More Pages: Grant Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100


What a great book.
Action packed, Thrilling and one of the best books i've read
Well worth reading

poor delivery but potentially usefulThe authors appear not to have much personal experience with sequence analysis and their exposition seems to be dominated by suggestions from not very honest or objective colleagues. At least that much can be inferred from the list of references given at the end of the book and the content of sequence-analysis-oriented chapters 5, 6 and section 11.3 of chapter 11. On the other hand, chapters 9 (about BLAST statistics), 13 (about evolutionary models), and 14 (about phylogenetic trees) are excellent. Every practicing bioinformatician should read them as a required reading before doing anything with BLAST or with construction of evolutionary trees.
Chapter 12 about computationally intensive methods is also very well written. However, the authors fail to notify the reader that many of the methods (such as bootstrap) have a really bad reputation among researchers involved in sequence analysis. Perhaps at least one sentence of warning (with references) could be in order.
In summary: The book is a mixed blessing but I would recommend it to statisticians who desire to do some work in bioinformatics. I also believe that chapters 9, 13 and 14 should be read by all practicing bioinformaticians.
Pretty good overviewChapter one begins, appropriately, with an introduction to probability theory, with a consideration of discrete probability distributions of one variable beginning the chapter. The Bernoulli, binomial, uniform, geometric, generalized geometric, and Poisson distributions are discussed. The authors point out the use of geometric-like distributions in the BLAST application. The also caution the reader as to the difference between the mean and the average of a random variable. They then move on to consider continuous distributions, discussing briefly the uniform, Normal, exponential, gamma, and beta distributions. Moment-generating functions are also introduced, and they prove a "convexity" theorem for these functions that is important in the BLAST application. The authors also introduce the relative entropy and generalized support statistics, the later also being used in BLAST.
The next chapter is an overview of probability theory in many random variables. The results in chapter one are discussed in this context, and the authors give an interesting application to the sequencing of EST libraries. The authors also point out that the variance of the maximum of a collection random variables is finite as the number of variables increases, a fact that is used quite often in bioinformatics. Transformations of random variables are also discussed, with the goal of showing how these can be used to find the density function of a single random variable, this also being important in BLAST.
The most important subject of the book begins in chapter 3, wherein the authors introduce statistical inference. They begin with a very brief discussion of the differences between the frequentist and Bayesian approaches to statistical inference and then move on to classical hypothesis testing and nonparametric tests. This chapter is of great value to those readers, for example biologists/would-be bioinformaticists who are approaching statistics for the first time.
Chapter 4 introduces concepts that are of upmost importance in probabilistic computational biology, namely Markov chains. The discussion in this chapter sets up the strategies used in the next chapter on analyzing a single DNA sequence and a latter chapter on hidden Markov models. Shotgun sequencing is discussed as a tool to determine the an actual DNA sequence, and the authors discuss the probabilistic issues that arise in the reconstruction of long DNA sequences from shorter sequences. Missing in this chapter is a mathematical analysis of the advantages/disadvantages between shotgun and whole genome sequencing strategies.
Chapter 6 then generalizes the analysis of chapter 5 to multiple DNA and protein sequences. It is here that one begins to talk about alignments between sequences, which bring about some very subtle mathematical problems in computational biology. The computational complexity of the (global) alignment problem entails the use of softer techniques, such as dynamic programming, which is discussed in this chapter. The (local) alignment problem is also discussed in some detail, using the linear gap model. The alignment problem and the issues with scoring for protein sequences are also discussed in detail. The reader first encounters the famous PAM and BLOSUM matrices in this chapter. The authors do not discuss any connections with the protein folding problem, unfortunately.
The next chapter introduces the basic probability theory behind the BLAST algorithm, namely random walks. They do so with emphasis on moment generating functions, which might be a little abstract for the biologist reader.
The authors return to tatistical estimation and hypothesis testing in chapter 8, with maximum liklihood and fixed sample size tests discussed in some detail. Again connecting with the BLAST algorithm, the sequential probability ratio test is treated.
The authors finally get down to the BLAST algorithm in chapter 9, using an older version of the software (1.4). The connection of the algorithm with random walks and how to assign scores is immediately apparent, as is the ability of BLAST to do database queries against a chosen sequence. The algorithm is compared with the sequential analysis discussed in the last chapter.
The authors return to Markov chains in chapter 10, and give some numerical examples. In addition, they treat the important topic of Markov chain Monte Carlo via the Hastings-Metropolis algorithm, Gibbs sampling, and simulated annealing. An application of simulated annealing to the double digest problem is described. The authors also spend a litte time discussing continuous-time Markov chains.
Hidden Markov models are finally discussed in chapter 11. These have been the most effective tools in sequence analysis and the authors give a nice overview of their construction and properties in this chapter. The Pfam package is discussed as a software implementation of HMMs for determining protein domains. Unfortunately, they do not discuss the excellent package HMMER for implementing HMMs in sequence analysis.
Chapter 12 discusses computationally intensive methods in classical inference. One of these methods, the bootstrap procedure, which is used for large sample sizes, is described. Used to estimate confidence intervals in situations where there is not enough information to employ classical methods, the authors detail a method using quantiles to estimate the confidence interval for the standard deviation of the expression intensity of a gene. This is followed by a return to the multiple testing problem of chapter 3 in the context of the data analysis of expression arrays.
I did not read the last two chapters on evolutionary models and phylogenetic tree estimation so I will omit their review.
guide into the right directionThis book is the first exception I know of. It builds, and rests on, solid foundations of genetic stochastic processes and still goes all the way to real-life problems. Let me illustrate this by means of an example, rather than enumerating all the topics in the book.
Chap. 14, entitled `phylogenetic tree estimation' (as opposed to the more common term `phylogenetic tree reconstruction' - not without reason, I presume) builds on, and is firmly interlaced with, Chap. 13 about `evolutionary models', which systematizes the zoo (if not jungle) of substitution models in both discrete and continuous time. On this basis, the overview of tree-building methods makes a lot of sense. Even better, it does not stop here, but presents an application (to real sequence data), followed by a careful analysis of where the various methods agree, and where - and maybe why - they disagree. This way, it clears away some common misconceptions; in particular, it presents a careful analysis of what bootstrap does and what it does not in this context. The chapter closes with a discussion of unresolved problems (like inhomogeneity of substitution rates), and methods and possible pitfalls related to testing of nested and non-nested hypotheses in tree estimation.
The book is written in an informal style without being imprecise, which makes it pleasant reading. It is particularly suitable for teaching at a high level. This is enhanced by realistic (and even real-life) examples that furnish the text, as well as carefully chosen exercises at the end of each chapter.
Certainly, this first edition of `Statistical Methods in Bioinformatics' cannot be the last word in this fast-moving field. But it is an excellent guide into the `right' direction.


Black Oak #2 fun, if not a bit confusing
"Episode 2" promises much but explains less
"This week, on Black Oak . . ."While The Hush of Dark Wings has the same overall tone as the first book, the plot is considerably less complex. At one point, the characters even realize how little time has passed over the course of the story. The book serves primarily as an introduction for (presumably) new regular Vivian Chambers. We also learn more about how the mysterious Ethan Proctor works and how he thinks, if not much more about his background. The paranormal mystery is weird and creepy, with some particularly vivid and graphic scenes. Graphic, that is, in the Charles Grant sense, where he gives the reader just enough information that you imagine something truly gruesome, without being spoon-fed all the gory details.
It's easy to make comparisons to X-Files, and I'm sure this series, like Chet Williamson's Searchers trilogy, owes its existence to that TV series' popularity. What makes Black Oak distinct is its varied cast of characters. Grant manages to create vivid personalities who come to life in front of the reader. I find myself looking forward to the next installment, not only to find out what happens next, but also to spend more time with these people and learn more about them. The Black Oak books may be quick reads, but they're a lot of fun, and may be one of the best TV series in print.


Very enjoyable.
Candy Factory Fun
A great murder mystery on par with Sue Grafton's A-Z series

Somewhat helpful, but narrow focus
Good commentary
The best practical commentary on Luke I've seen so far.

Good stories!
Fascinating and chilling
spooky

Nothing very new with this book
Caution needed for contact information
Gorgeous photos...The above I wrote before I purchased the book. Now that I own it, it's even better. Even the very beginning of the book with its snippet of Scottish history is wonderful and whets the reader's appetite to learn more about Scotland.


A Eurocentric view of India
Nice textbook
My favorite one-volume history of IndiaThe first 2/3 of the book covers the pre-British period -- a good fraction. While relating more of the military viscitudes than I would like, there is some consideration of social, religious, and economic issues as well as ruling strategies. And the focus on 'great empires' is less than in most Indian histories, which is good since India has spent much more time disunited than united.
Kulke and Rothermund break with the Hindu/Islamic/British periodization of Indian history, breaking periods before the Guptas and before the Mughals. All in all, it is a substantial improvement over Romila Thapar's effort, and a huge improvement over Stanley Wolpert's book.


Uninteresting and underwritten characters
serious, troubling account of childhood in unsettling familyJaffe's significant talents find best expression when exploring the psychological consequences of growing up in an environment which permits neither ease or coherence. Despite learning, at an early age, the notion of social responsibility, the children "had rubbed against things too sharp for the hands of the young. They'd been spittoons for words of terrific cruelty, they'd felt the sting of noses turned bloody. Awfulness that usually began in defense of things they didn't completely understand: their mother's work or their father's mind."
In addition, the author skillfully interweaves Mercer's anxieties about the ramifications of her life's work on her children's safety. "...This is what worried Mercer most: someday, intelligently, one or more of her children might come to the decision that their mother had placed them all in trouble's way for a belief they did not share." Kendall's increased instablity further isolates the Boones from a neighborhood steeped in hypocrisy and isolated anger. Jaffe's subtle depiction of the Boones' neighbors is superb. Lukin seethes with intolerance, disdain and fear at the Boones, a family that simply does not fit in with the truncated hopes of a working-class community. After Kendall's institutionalization, the neighborhood heaves a sigh of relief, however guiltily, that at least one detriment to community stability has been removed.
As the children age, their realizations mature. Garrett "accepted the parallels in his parents' lives: one needing protection from others, one needing only protection from himself." Not until young adulthood does Clem have a serious conversation with her mother about Mercer's decision to provide abortions, and the mother's measured response is one of the most eloquent defenses of the right to choice imaginable. "'I'd imagine no one wishes there weren't a need for abortions more than the doctors who perform them...But I can't just hide my eyes and hope it'll disappear. The only satisfaction - if that's even the word - I can take from doing abortions is knowing I gave the patients the best medical care I was capable of. A proficient set of hands.'"
"Skateaway" is not without its flaws. Written in three distinctive parts -- childhood, adolescence and adulthood -- the novel never fully coheres. Jaffe also has difficulty with the narrative; constant flashbacks tend to interfere with understanding rather than enchance it. The writing tends to be uneven as well; some pages have lyrical beauty while others are mundane. Nevertheless, the strengths of the novel far outweigh the weaknesses. A devastating conclusion reaffirms the undercurrent of fear swirling in "Skateaway." Jaffe poses very troubling questions and does not flinch in attempting to provide thoughtful and compelling answers. His characters' unique personalities and utterly believable means of responding to their unusual home circumstances elevate the importance of this novel.
REALLY ENJOYABLE EASY TO RELATE TO THIS FAMILY