Book Description
Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The text avoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles. An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.
Customer Reviews:
Clear, rigorous, fascinating.......2007-01-20
I'm a Ph.D. student in biophysics. This is the best treatment of systems biology that I've encountered. It treats both the math and the biology with clarity, rigor, and respect. It simplifies without dumbing down. It's beautifully written. If you doubt that systems biology is a real scientific discipline, this book will change your mind.
Building Mathematical Models of Cells.......2006-09-25
The history of science over the past few centuries is to become ever more specialized. The physicists, becomming ever more concerned with the very large (stars, galaxies, the cosmos) or the very tiny (first atoms, then atomic components, now sub-components. The biologists on the other hand were studying much larger things, such as the cells that make up life. Both sciences developed techniques to facilitate their study.
In recent years, researchers have discovered that sometimes these specialized techniques can be used to develop greater insight into what is happening in other sciences.
In this book, Dr. Alon uses his training in physics to examine certain aspects of biology and to use the terminology and mathematics to describe the way these biological networks work.
The goal of the book is to begin the formulation of general laws that apply to biological networks. This is done by providing a mathematical framework in which some of the design principles of biological systems can help to understand biological networks. In looking at the results, an underlying simplicity not seen before appears in biological systems.
Great Job.......2006-09-09
A superb intro to the field. The math is moderate and helpful. Network concepts and their ties to examples and theory are clearly and succinctly presented. This is a textbook but reads easily like a book. Covers key elements while connecting them by at least mention to up-to-date further research. The basics and the grandeur of systems biology. I am trying to remember now anything on the negative side and cannot.
Book Description
Biology is in the midst of a era yielding many significant discoveries and promising many more. Unique to this era is the exponential growth in the size of information-packed databases. Inspired by a pressing need to analyze that data, Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences. This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps. It examines problems associated with reading DNA sequences and comparing sequences to finding common patterns. The author then considers that statistics of pattern counts in sequences, RNA secondary structure, and the inference of evolutionary history of related sequences. Introduction to Computational Biology exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology.
Customer Reviews:
A modern classic.......2003-10-15
The first name people learn in bioinformatics is the Smith-Waterman algorithm. Some people never learn anything else. This is by that Waterman. Although written in 1995, it still has some of the best discussion I've seen on the topics it addresses.
The first few chapters deal with the "digest problem," reconstructing a DNA or protein sequence from the fragment sizes of enzyme digests. The technique is not used as much now as it was then, but it's always good to know the background of modern techniques.
The digest problem doesn't stand alone, though. It introduces concepts - islands, anchors, etc. - that still matter. The problems in reconstructing molecules from digests yield the same kinds of intermediate results and the same ambiguities that arise in modern sequencing. As Waterman advances the discussion, shotgun sequencing appears as a logical extension, at least mathematically, of digest assembly.
Sequence assembly involve end matching, perhaps in the presence of sequencing errors. That introduces the topic for which Waterman's name is famous, approximate string matching. The next few chapter progress through dynamic programming and multiple alignments. The logical connections between the techniques shown are so tight that chapter boundaries are almost artificial. It was a real pleasure to see the computational and practical relationships laid out.
The final topics, RNA structure and phylogenetic trees, lack the continuity that characterized the first dozen chapters. The RNA structure may be the weakest chapter in the book, but still a very competent introduction.
Throughout, Waterman emphasizes mathematical rigor without insisting on uninformative theorems. Every topic is presented in rich detail, with special attention to scoring and background models. Perhaps there are newer discussions of some topics. I don't know of any clearer discussions, though. Best, I think, is how Waterman prepares the reader to ask all the right questions in any future discussion: what are the elements of the computation, how can elements be recombined, how good is a result, and how does the result stand out from the statistical background.
The final chapter is what a bibliography should be. It doesn't just list authors, titles, and dates of publication. It actually discusses the contribution that each source made to this book. Rather than leave the reader to wander aimlessly among obscure titles, Waterman shows which sources are most informative on which topics. I wish more authors took the time for such commentary.
This is a book worth having. It covers topics that I haven't seen elsewhere, and shows how many different topics relate to each other. It is rigorous without giving distracting detail. Most of all, it keeps the biology in sight of all calculations. Some authors seem to forget that anything exists but the arithmetic; Waterman puts the math clearly in the service of its subject. I enjoyed it immensely, and look forward to applying its content in my own research.
Packed full of good information.......2000-08-13
This book gives a good survey of the different techniques employed by computational biologists. After a brief review of molecular biology in Chapter 1, the author treats the mathematical modeling of restriction maps in Chapter 2 using graph theory. His presentation is somewhat hurried, but he does give references and gives the reader three exercises at the end of the chapter. Multiple maps are treated in Chapter 3, wherein the author first makes use of probability theory, via the Kingman subadditive ergodic theorem. The proof is omitted but the author does a good job of explaining its use in studying the double digest problem (DDP). The best part of this chapter is the author's explanation of the difficulties of using Kingman's results for solving the DDP, and goes on to discuss multiple solutions of the DDP. Graph theory is again used in the discussion. This sets up the discussion in Chapter 4, which outlines algorithms for the DDP. The author gives a very compact introduction to P- and NP-complete problems in the theory of computation, then proves that DDP is NP-complete. The author does a good job of discussing subsequent approximate methods used for the DDP, such as simulated annealing. Markov chains are introduced in the book here for the first time, but due to the shortness of the presentation, the reader should do outside reading as a back-up. The author does a great job of explaining the difficulties if measurement error is introduced in the DDP at the end of the chapter. Cloning is discussed in Chapter 5, with tools from probability theory used to deal with partial digest libraries. The chapter is really short though, and the working the problems at the end of the chapter is essential for the understanding the results of this chapter. The author switches gears in the next chapter, wherein physical maps are discussed. The discussion is fairly detailed and interesting. Sequencing is discussed in the next two chapters, and the treatment is very good. Hashing is introduced here, and psedocode is given throughout. The very important method of dynamic programming is outlined in Chapter 9, which is beautifully written, and again pseudocode abounds throughout. Genetic mapping is left out though, but the this, the longest chapter of the book, is a detailed introduction to this area. The results in this chapter are used to study multiple sequence alignment in Chapter 10, wherein hidden Markov models are introduced for the first time. The discussion of these models is very curt, but there are other books and notes available if the reader needs further guidance. The best chapter of the book follows, which discusses probability and statistics for sequence alignment. The theory of large deviations is brought in, and the author does an excellent job of discussing this important, and powerful theory. The reader's level of mathematical sophistication is assumed to be a lot greater than the rest of the book in this chapter. Knowledge of measure theory and martingales are assumed here. The author uses the very powerful tool of relative entropy, so indispensable in other applications of probability. The problem set at the end of the chapter is challenging but working them through is definitely worth the time involved. The next chapter also uses some heavy guns from probability theory to study sequence patterns. The author returns to matter of a more empirical nature in Chapter 13, which deals with RNA secondary structures. The reader with a background in simple combinatorial theory should find the reading straightforward and informative. Continuous-time Markov chains are introduced in the next chapter to study trees and sequences. The treatment here is rather hurried, so again the reader should work the exercises at the end of the chapter. The book ends with a discussion of the literature and references. All in all a very nice book, worth the price, and worth spending time reading. The only minus might be the total omission of actual source code, but that really was not the intent of the book. Readers with a strong mathematical background will like the book, as well as anyone interested in going into the area of computational biology.
Book Description
This general introduction to the mathematical techniques needed to understand epidemiology begins with an historical outline of some disease statistics dating from Daniel Bernoulli's smallpox data of 1760. The authors then go on to describe simple deterministic and stochastic models in continuous and discrete time for epidemics taking place in either homogeneous or stratified (nonhomogeneous) populations. They offer a range of methods for constructing and analyzing models, mostly in the context of viral and bacterial diseases of human populations. These models are contrasted with models for rumors and macro-parasitic diseases. Questions of fitting data to models, and the use of models to understand methods for controlling the spread of infection, are discussed. Exercises and complementary results at the end of each chapter extend the scope of the text.
Customer Reviews:
A Foundation Book.......2007-05-16
This book tells what we knew about the mathematics of epidemics up until 1990. The differential equations (beginning with Bernoulli and moving forward) are presented well. That is, the variables are defined in the text and not too many steps are skipped in the derivations. The high point in this type of epidemiology came in 1927, when Kermack and McKendrick wrote the continuous-time epidemic equations. Diseases were characterized by the parameter rho, the relative removal rate. Up until the 1990s, we were just fitting our data to this model, and estimating rho.
Along came 'computational biology', or 'agent-based models' or 'numerical methods'. After 1990, these new techniques allowed us to escape from the perfect-mixing assumption that caused the Kermack and McKendrick model to depart from reality. With computation, we were able to see the impact of social networks, targeted innoculuations, and to test the value of different intervention strategies. See March 2005 Scientific American. None of those advances are discussed in this book. As a historical treatise, however, it is a superb addition to the library.
Great Service.......2007-02-02
My book arrived before estimated time and in better condition than described. I am a math dork and given the choice I would purchase from this seller.
Excellent Text.......2005-05-14
This is a broad, wonderful introduction to the mathematics of epidemic modeling. The authors have done an outstanding job at pointing out the mathematics of both deterministic and stochastic epidemic models.
Careful study of this small text will prepare one for a serious look at the current research on the subject. This material is far from ``old fashioned" as one reviewer wrote, indeed, this text is a welcome introduction to the subject!
Old-fashioned.......2004-11-04
The authors mainly give an introduction how to do the calculations by hand for several epidemic models. However, some of their tricks for doing the calculations are not very interesting anymore in times where computers are available. More imporatant, they hardly ever explain why they choose a particular model, what they want to calculate and how to interpret the results of the calculations. So reading the book does not give you much insight in epidemic modelling, only in doing some calculation. Furthermore they ignore all kind of recent approaches in epidemic modelling. (Most references are quite old (before 1990) and the few more recent references are most of the time only mentioned without going into detail.)
Book Description
Focusing on discrete models across a variety of biological subdisciplines, this introductory textbook includes linear and non-linear models of populations, Markov models of molecular evolution, phylogenetic tree construction from DNA sequence data, genetics, and infectious disease models. Assuming no knowledge of calculus, the development of mathematical topics, such as matrix algebra and basic probability, is motivated by the biological models. Computer research with MATLAB is incorporated throughout in exercises and more extensive projects to provide readers with actual experience with the mathematical models.
Book Description
KEY BENEFIT: This reference introduces a variety of mathematical models for biological systems, and presents the mathematical theory and techniques useful in analyzing those models. Material is organized according to the mathematical theory rather than the biological application.
Contains applications of mathematical theory to biological examples in each chapter. Focuses on deterministic mathematical models with an emphasis on predicting the qualitative solution behavior over time. Discusses classical mathematical models from population , including the Leslie matrix model, the Nicholson-Bailey model, and the Lotka-Volterra predator-prey model. Also discusses more recent models, such as a model for the Human Immunodeficiency Virus - HIV and a model for flour beetles.
KEY
MARKET: Readers seeking a solid background in the mathematics behind modeling in biology and exposure to a wide variety of mathematical models in biology.
Average customer rating:
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An Introduction to Mathematical Physiology and Biology (Cambridge Studies in Mathematical Biology)
J. Mazumdar
Manufacturer: Cambridge University Press
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Mathematical Physiology
ASIN: 0521646758 |
Book Description
This textbook is concerned with the mathematical modeling of biological and physiological phenomena for mathematically sophisticated students. A range of topics are discussed: diffusion population dynamics, autonomous differential equations and the stability of ecosystems, biogeography, pharmokinetics, biofluid mechanics, cardiac mechanics, the spectral analysis of heart sounds using FFT techniques. The last chapter deals with a wide variety of commonly used medical devices. This edition includes new chapters on epidemiology, including modeling the spread of AIDS through a population. Coverage is based on courses taught by the author over many years and the material is class tested. The reader is aided by many exercises that examine key points and extend the presentation in the body of the text. All students of mathematical biology will find this book to be a highly useful resource.
Average customer rating:
- The most mathematically cogent introduction to electrophysiology
|
Introduction to Theoretical Neurobiology (Cambridge Studies in Mathematical Biology)
Henry C. Tuckwell
Manufacturer: Cambridge University Press
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Introduction to Theoretical Neurobiology (Cambridge Studies in Mathematical Biology)
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Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems
ASIN: 0521022223 |
Book Description
The human brain contains billions of nerve cells whose activity plays a critical role in the way we behave, feel, perceive, and think. This two-volume set explains the basic properties of a neuron--an electrically active nerve cell--and develops mathematical theories for the way neurons respond to the various stimuli they receive. Volume 1 contains descriptions and analyses of the principle mathematical models that have been developed for neurons in the past thirty years. It provides a brief review of the basic neuroanatomical and neurophysiological facts that will form the focus of the mathematical treatment. Tuckwell discusses the mathematical theories, beginning with the theory of membrane potentials. He then goes on to treat the Lapicque model, linear cable theory, and time-dependent solutions of the cable equations. He concludes with a description of Rall's model nerve cell. Because the level of mathematics increases steadily upward from Chapter Two some familiarity with differential equations and linear algebra is desirable.
Customer Reviews:
The most mathematically cogent introduction to electrophysiology.......2007-02-28
Of all the introductory texts on electrophysiology, this one is by far the most mathematically literate. This is a two volume set. Volume 1 covers Nernst Plaank equilibrium equations, integrate and fire neurons, linear cable theory and the Rall model of dendrites. Volume 2 delves into the theory of the action potential - Hodgkin Huxley eqs and the various spinoffs, and some stochastic theory of spontaneous activity. This book was published in 1988, so it predates much of the more recent electrophysiological theory including the zoo of channels and current sources that have been more recently characterized, or the theory of recurrent networks, for example. Also, there are other books - Aidley's Physiology of Excitable Cells, or Kandel and Schwartz - that convey more sense of the underlying biology. But for a mathematically coherent treatment of the bedrock concepts in electrophysiology, nothing else comes close.
Book Description
The second part of this two-volume set contains advanced aspects of the quantitative theory of the dynamics of neurons. It begins with an introduction to the effects of reversal potentials on response to synaptic input. It then develops the theory of action potential generation based on the seminal Hodgkin-Huxley equations and gives methods for their solution in the space-clamped and nonspaceclamped cases. The remainder of the book discusses stochastic models of neural activity and ends with a statistical analysis of neuronal data with emphasis on spike trains. The mathematics is more complex in this volume than in the first volume and involves numerical methods of solution of partial differential equations and the statistical analysis of point processes.
Customer Reviews:
The most mathematically cogent introduction to electrophysiology.......2007-02-28
Of all the introductory texts on electrophysiology, this one is by far the most mathematically literate. This is a two volume set. Volume 1 covers Nernst Plaank equilibrium equations, integrate and fire neurons, linear cable theory and the Rall model of dendrites. Volume 2 delves into the theory of the action potential - Hodgkin Huxley eqs and the various spinoffs, and some stochastic theory of spontaneous activity. This book was published in 1988, so it predates much of the more recent electrophysiological theory including the zoo of channels and current sources that have been more recently characterized, or the theory of recurrent networks, for example. Also, there are other books - Aidley's Physiology of Excitable Cells, or Kandel and Schwartz - that convey more sense of the underlying biology. But for a mathematically coherent treatment of the bedrock concepts in electrophysiology, nothing else comes close.
Average customer rating:
- Don't start with this book
- Unsuitable for its stated purpose.
- Interesting but not very good for beginners
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Computational Molecular Biology: An Introduction
Peter Clote , and
Rolf Backofen
Manufacturer: Wiley
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Bioinformatics: Sequence and Genome Analysis
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Bioinformatics and Functional Genomics
ASIN: 0471872520 |
Book Description
Recently molecular biology has undergone unprecedented development generating vast quantities of data needing sophisticated computational methods for analysis, processing and archiving. This requirement has given birth to the truly interdisciplinary field of computational biology, or bioinformatics, a subject reliant on both theoretical and practical contributions from statistics, mathematics, computer science and biology.
* Provides the background mathematics required to understand why certain algorithms work
* Guides the reader through probability theory, entropy and combinatorial optimization
* In-depth coverage of molecular biology and protein structure prediction
* Includes several less familiar algorithms such as DNA segmentation, quartet puzzling and DNA strand separation prediction
* Includes class tested exercises useful for self-study
* Source code of programs available on a Web site
Primarily aimed at advanced undergraduate and graduate students from bioinformatics, computer science, statistics, mathematics and the biological sciences, this text will also interest researchers from these fields.
Customer Reviews:
Don't start with this book.......2004-02-13
In general I agree with the two previous reviews.
This book is not very good as an introduction. First read some other book such as Setubal and Meidanis, "Introduction to Computational Molecular Biology"; or Krane & Raymer, "Fundamental Concepts of Bioinformatics". These books have more readable narrative and examples.
The writing in this book is obtuse. It is written like an advanced abstract math book, not like an ostensibly applied science book. The notation is unnecessarily intricate. Even though it says "Introduction" in the title, there are very few tutorial examples. This is just for mathematicians/computer scientists: no biologist I have ever known would/could read this and really understand the algorithms.
This book does, however, have one of the more complete detailed descriptions of various algorithms used for sequence matching, etc. If you have read some other books and are looking for more details on algorithms, then this is your book. But I'm still waiting for THE ultimate Computational Biology book!
Unsuitable for its stated purpose........2001-03-21
The book purports to be a "self-contained introduction" to computational biology. It fails on both counts due to its excessive ambition, its opaque pedagogy, and a large number of significant typographical errors, such as entire subroutines missing from pseudocode examples. Undergraduates seeking an accessible survey are advised to look elsewhere.
That said, the mathematical rigor of the text makes it ideal for students who have moved beyond the need for accessible surveys and wish to improve their fundamental understanding of the field.
Interesting but not very good for beginners.......2000-11-23
This is an unusual book. The authors obviously have not been aquinted with biomolecular sequence analysis and fail to give state-of-the-art references to research work in this field. The same comment applies to the description of applications of Shannon communication theory to DNA and protein sequence analysis. The enormous impact of these applications in the 1970s, 1980s and 1990s is not reflected in the book and one could wonder why the authors bother to write of Shannon theory at all. In addition to the above misgivings the authors decided to confuse the reader by including a discussion of quite controversial relationship between Shannon entropy and thermodynamic entropy. Both computational and laboratory biologists will not benefit from this kind of confusion. Mathematicians and computer scientist will probably be mislead by a superficial treatment of this quite intricate topic. Physicists and chemist will probably be able to sort out useful information from over-interpretations but they may wonder why this issue is discussed in a computational biology text.
Despite the above critique I like the book. Organization of this text is interesting and distinctly different form other books in the field. Chapters on sequence alignment and phylogenetic trees are most interesting and original. They should probably be read in conjunction with more systematic textbooks such as Gusfield's "Algorithms on strings, trees and sequences" or Li's "Molecular evolution." Despite many misgivings (see the beginning paragraph of this review) the mathematical primer (chapter 2) is very much worth reading for its originality and compactness. Particularly sections about probability distributions and combinatorial optimization can be useful for non-mathematicians and interesting for those who are mathematically literate. However, care should be exercised (see the beginning paragraph) while reading sections about entropy and about optimality of the genetic code. Chapter 1 about principles of molecular biology is not very good for non-biologists because it is too compact. Chapter about structure prediction is also too compact to be either understandable to non-specialists or enjoyable by the experts. If the authors' ambitious approach was to be sustained, this chapter should probably be expanded to the size of entire book. Exercises at the end of every chapter of the book are interesting and worth the reader's attention. It would probably be good to have access to solutions of all exercises but it is a minor problem.
In summary: it is an interesting book but it should be read in conjunction with other texts. It should not be recommended to the beginners in computational biology. Mathematically seasoned readers will enjoy reading selected parts of this book. It would be nice if the publisher could consider lowering price of this book (already in paperback.)
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An Introduction to Structured Population Dynamics (CBMS-NSF Regional Conference Series in Applied Mathematics)
J. M. Cushing
Manufacturer: Society for Industrial Mathematics
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ASIN: 0898714176 |
Book Description
Interest in the temporal fluctuations of biological populations can be traced to the dawn of civilization. How can mathematics be used to gain an understanding of population dynamics? This monograph introduces the theory of structured population dynamics and its applications, focusing on the asymptotic dynamics of deterministic models. This theory bridges the gap between the characteristics of individual organisms in a population and the dynamics of the total population as a whole. In this monograph, many applications that illustrate both the theory and a wide variety of biological issues are given, along with an interdisciplinary case study that illustrates the connection of models with the data and the experimental documentation of model predictions. The author also discusses the use of discrete and continuous models and presents a general modeling theory for structured population dynamics.
Books:
- Animal Architects: Building and the Evolution of Intelligence
- Applied Longitudinal Data Analysis: Modeling Change and Event Occurrence
- Applied Numerical Methods with MATLAB for Engineers and Scientists
- Applied Numerical Methods with MATLAB for Engineers and Scientists
- Applied Numerical Methods with MATLAB for Engineers and Scientists
- Bioaerosols Handbook
- Brief Calculus: An Applied Approach
- Children's Mathematics: Cognitively Guided Instruction
- Combinatorial Optimization
- Competing on Analytics: The New Science of Winning
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