Introduction to Bioinformatics Algorithms (Computational Molecular Biology)
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Mastering Perl for Bioinformatics
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Mastering Regular Expressions
ASIN: 047085331X |
Book Description
Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Structuring its presentation around four main areas of study, this book covers the skills vital to the day-to-day activities of today’s bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material.
Working with Perl presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease.
Working with Data applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS-PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples.
Working with the Web presents a discussion of the Web-based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet.
Working with Applications shifts gear from creating custom programs to using them. The tools described include Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.
Download Description
Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Structuring its presentation around four main areas of study, this book covers the skills vital to the day-to-day activities of today's bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material. Working with Perl presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease. Working with Data applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS-PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples. Working with the Web presents a discussion of the Web-based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet. Working with Applications shifts gear from creating custom programs to using them. The tools described include Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.
Customer Reviews:
Worst bioinformatics book I have read.......2005-04-11
I have been programming and working as a biologist for the past 6 years, but I have had only a small exposure to Perl. When I read this book description, I was excited since it indicated that Perl would be taught from the ground up and from the bioinformatics perspective. While the perspective is as advertised, this is still a terrible book. Unless you know something about Perl (and programming in general) before you begin, you will be lost. The authors organize some material well, but often relevant items are completely missing. They almost completely abandon Windows users when it would only take a few more sentences to address the difference between Unix and Windows. The end of chapter exercises are poorly thought out and do not provide sufficient practice for the novice. Frequently I found myself referring to "Beginning Perl for Bioinformatics" to make sense of the Moorhouse and Barry book.
Book Description
This book looks at the mathematical foundations of the models currently in use. This is crucial for the correct interpretation of the outputs of the models. A bioinformatician should be able not only to use software packages, but also to know the mathematics behind these packages.
From this point of view, mathematics departments throughout the world have a major role to play in bioinformatics education by teaching courses on the mathematical foundations of the subject. Based on the courses taught by the author the book combines several topics in biological sequence analysis with mathematical and statistical material required for such analysis.
Average customer rating:
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Introduction to Bioinformatics (Chapman & Hall / Crc Mathematical & Computational Biology Series)
Anna Tramontano
Manufacturer: Chapman & Hall/CRC
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Essential Bioinformatics
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ASIN: 1584885696 |
Book Description
Guiding readers from the elucidation and analysis of a genomic sequence to the prediction of a protein structure and the identification of the molecular function, Introduction to Bioinformatics describes the rationale and limitations of the bioinformatics methods and tools that can help solve biological problems. Requiring only a limited mathematical and statistical background, the book shows how to efficiently apply these approaches to biological data and evaluate the resulting information. The author, an expert bioinformatics researcher, first addresses the ways of storing and retrieving the enormous amount of biological data produced every day and the methods of decrypting the information encoded by a genome. She then covers the tools that can detect and exploit the evolutionary and functional relationships among biological elements. Subsequent chapters illustrate how to predict the three-dimensional structure of a protein. The book concludes with a discussion of the future of bioinformatics. Even though the future will undoubtedly offer new tools for tackling problems, most of the fundamental aspects of bioinformatics will not change. This resource provides the essential information to understand bioinformatics methods, ultimately facilitating in the solution of biological problems.
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