Mathematics of Genome Analysis

Book Description

The massive research effort known as the Human Genome Project is an attempt to record the sequence of the three trillion nucleotides that make up the human genome and to identify individual genes within this sequence. The description and classification of sequences is heavily dependent on mathematical and statistical models. This short textbook presents a brief description of several ways in which mathematics and statistics are being used in genome analysis and sequencing.

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Customer Reviews:

Narrow and shallow.......2003-10-10

Genome analysis is a huge field - any title that promises to address it all has taken on a huge task.

This brief book does not deliver on the title's promise. It provides a cursory introduction to the assembly problem. That intro is so brief, however, that I don't think a reader will come away understanding what genome assembly is really about.

It continues with a disappointing analysis of nucleotide frequencies. The probability analysis is competent enough, within its limits, but I don't see any mention of why the analysis is interesting, or how to extend it the same techniques proteins. The author proposes spectral analysis as a tool, and argues for Walsh vectors as basis functions. Spectral analysis is offbeat, to say the least, but the author does not explain what (if any) biological insight the technique generates. More mainstream tools, including Markov Models, get little or no mention.

The chapter on sequence comparison is so short and skips so much critical material, that I'm tempted to call it negligent.

Perhaps you have specific reason for wanting the narrow and idiosyncratic view that Percus brings. ...

Short but helpful.......2002-01-02

This book is a short overview of some of the important mathematical techniques used to study genome sequences. In spite of the length of the book, the author does a fine job of introducing these techniques. Students of computational biology will especially benefit from its perusal.

The first section is a brief overview of the structure of DNA, m-RNA, and t-RNA. Recognizing that DNA is two large for direct analysis, restriction fragments are discussed in the second section, with emphasis on the restriction-enzyme fingerprint. The author's goal is to find the probability of occurences of a 6-letter word in a strand and the mean distance between occurrences of this word (assuming no overlap between the words or the occurences and equal probabilities for the bases). The effect of successive pair correlation (Markov chain effect) is considered briefly. This is followed by a calculation of the probability that a base pair is contained in a given clone. The author omits any discussion of algorithms for optical mapping, but does give a brief discussion of restriction maps.

The mathematics becomes more rigorous in chapter two, wherein the author analyzes a chain that exists as a set of cloned subchains with unknown overlap. This is the 'fingerprint assembly' problem the object of which is to produce a physical map of the full sequence. The fingerprint of the clone is a collection of lengths of a particular restriction fragments. This algorithm involves a sequence of contiguous clones called 'islands'; and 'contigs', which are two or more clones. The average number and size of islands are calculated assuming that the clones have equal length and identical overlap threshold. The method of anchoring is also discussed as a second method for obtaining the physical map of the genome. The author then considers the problem of covering the whole sequence by first placing n markers on a genome and covering by intervals centered at these markers. This is the restriction-fragment-length polymorphism analysis, the combinatorics of which the author solves by using Laplace and Fourier transforms. He also considers adaptive and non-adaptive pooling, in order to find a particular set of proteins on a large fragment.

The third chapter addresses sequence statistics, with the author addressing the nonhomogeneity of sequences and the correlation dependence in the bases. The chi-square test is discussed is some detail and the author discusses the accuracy of the Markov chain assumption. Noting that very long chains would be needed to determine the parameters for the expressions for the conditional correlations, he uses the maximum likelihood method to find the intrinsic correlation length, and then estimates the parameters by modeling the parameter set.

The author then studies the isochore regions and discusses their detection via the Jensen-Shannon entropy. Asking whether there are correlations between these long regions and within them motivates him to consider the long-range properties of DNA. This leads to the examination of a long fragment of a single strand of DNA, and with the assumption that strand-symmetry holds, the correlation coefficients are studied, with the decay properties of the auto- and cross-correlation discussed. Then, distinguishing only dual pairs, the author considers the probability that a pair is separated by an integer after an integral number of steps, a calculation that reduces to finding the largest eigenvalue of a 'transfer matrix', a procedure well-known in statistical physics.

Next, a consideration of simple sequence repeats leads to a difference equation that is solved by the method of moments. Windows of bases are then discussed, in order to improve on the statistics. Correlations within and between windows are calculated. Interestingly, the consideration of long-range correlations gives a power-law dependence for the correlations, which is related to the Hurst index for self-similar patterns. Readers get their first taste of hidden Markov models in this chapter, which are currently very popular in sequence analysis. Even more interesting is the discussion of walking Markov models, wherein a first-order base-to-base Markov chain is chosen to depend on a hidden parameter, and the time evolution is shown to satisfy a Fokker-Planck (diffusion) equation. Spectral analysis and information theoretic criteria are also discussed.

In the next chapter of the book, the author considers the most important part of sequence analysis, namely the comparison between sequences according to their linear ordering. The problem is to find the probability of a common subsequence of two linear chains with a given length. The first calculation assumes that the matches are mutually exclusive, and the result is an upper bound on the probability. The author then considers the matches to be independent events, and again bounds are given for the probability, the so-called Chen-Stein estimate). He also gives an estimate of the probability in terms of an asymptotic series. Extreme value methods are then used to calculate the expectation value and the variance of the length of the longest match. An interesting exercise is assigned for the reader; namely of finding the effect on the Fourier and Walsh power spectrum with the assumption that the base correlations are fractal in form. The alignment problem is then generalized to include replication errors, mutations, etc. The chapter ends, appropriately, with a discussion of multisequence comparison. The author poses the problem as one of finding the best match of a word to an n-tuple of words, which he tackles first using 'information content'. The category analysis of separating subsequence configurations into clusters is briefly discussed via simulated annealing, discriminant analysis, Bayesian analysis, and neural networks.

Book Description

The emergence of genomics, the study of genes, is one of the major scientific revolutions of this century. Microarrays, a method used to analyze numerous DNA samples rapidly, enables scientists to make sense of this mountain of data using statistical analysis. They are being used in such areas of biomedical research as studying patterns for gene activity that cause cancers to spread. This book presents a comprehensive methodology for analyzing DNA microarray and protein array data.
The most comprehensive treatment of this important emerging field, Exploration and Analysis of DNA Microarray and Protein Array Data includes:
A review of basic molecular biology and a chapter introducing microarrays and their preparation
Chapters on processing scanned images, preprocessing microarray data, group comparative experiments, and other designs
Discussions of clustering, protein arrays, and applications for diagnostic tools
Ample exercises assist absorbtion

Customer Reviews:

Excellent!.......2004-03-30

This book provides an excellent overview of various methods in DNA microarray analysis. It explains most of the theories behind the algorithms, so that you know why the analyses are done in certain way. In fact, I find I get more insights from the book as compare to the research papers which tend to be brief.

Mathematical and Statistical Methods for Genetic Analysis

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Read this book and you might learn something
OK, but not for me
nice introduction to math. and stoch. models in genetics
Mathematical Details of Genetics
Mathematical details about genetics

Mathematical and Statistical Methods for Genetic Analysis
Kenneth Lange
Manufacturer: Springer
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Binding: Hardcover

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ASIN: 0387953892

Book Description

During the past decade, geneticists have cloned scores of Mendelian disease genes and constructed a rough draft of the entire human genome. The unprecedented insights into human disease and evolution offered by mapping, cloning, and sequencing will transform medicine and agriculture. This revolution depends vitally on the contributions of applied mathematicians, statisticians, and computer scientists. Mathematical and Statistical Methods for Genetic Analysis is written to equip students in the mathematical sciences to understand and model the epidemiological and experimental data encountered in genetics research. Mathematical, statistical, and computational principles relevant to this task are developed hand in hand with applications to population genetics, gene mapping, risk prediction, testing of epidemiological hypotheses, molecular evolution, and DNA sequence analysis. Many specialized topics are covered that are currently accessible only in journal articles. This second edition expands the original edition by over 100 pages and includes new material on DNA sequence analysis, diffusion processes, binding domain identification, Bayesian estimation of haplotype frequencies, case-control association studies, the gamete competition model, QTL mapping and factor analysis, the Lander-Green-Kruglyak algorithm of pedigree analysis, and codon and rate variation models in molecular phylogeny. Sprinkled throughout the chapters are many new problems. Kenneth Lange is Professor of Biomathematics and Human Genetics at the UCLA School of Medicine. At various times during his career, he has held appointments at the University of New Hampshire, MIT, Harvard, and the University of Michigan. While at the University of Michigan, he was the Pharmacia & Upjohn Foundation Professor of Biostatistics. His research interests include human genetics, population modeling, biomedical imaging, computational statistics, and applied stochastic processes. Springer-Verlag published his book Numerical Analysis for Statisticians in 1999.

Customer Reviews:

Read this book and you might learn something.......2004-05-21

This book is not for the novice dabbling in statistical genetics. This is a highly sophisticated, thought provoking book targeted to individuals with considerable mathematical ability and training. As such, this book is an invaluable tool for individuals hoping to make a real impact in the field of statistical genetics. I particularly enjoyed the chapter on Markov Chain Monte Carlo methods for pedigree data.

OK, but not for me.......2003-09-24

I'm interested in molecular genetics, this seems to be more about population genetics. There is some material, towards the back, about phylogeny. I can bash that a bit to make it match my needs, but it's still a bit of a stretch.

It seems to be a pretty good presentation of population genetics, the kind of genetics taught in high schools in the 70s. I can't comment on this book's merits, but I can warn the biochem types to spend their money elsewhere.

nice introduction to math. and stoch. models in genetics.......2002-07-09

This second edition updates the first with the many advances in the rapidly growing field of genetics. It provides a nice treatment of the mathematical and stochastic models that are useful in genetic studies.

It is a little disappointing that it does not go into the microarray technology that has become so important for experimentation in the last few years. Other recent books that cover statistical aspects of genetic research are Weir (1996) "Genetic Data Analysis II" Sinauer Associates (publisher) and Yang (2000) "Introduction to Statistical Methods in Modern Genetics" Gordon and Breach Science Publishers.

Mathematical Details of Genetics.......2001-03-01

This book has an excellent coverage on the mathematical subtlies of genetics. The complicated theories are complimented by numerous examples. The exercise at the end of each chapter has a collection of probing questions that tests the understanding of the topics covered in the respective chapter. However, there is no discussion on association studies and quantitative traits which are two of the most active areas of genetic epidemiology. Moreover, the coverage on linkage is not adequate.

Mathematical details about genetics.......2001-02-27

The book has an excellent coverage of the mathematical subtlities of genetics. Theories are illustrated through numerous examples and the exercises at the end of each chapter contain probing questions which would test the understanding of the topics covered in the respective chapters. However, there are no chapters devoted to quantitative traits and association analysis, which are currently active areas of research. The coverage of linkage is also not adequate.

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Customer Reviews:

Paint and coating raw matirials.......2000-01-10

I have no review, but I prepare my first one

Handbook of Paint and Coating Raw Materials: Chemical Products With Trade Name Cross-Reference

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Handbook of Paint and Coating Raw Materials: Chemical Products With Trade Name Cross-Reference

Manufacturer: Gower Publishing Company
ProductGroup: Book
Binding: Hardcover

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ASIN: 0566078236

Handbook of Paint and Coating Raw Materials: Trade Name Products

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Handbook of Paint and Coating Raw Materials: Trade Name Products

Manufacturer: Gower Publishing Company
ProductGroup: Book
Binding: Hardcover

General | Reference | Subjects | Books
ASIN: 0566078244

Book Description

The Handbook of Paint and Coating Raw Materials, in its second edition, contains more that 50% additional trade names and generic chemicals with expanded information for individual entries. It describes more than 18,000 trade name and generic chemical ingredients that are used in the formulation of paint and coating products available from international manufacturers. With a worldwide focus on new or alternative materials for the development of efficient coatings, it is essential for professionals associated with this industry to have immediate access to current, accurate, and comprehensive information on these ingredients in order to make informed decisions on their selection. This reference provides such a resource. The chemicals and materials contained in this reference include: Accelerators, Adhesion Promoters, Antioxidants, Antiskinning agents, Fungicides, Coalescing agents, Diluents, Defoamer, Dispersants, Driers, Emulsifier, Fire retardants, Flow control agents, Gloss aids, Leveling agents, Marproofing agents, Pigments, Polymers, Resins, Slip agents, Thickeners, UV stabilizers, Viscosity control agents, Wetting agents, and many more! Paint and coating application areas include: Architectural Coatings, Powder Coatings, Wood Coatings, Marine Coatings, Maintenance Coatings, Highway/Traffic Marking Paints, Aerosol Paints, Coil Coatings, UV light curable coatings Product Features include: Click and Go Contents Menus-- contents always tracks where you are; click on a topic and it instantly appears Full-Text Search-- words, phrases and queries; from simple to complex Keyword Index Browser-- browse through thousands of key word entries organized by major categories; search as you type feature Multi-Book Access--This title's information is seamlessly accessible from other Synapse Library titles. Additional features: Print hit lists, search and index results, individual topics and sections Cut and paste fully formatted mouse-selected text into other applications View pop-up topics before jumping to them Annotate and create bookmarks on specific entries Minimum CPU speed and RAM requirements for Windows 95, 98, Me, NT, 2000, and XP Screen Resolution: 800x600 CD or DVD ROM Mouse or other Tracking Device Recommended System: 233 MHz Pentium II or faster Intel-compatible CPU Screen Resolution: 1280X1024 (256 or more colors) 128 MB (Windows 95, 98, Me, NT, 2000, and XP)

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Handbook of Paint and Coating Raw Materials
Michael Ash
Manufacturer: NY
ProductGroup: Book
Binding: Hardcover
ASIN: B000MUBYZ8

Book Description

The stark grief of a brother mourning a brother opens this novel with a stunning, unforgettable experience. Here, in a monumental saga of love and rage, Baldwin goes back to Harlem, to the church of his groundbreaking novel Go Tell It on the Mountain, to the homosexual passion of Giovanni's Room, and to the political fire that enflames his nonfiction work. Here, too, the story of gospel singer Arthur Hall and his family becomes both a journey into another country of the soul and senses--and a living contemporary history of black struggle in this land.

Customer Reviews:

A reader.......2005-09-23

From the moment I read the first page, I have loved this novel. I have read it several times and each time the characters come to life and I find myself caring about them. Hall has to deal with so many issues--least of all, is Ruth the woman he truly loves or should he be with the evangelist? Arthur-the gay gospel singer who sometimes would just as well have a drink or a man than sing the gospel, but who sang it so well when he chose to. Then there are the complex lives of their friends and parents that seem so real and yet so tragic. Baldwin created a masterpiece!

An artist of words.......2004-05-25

Probably one of the more underappreciated novels in American literature. It is unfair to charecterize Baldwin as merely a social critic of the civil rights era. He stands alongside Dickens as one of the great writers of any era, with the ability to articualte an understanding of human nature that trancends any era and stands second to none.

Love, Black, Gay and Providence.......2004-03-07

This novel is a testament in a way, the testament of a man who has lived long and well, too much even and too hard, in the world. A testimony too. Every single event in this novel about a black man who became a gospel singer and then a blues singer is the crystalisation of the whole history of Afro-Americans in the USA, the whole history of each character that is living the event through, the whole past and future of a present that is both crooked and promising. That is the very dilemma of this book, a dilemma that we feel and sense everywhere, on every page. Each moment in the life of these characters is the condensation of the cosmic, historical and human past of the individual and the sublimation of all possible wishes, desires, potentialities that this individual has developed in his situation and with his heritage. The novel may appear as very pessimistic because one cannot evade their heritage. But it is tremendously optimistic because one can always choose to realize their dreams, even if the situation around limits the possibilities and the chances to succeed. The aim of life is not to succeed, but it is not to fail, hence to move forward a few steps, and that one can always do it, even if it entails a lot of suffering and a lot of pain. Baldwin is also very optimistic about the world, about human beings, about Afro-Americans because he believes and tries to demonstrate that this forward progress of the pilgrims we are is fuelled by the happiness one gets from life, and that happiness comes from one's effort to accept what may provide happiness, no matter what that is, and the first thing to accept is love, no matter what form it may take. Yet there is a limit for Afro-Americans, a limit and a contradiction : they have great difficulties thinking in other terms than racial terms. They have been the victims as a « race » of deportation, slavery, discrimination, in a word a holocaust, and they cannot differenciate between the whites who are responsible for that fate, those who have made a direct profit out of it, even if many others have been able to enjoy some improved conditions thanks to the exploitation of black slaves, and the whites who have no responsibility in this historical process. How can we put on the same level, in the same boat the slave owners, the slave traffickers on one side, and the serfs that could only survive between famines, and the workers who were exploited too in the factories, and still are ? How can we put in the same bag the pharmaceutical firms that let Africans die because they don't want generic drugs to be produced and the workers of these pharmaceutical firms who are exploited just the same, even if in another way : the research and the patents the bosses want the poor to pay at the highest price, and in this very case most of these firms are American in the world, have been produced by workers who should be considered as the owners of their work and are, too often, paid a pittance when compared with the riches their bosses get out of this work. That's James Baldwin's dilemma. He hardly can discriminate between the white corn and the white chaff, and the white chaff is the workers, those who create the riches of the white corn. Some chapters become extremely poignant when this issue is brought up here and there and when Black Arthur cannot accept to love and be loved by white Guy, just because Guy is white and considered by principle as an accomplice of what the lords of the white « race » have done in history. And one of James Baldwin's concluding thoughts is : « To undo the horror, we repeat it ». And not to repeat the horror of the killing of a black man by some whites (like Peanut for instance), Baldwin makes his Arthur die in London, in a pub where he is the only black man, and by falling in a state of amazed drunkness on the stairs leading to the restrooms in the basement, at a moment when love had been slightly roughened by life into a distance that could have been avoided if love had not gone through a storm in what appears like nothing but a glass of water, the glass of water of everyday life.

Dr Jacques COULARDEAU

A stirring work..........2002-02-26

Highly recommended...This is an "intense" read...and you will find yourself going back and re-reading certain pages to make sure that you absorbed everything from the page. A stirring story of two brothers desperately seeking to find themselves and a true identity outside of the religious world they had been so immersed in...

A Literary Wonder.......2001-03-05

I first came across the book as a teenager, rooting around amidst the books my brother left behind. I was just coming out then, and decided to try and read it. Much of it flew over my head then, but upon returning to it as an adult, I found much here to treasure. The characters not only inhabit the pages, but leap right off them at times, and the reader feels like he would want to sit in a room with them, talk with them, laugh with them and grieve with them. As a black gay man, it's nearly an autobiographical read, showing how far ahead of his time Baldwin was. It definitely comes highly recommended from this reader.

James Baldwin Reads from Just Above My Head

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James Baldwin Reads from Just Above My Head
James Baldwin
Manufacturer: Amer Audio Prose Library Inc
ProductGroup: Book
Binding: Audio Cassette

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ASIN: 1556440936

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JUST ABOVE MY HEAD
James BADLWIN
Manufacturer: see notes for publisher info
ProductGroup: Book
Binding: Hardcover
ASIN: B000L6H7MW

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Just Above My Head
James Baldwin
Manufacturer: NY The Dial Press 1978.
ProductGroup: Book
Binding: Hardcover

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Just Above My Head
James, 1924-1987 Baldwin
Manufacturer: see notes for publisher info
ProductGroup: Book
Binding: Hardcover
ASIN: B000NOWPU6

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Just Above My Head
James Baldwin
Manufacturer: The Dial Press
ProductGroup: Book
Binding: Hardcover

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Just Above My Head
James Baldwin
Manufacturer: Dial Press
ProductGroup: Book
Binding: Hardcover

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Just Above My Head -
James Baldwin -
Manufacturer: Dial Press -
ProductGroup: Book
Binding: Hardcover

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Just Above My Head
James Baldwain
Manufacturer: The Dial Press
ProductGroup: Book
Binding: Hardcover
ASIN: B000KEWXD8

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Just Above My Head
James Baldwin
Manufacturer: DIAL PRESS
ProductGroup: Book
Binding: Hardcover

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