Nonneutral Evolution: Theories and Molecular Data

Book Description

All organisms--from the AIDS virus, to bacteria, to fish, to humans--must evolve to survive. Despite the central place of evolution within biology, there are many things that are still poorly understood. For Charles Darwin, the driving force behind all evolution was natural selection. More recently, evolutionary biologists have considered that many mutations are essentially neutral with respect to natural selection. Many questions remain. Are molecular differences between species adaptive? Are differences within species adaptive? Modern biotechnology has enabled us to identify precisely the actual DNA structure from many individuals within a population, and thus to see how these DNA sequences have changed over time and to answer some of these questions. At the same time, this knowledge poses new challenges to our ability to understand the observed patterns. This exciting volume outlines the biological problems, provides new perspectives on theoretical treatments of the consequences of natural selection, examines the consequences of molecular data, and relates molecular events to speciation. Every evolutionary biologist will find it of interest.

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Essential Mathematical Biology
Nicholas F. Britton
Manufacturer: Springer-Verlag London
ProductGroup: Book
Binding: Paperback

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ASIN: 185233536X

Book Description

Essential Mathematical Biology is a self-contained introduction to the fast-growing field of mathematical biology. Written for students with a mathematical background, it sets the subject in its historical context and then guides the reader towards questions of current research interest, providing a comprehensive overview of the field and a solid foundation for interdisciplinary research in the biological sciences.

A broad range of topics is covered including: Population dynamics, Infectious diseases, Population genetics and evolution, Dispersal, Molecular and cellular biology, Pattern formation, and Cancer modelling.

This book will appeal to 3rd and 4th year undergraduate students studying mathematical biology. A background in calculus and differential equations is assumed, although the main results required are collected in the appendices. A dedicated website at www.springer.co.uk/britton/ accompanies the book and provides further exercises, more detailed solutions to exercises in the book, and links to other useful sites.

Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)

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Informative, but not information I can use
Excellent survey of the field
it's about time!!!

Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
James M. Bower
Manufacturer: M.I.T. PRESS
ProductGroup: Book
Binding: Hardcover

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ASIN: 0262024810

Book Description

The advent of ever more sophisticated molecular manipulation techniques has made it clear that cellular systems are far more complex and dynamic than previously thought. At the same time, experimental techniques are providing an almost overwhelming amount of new data. It is increasingly apparent that linking molecular and cellular structure to function will require the use of new computational tools.

This book provides specific examples, across a wide range of molecular and cellular systems, of how modeling techniques can be used to explore functionally relevant molecular and cellular relationships. The modeling techniques covered are applicable to cell, developmental, structural, and mathematical biology; genetics; and computational neuroscience. The book, intended as a primer for both theoretical and experimental biologists, is organized in two parts: models of gene activity and models of interactions among gene products. Modeling examples are provided at several scales for each subject. Each chapter includes an overview of the biological system in question and extensive references to important work in the area.

Customer Reviews:

Informative, but not information I can use.......2004-05-03

Regulatory networks are central to every aspect of computational biology. Determining what they are, and what genes, proteins, and post-translational modifications interact is a major and exciting field of study.

I just didn't come away from this book with that excitement. I was hoping for more about the large-scale regulation networks, but these papers go down to the quantum mechanics of interactions between pairs of molecules. I appreciate that the exact interactions matter, and that computation is probably the only way to examine some kinds of interactions (e.g. the ones in lethal mutations). It's just not what I think of as a "network."

I was also hoping for some more specifics about the computation techniques. There were some interesting insights here. For example, I never thought about the similarities between steady state chemical equilibrium and steady state Markov model behavior before, but the formalisms have striking similarities. I was also interested in some of the information-based measures for determining how well a model represents a system. I learned that the statistical assumptions behind normal chemical "equilibrium" break down at the scale of bacteria - instead, presence or absence of individual molecules matters more. Still, those were isolated kinds of facts and never came together into a whole for me.

The range of views was worthwhile. On the whole, though, the models all seemed very low-level to me, probably not well suited to handling more than a few dozen interactions, and the computation specifics were not always explicit. I'm still looking for a book with more information that I can apply directly.

Excellent survey of the field.......2001-08-04

An excellent survey for anyone contemplating doing research in this area. The authors make a special effort to identify the open research problems, what has been done to date and what there is very little of. This book will bridge the gap for anyone with a background in Molecular Biology that wants to build computer models for cellular and genetic activities. It is especially focused on gene regulation, but also covers other modeling areas such as diffusion. In reading this book, you will appreciatge both the good start this field is off to, but also the long way to go before a complete cell can be modeled. A great area to do pioneering work.

it's about time!!!.......2001-04-03

For many years, biologists have been accumulating descriptions of biological "parts" with an almost complete lack of a framework for understanding how those parts might really work together. This book represents the first and so far only example I have seen of an effort to describe modeling techniques that are right now being developed to construct such a framework. There are other books on "computational biology", but most of them are focused only on measuring and comparing different strands of molecules -- this book describes how computational techniques are starting to be applied to actually trying to understand how those molecules work together to generate life. On the outside jacket of the book, Bruce Alberts, President of the National Academy of Science, AND the guy whose book on molecular biology I had to buy for a lot of money when I was in college, describes the authors of this book as being "Brave". I would say it is an introduction to a "Brave New World". This has to be where biology is going -- Each of the chapters are written by different people, and as such there is some variation in readability. I also wish that the color illustrations were part of the chapter they refer to instead of being grouped in the middle. But most of the chapters start with enough of an overview to be understandable to anyone with a decent background in biology. And WOW -- biology is going to get much more exciting!! Oh one other thing -- the art on the inside of the jacket is wonderful - especially in contrast to the black cover with its standard diagram of metabolism -- I wonder if there is a message there :-) .

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Someone who would like to do undergraduate research?

Applied Molecular Genetics
Roger L. Miesfeld
Manufacturer: John Wiley & Sons
ProductGroup: Book
Binding: Paperback

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ASIN: 0471156760

Book Description

This text explains the key biochemical and cell biological principles behind some of today's most commonly used applications of molecular genetics, using clear terms and well-illustrated flow schemes. The book is divided into several sections and moves from basic to advanced topics while providing a concise overview of fundamental concepts in modern biotechnology. Each chapter concludes with a Laboratory Practicum describing a hypothetical research objective and the sequence of steps that are most often used to investigate biological questions using molecular genetic methods. In addition, the book provides informative summaries of the latest advances in molecular genetics, using attractive illustrations and a comprehensive reference list.

This text also introduces the use of Internet resources through the World Wide Web as a powerful new tool in molecular genetic research. Seven appendices are included in the book, providing a convenient information resource for properties of nucleic acids, protein and restriction enzymes, a description of common E. coli genetic markers and gel electrophoresis parameters, as well as a list of useful Internet address sites.

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Someone who would like to do undergraduate research?.......2000-09-29

This book is very simple to understand molecular biology work in the lab. Actually, the real advantage of this book is each chapter has an assignment (called "praticum" in this book) and that could be tried to learn DNA work in the lab. This book has included DNA works such as PCR, cloning, transfection (and transformation) and so on, except protein work such as protein purification, SDS-PAGE gel etc.. If any undergraduate student who would like to do independent research or undergrad research, this book would be helpful to figure out what kind of real techniques should be required based on your molecular biology background by your class.

Recent Progress In Bioconversion Of Lignocellulosics (Advances in Biochemical Engineering and Biotechnology)

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Recent Progress In Bioconversion Of Lignocellulosics (Advances in Biochemical Engineering and Biotechnology)
G.T. Tsao
Manufacturer: SPRINGER-VERLAG
ProductGroup: Book
Binding: Hardcover

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ASIN: 3540655778

Product Description

Recent Progress in Bioconversion of Lignocellulosics (Advances in Biochemical Engineering / Biotechnology)

Statistical Genetics of Quantitative Traits: Linkage, Maps, and QTL (STATISTICS FOR BIOLOGY AND HEALTH)

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Statistical Genetics of Quantitative Traits: Linkage, Maps, and QTL (STATISTICS FOR BIOLOGY AND HEALTH)
Rongling Wu
Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 0387203346

Book Description

The book introduces the basic concepts and methods that are useful in the statistical analysis and modeling of DNA-based marker and phenotypic data that arise in agriculture, forrestry, experimental biology, and other fields. It concentrates on the linkage analysis of markers, map construction and quantitative trait locus (QTL) mapping and assumes a background in regression analysis and maximum likelihood approaches. The strengths of this book lie in the construction of general models and algorithms for linkage analysis and QTL mapping in any kind of crossed pedigrees initiated with inbred lines of crops and plant and animal model systems or outbred lines in forest trees and wildlife species.

The book includes a detailed description of each approach and the step-by-step demonstration of live-example analyses designed to explain the utilization and usefulness of statistical methods. The book also includes exercise sets and computer codes for all the analyses used.

This book can serve as a textbook for graduates and senior undergraduates in genetics, agronomy, forest biology, plant breeding and animal sciences. It will also be useful to researchers and other professionals in the areas of statistics, biology and agriculture.

Drosophila Cytogenetics Protocols (Methods in Molecular Biology (Cloth))

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Drosophila Cytogenetics Protocols (Methods in Molecular Biology (Cloth))
Daryl S. Henderson
Manufacturer: Humana Press
ProductGroup: Book
Binding: Hardcover

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Drosophila: A Practical Approach (Practical Approach Series)

ASIN: 1588290506

Book Description

Leading drosophilists describe in step-by-step detail all the essential techniques for studying Drosophila chromosomes and suggest new avenues for scientific exploration. The chapters emphasize specimen preparation (from dissection to mounting) and cover both polytene and mitotic/meiotic chromosomes in depth. Each fully tested and readily reproducible protocol offers a background introduction, equipment and reagent lists, and tips on troubleshooting and avoiding pitfalls. A cutting-edge FISH and immunolocalization technique will be important for discovering how DNA sequence influences higher-order chromosome architecture and ultimately gene expression.

The Molecular Origins Of Life: Assembling the Pieces of the Puzzle

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The Molecular Origins Of Life: Assembling the Pieces of the Puzzle
Andre, Ed. Brack
Manufacturer: Cambridge University Press
ProductGroup: Book
Binding: Paperback

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ASIN: 0521564751

Book Description

The origin of life was probably the result of a singular event in the Earth's history, and reconstructing this event is like assembling a puzzle made up of many pieces. These pieces are composed of information acquired from many different disciplines. The aim of this book is to integrate the most recent discoveries in astronomy, planetology, paleontology, biology and chemistry, and use this knowledge to present plausible scenarios that give us a better understanding of the likely origin of life on Earth. Eighteen experts contribute chapters that discuss everything from the environment and atmosphere of the early Earth, to the appearance of organic molecules in the prebiotic environment, to primitive chiral chemical systems capable of self-replication and evolution by mutation. The book also discusses various clues to the origin of life that can be obtained by a study of the past and present microbial world, as well as from other planets.

Evolutionary Dynamics: Exploring the Interplay of Selection, Accident, Neutrality, and Function (Santa Fe Institute Studies on the Sciences of Complexity)

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Evolutionary Dynamics: Exploring the Interplay of Selection, Accident, Neutrality, and Function (Santa Fe Institute Studies on the Sciences of Complexity)

Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Paperback

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ASIN: 0195142659

Book Description

This book is an assessment and review of the recent progress in integrating evolutionary modeling and computation, molecular and developmental evolution, and nonlinear population dynamics into evolutionary theory. It brings together a wide range of eminent researchers in evolutionary dynamics in order to formulate a comprehensive theory that builds on nonlinear mathematics and physics. The text is divided into four sections: macroevolution; ephochal evolution; population genetics, dynamics, and optimization; and evolution of cooperation, each containing several in-depth chapters and discussions.

Introduction To Computational Molecular Biology

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Detailed broad overview of algorithms
Strong on algorithm analysis
Concise and to-the-point
Not a good introduction book
Not a good introduction book

Introduction To Computational Molecular Biology
Joal Carlos Setubal
Manufacturer: WADSWORTH
ProductGroup: Book
Binding: Hardcover

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ASIN: 0534952623

Book Description

Until now, those interested in the emerging field of computational molecular biology have used surveys and technical articles collected from many sources. Introduction to Computational Molecular Biology brings together major results in the field, in coherent and readable format. Setubal and Meidanis present a representative sample of problems in molecular biology, focusing on the algorithms that have been proposed to solve them. Readers will find background material on molecular biology, definitions of key terms, descriptions of models, and a full sample of algorithmic results. Key theoretical computer science concepts are emphasized, such as the improvement in asymtotic running time with better algorithms, the contrast between heuristics and an algorithm with guarantees, and the difficulty posed by NP-complete problems. Algorithms for sequence comparison, including the popular BLAST and FAST programs, are covered. Introduction to Computational Molecular Biology serves readers from both the mathematical and computing sciences as well as molecular biology. The authors assume a basic chemistry background and some training in college-level discrete mathematics and algorithms.

Customer Reviews:

Detailed broad overview of algorithms.......2005-11-16

We used this book in a bioinformatics class. It can take a whole semester to discuss this little book. The approach here is algorithmic. It explains fundamental bioinformatics algorithms in detail. In comparison to Pevzner's Computational Molecular Biology, it's more practical, and has less mathematical formalisms. This book peaks inside the black box of bioinformatics algorithms.
It's rigourous and for mathematics and computer science folks, and some material is difficult. Biologists may have a hard time with it, because of algorithm analysis and the required familiarity with graph theory. On the other hand, computer science folks shouldn't really take the introductory chapter on biology seriously.
Take a look at its Table of Contents to see what it covers, there's no point repeating it here.
Must have for anyone interested in implementing bioinformatics algorithms. On the other hand, if you're a biologist simply interested in how to use bioinformatics in your work, e.g., BLAST, there's no point reading this book.

Strong on algorithm analysis.......2005-02-03

This is a good book on some of the algortihms used in bioinformatics. That term may not have been in wide use back in `97, leading to the title that suggests a lot more focus on the molecules than is in fact present.

The book starts with two brief chapters on biology and mathematical basics - graph theory and algorithm analysis. I'm sorry to say that these really are too brief. A reader who comes in with little knowledge of either topic will probably leave with about the same level of knowledge.

After that, the authors give coverage of the basics, as `97 writers saw them: approximate string matching, fragment assembly, mapping, trees, and a discussion of the reversals that occur in DNA over evolutionary time. Each topic is presented carefully, in a number of variations, and with formal analysis of the algorithmic complexity. That last won't do much for the biologists in the crowd, but gives programmers a good idea of how each technique will behave as the problems grow larger (and they always do). The presentation generally stick with the most popular algorithms, emphasizing detailed presentation over breadth of coverage. Multiple alignment, in particular, could have used a lot more pages. Also, topics like assembly and restriction digests aren't at the forefront of analysis any more. They're important, but good algorithms exist in widely available tools, and more advanced analyses tend to attract more attention these days. The section on genome rearrangements is quite good, but seems to stand alone - it could have been one input into tree building, but the authors don't draw any clear relationships between the reorderings and any other problems.

The section on structure prediction is definitely showing its age. RNA structure prediction has come a long way since this was written, and protein structure prediction has come even farther. Discussions of the basic ideas are good, but a more recent reader will want a lot more development. The final section, on using DNA as a material for performing computations, is interesting but hardly mainstream. The authors use one or two problems as case studies, but don't present the kinds of tools that can be applied to lots of different problems, just a few point solutions.

This book's value, today, lies mostly in the clarity of its complexity analysis and in the pseudocode that gives a programmer a step in the right direction. It has a few unusual items, like a highly generalized gap model for approximate string matching. On the whole, though, more recent books present most of the same material at least as well, and cover more up-to-date topics.

When it was new, I might have given this book a five star rating. Times have changed, though, and I have to rate this book among the others on the shelves now.

//wiredweird

Concise and to-the-point.......2002-02-21

This is a really nice introduction to the most commonly used algorithms in bioinformatics. It is not really a general introduction to molecular biology or to computer science, and to make best use of this book a reader probably needs some prior exposure to both. But, for someone who has had a basic course in say genetics, and a basic programming course that covers simple data structures and algorithms etc., this volume provides all they will need to understand what is really happening when they run a BLAST search, for instance. A serious computer-science type person will probably not find the alogorithms described here very interesting, because they aren't meant to be elegant or interesting, just useful. I think a reader would have to have some direct interest in bioinformatics per se in order to enjoy this book. One thing that I find particularly nice is that the length of the chapters is just right so that you can read through a chapter in a single sitting, and because the chapters are largely independent of one another, its a handy book to have around and pick up when one has a little spare time. I recommend it very strongly.

Not a good introduction book.......2001-11-17

I do not think it is a good introduction book for biologists to learn computational biology. The authors should have used more figures and examples to illustrate the concepts. Also, I do not like the norrow margins of this book. I like to write comments and my understanding in the books when I read. There is simply no place to write.

Not a good introduction book.......2001-11-17

I do not think it is a good introduction book. The authors should have used more figures to illustrate the concepts. Also, I do not like the norrow margins of this book. I like to write comments and my understanding in the books. There is simply no place to write!

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