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| By: El-Ghazali Talbi, Albert Y. Zomaya ISBN: 0471784095 Publisher: Wiley-Interscience Release Date: 17 December, 2007 Bioscience book rank: 1325858 | ||
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| By: Paul Harrison ISBN: 0471495638 Publisher: Wiley Release Date: 05 December, 2001 Bioscience book rank: 863246 | ||
| By: Jaroslaw Meller, Wieslaw Nowak ISBN: 0820487937 Publisher: Peter Lang Publishing Release Date: 03 September, 2007 Bioscience book rank: 1472861 | ||
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| By: Shui Qing Ye ISBN: 1584888105 Publisher: Chapman & Hall/CRC Release Date: 20 August, 2007 Bioscience book rank: 874108 | ||
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| By: Andrzej K. Konopka, M. James C. Crabbe ISBN: 0824709829 Publisher: CRC Release Date: 01 September, 2004 Bioscience book rank: 1372386 | This is a surprisingly complete practical text. It can be appreciated by computer literate novices as well as by practicing bioinformaticians. Each chapter can, in principle, be read separately from others but reading entire book from cover to cover could be a better strategy for the readers who would like to become professional computational biologists in the future. It would be good if future editions of this handbook contained a more elaborated description of contents and a more exhaustive index. This could facilitate navigating through this quite large text. That is to say the subject index in the current edition is all right but could be improved in the future. It would also be nice if the publisher could make this excellent book affordable for a larger audience by lowering the price. | |
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| By: Anna Tramontano ISBN: 1584885696 Publisher: Chapman & Hall/CRC Release Date: 06 December, 2006 Bioscience book rank: 570245 | ||
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| By: T. Koski ISBN: 1402001363 Publisher: Springer Release Date: 01 May, 2002 Bioscience book rank: 296518 | The intended audience of this book are mathematicians. To understand this book, you should have prior coursework experience in at least several upper division undergraduate courses in mathematical statistics and probability theory. The structure of this book is also that of a typical math book; full of proposition, corollary, lemma, etc, and very limited use of illustrations (e.g., there is no single figure up to chapter 6).<p>I wanted a book with a mathematical sophistication simliar to Durbin's book, but this book is way more than that. On the other hand, I showed this book to a mathematics graduate student and she said this book is perfect for her. So I guess this book is written by a mathematician only for mathematicians. The book gives outstanding coverage of all that goes into building HMMs - one of the most important tools in genome analysis and structure prediction. It covers the field in extreme depth. More depth, in fact, than needed for building useful HMM systems. It not only presents the forward and backward algorithms leading up to Baum-Welch, it presents all the extras - convergence, etc.<p>This additional depth of coverage may go beyond many readers' needs. It is very helpful, though, for people who need more than the usual algorithms. By giving the background in such detail, a persistent reader can follow to a certain point, then create modifications with a clear idea of where the new algorithm actually comes from.<p>Regarding the current practice of HMM usage, I found it a bit thin. Widely-known tools based on HMMs are mentioned only occasionally and in passing, and HMM-based alignment is discussed only briefly. Well, this book isn't for the tool user. Perhaps more important, I found scant mention of scoring with respect to some background probability model ("null" model, as it's called here). <p>My one real complaint, and this is truly minor, is the quality of illustration. The line-drawings look like Word pictures - not necessarily a bad thing, if done well. These aren't particularly professional-looking, though, and oddly stretched or squashed in many cases. Still, they're readable enough and make all the needed points. <p>A lesser point, and not the author's fault, is the editorial implication that this book introduces probabilitic models in general. It does not. This is strictly about HMMs, not Bayesian nets, bootstrap techniques, or any of the dozens of other probabilistic models used in bioinformatics. That is not a flaw of the book, just a flaw in how it's represented.<p>If you are dedicated to becoming an expert in HMM construction and application, you must have this book. It's a bit much, though, for people who just want the results that HMMs give. The field of computational biology has expanded greatly in the last decade, mainly due to the increasing role of bioinformatics in the genome sequencing projects. This book outlines a particular set of algorithms called hidden Markov models, that are used frequently in genetic sequence search routines. The book is primarily for mathematicians who want to move into bioinformatics, but it could be read by a biologist who has a strong mathematical background. The book is detailed at some places, sparse in others, and reads like a literature survey at times, but many references are given, and there are very interesting exercises at the end of each chapter section. In fact it is really imperative that the reader work some of these exercises, as the author proves some of the results in the main body of the text via the exercises. <p> Some of the highlights of the book include: 1. An overview of the probability theory to be used in the book. The material is fairly standard, including a review of continuous and discrete random variables, from the measure-theoretic point of view, i.e the author introduces them via a probability space which is set with its sigma field, and a probability measure on this field. The weight matrix or "profile" as it is sometimes called, is defined, this having many applications in bioinformatics. Bayesian learning is also discussed, and the author introduces what he calls the "missing information principle", and is fundamental to the probabilistic modeling of biological sequences. Applications of probability theory to DNA analysis are discussed, including shotgun assembly and the distribution of fragment lengths from restriction digests. A collection of interesting exercises is included at the end of the chapter, particularly the one on the null model for pairwise alignments. 2. An introduction to information theory and the relative entropy or "Kullback distance", the latter of which is used to learn sequence models from data. The author defines the mutual information between two probability distributions and the entropy, and calculates the latter for random DNA. He also proves some of the Shannon source coding theorems, one being the convergence to the entropy for independent, identically distributed random variables. The Kullback distance is then defined, as a distance between probability distributions, with the caution that it is not a metric because of lack of symmetry. 3. The overview of probabilistic learning theory, where 'learning from data' is defined as the process of inferring a general principle from observations of instances. 4. The very detailed treatment of the EM algorithm, including the discussion of a model for fragments with motifs. 5. The discussion of alignment and scoring, especially that of global similarity. Local alignment is treated in the exercises. 6. The discussion of the learning of Markov chains via Bayesian modeling applied to a training sequence via a family of Markov models. Frame dependent Markov chains are discussed in the context of Markovian models for DNA sequences. 7. The discussion of influence diagrams and nonstandard hidden Markov models, in particular the excellent diagrams drawn to illustrate the main properties, and excellent discussion is given of an "HMM with duration" in the context of the functional units of a eukaryotic gene. This is important in the GeneMark:hmm software available. 8. The treatment of motif-based HMM, in particular the discussion of the approximate common substring problem. 9. The discussion of the "quasi-stationary" property of some chains and the connection with the "Yaglom limit". 10. The treatment of Derin's formula for the smoothing posterior probability of a standard HMM. The author shows in detail that the probability of a finite length emitted sequence conditioned on a state sequence of the HMM depends only on a subsequence of the state sequence. 11. The treatment of the lumping of Markov chains, i.e. the question as to whether a function of a Markov chain is another Markov chain. 12. The very detailed treatment of the Forward-Backward algorithm and the Viterbi algorithm. 13. The discussion of the learning problem via the quasi-log likelihood function for HMM. 14. The discussion of the limit points for the Baum-Welch algorithm. Since the Baum-Welch algorithm deals with iterations of a map, its convergence can be proved by finding the fixed points of this map. These fixed points are in fact the stationary points of the likelihood function and can be related to the convergence of the algorithm via the Zangwill theory of algorithms. Unfortunately the author does not give the details of the Zangwill theory, but instead delegates it to the references (via an exercise). The Zangwill theory can be discussed in the context of nonlinear programming, with generalizations of it occurring in the field of nonlinear functional analysis. It might be interesting to investigate whether the properties of hidden Markov models, especially their rigorous statistical properties, can all be discussed in the context of nonlinear functional analysis. | |
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| By: Satoru Miyano, Jill Mesirov, Simon Kasif, Sorin Istrail, Pavel Pevzner, Michael Waterman ISBN: 3540258663 Publisher: Springer Release Date: 23 June, 2005 Bioscience book rank: 1583863 | ||
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| By: Pavel A. Pevzner ISBN: 0262161974 Publisher: The MIT Press Release Date: 21 August, 2000 Bioscience book rank: 840035 | Dr. Pevzner writes with a very lucid and conversational style about very complex and seemingly inscrutable topics. As a biologist who works primarily with computational tools in the field of genomics, this resource has helped to provide me with more than a rudimentary understanding of the algorithms and logic lurking in the methods of sequence analysis. Explaining dynamic programming to a biologist with rudimentary programming skills is a daunting task. However, his description of sequence alignment algorithms (including dynamic programming) in chapter 6 is quite readable and the information is very accessible. I highly recommend this book if you want a comprehensive understanding of the computational biologists toolkit. Pevzner has written a very useful book on bioinformatics algorithms, and one that seems reasonably up to date. The table of contents follows a classic plan: restriction maps, assembly and sequencing, 2- and N- way string comparisons, and analysis of rearrangements. There's a good but brief section on mass spec analysis - unfortunately, that chapter is called "Proteomics" even though the term covers a lot more than MS. Other sections skim the surface of hidden Markov models and Gibbs sampling for finding patterns ("motifs") in DNA. <br /> <br />A few chapters have unusual strengths. The "Conway Equation" gives more insight in analysis of motif significance than other introductory books do. The section in sequence comparison pays a lot more attention to BLAST-like algorithms than other books do, also - modern material you'd normally see only in the journals. Also, the section on rearrangements gives some ideas about using rearrangement data for phylogenetic analysis. That really gives the material meaning. Rearrangements aren't just string operations, they're features of evolution, and they can be compared to each other. No matter what the discussion, Pevzner keeps maintains a readable and enjoyably informal tone. <br /> <br />The book does have some weaknesses, though. It's a bit advanced for an undergrad intro, but bottoms out before the Baum-Welch algorithm, for example. Discussion of microarrays for sequencing seems dated. Pevnzer describes their use in sequencing, a rarity now, but skips their use in functional gneomics, where they are used most often. Illustration style is erratic and many diagrams are oddly stretched (3.5, 5.7, 8.3, and others, some much worse). Formal analysis of the algorithms is weak, but Pevzner somewhat makes up for that with better statistical analysis than many authors give. Also, even though the book was reprinted in 2001, it still estimates 100K genes in the human genome. <br /> <br />This is a good second book, maybe the one to read after Pevzner's newer "Introduction". It covers most of the basics and gives fairly usable pseudocode. Most of all, it always keeps the biology in mind. That, by itself, makes this book stand out. <br /> <br />//wiredweird An excellent book for studying computational molecular biology from an algorithmic perspective. (But if you never took mathematics seriously, you are forewarned.) | |
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| By: John M. Hancock, Marketa J. Zvelebil ISBN: 0471436224 Publisher: Wiley-Liss Release Date: 09 August, 2004 Bioscience book rank: 1389869 | ||
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