Reviews (20)

more challenging than trying to unravel the human genome.
I used this book to teach a bioinformatics course in a foreign language because it was only one of two available in both english and chinese.I'm not sure it wouldn't have been less confusing to simply use a english textbook and let the students translate the text for themselves.To give the author credit, he has compiled an enormous quantity of information and made it available in a single location and that is no mean feat.At the very least, it is a valuable starting point to find both useful references to better explanations and software appropriate to almost any analysis you might want to do.On the downside, the prose is a tangled mess and is beyond comprehension in places.there are points where, even though i understand the underlying theories used throughout the book, i still couldn't figure out some of the examples used to illustrate particular methods.For example, there are some figures which have captions which run for a page and a half.Finally, in the majority of cases, the figures are taken directly from key papers on each topic, and associated explanations consist of sentences copied verbatim from the text. I may be doing the author a gross injustice here, but in many of the explanations, i was left with the same impression i get when reading students papers when they have copied something out of a textbook, without really understanding what is going on.Having said all of the above, i would still recommend taking a look at this book, but be ready to access the excellent list of references if you want a more insightful understanding of many of the methods described throughout.

Leaves something to be desired
I took Dr. Mount's class at the U. or Arizona, and he's a really smart guy, but the man can't explain anything. It's not just his book either; his lectures are just as cryptic. I went to class thinking I understood the concepts, but then I got totally confused when he lectured. I would try to clarify things with the book, and again, I'd get even more confused. Someone who reviewed this book earlier said that he tends to use 10 words where he should use 1; I couldn't agree more. The figures in this book also need a major overhaul, and he should definitely include more examples of the many complex concepts he talks about. While I have no doubt that there is plenty of useful information in there, getting anything out of it is a chore. I would only recommend this book to someone who already had a strong knowledge of bioinformatics concepts.

Bioinformatics: Sequence and Genome Analysis by David W. Mount [Paperback]
Book is a good reference textbook for Bioinformatics.Of course the material covered is technical and dense, but that is unavoidable for the subject matter that the book covers. ... Read more

Subjects:  1. Amino acid sequence    2. Bioinformatics    3. Data processing    4. Genetics    5. Life Sciences - Genetics & Genomics    6. Nucleotide sequence    7. Science    8. Science/Mathematics    9. Genetics (non-medical)   

Reviews (7)

More for mathematicians than computer scientist
This book introduces the concepts of kernel-based methods and focuses specifically on Support Vector Machines (SVM). It is hard to read and a good background in mathematic is clearly needed. The book has a strong emphasis on SVM starting from the very first line of text. Concepts are well explained, although equations are not clear. The notation doesn't facilitate the reading at all. The book covers linear as well as kernel learning. The kernel trick is well described. It is easy to understand ideas behind SVM while reading the corresponding chapter. Finally a small chapter on SVM applications is proposed. Unfortunately, it only contains typical SVM applications (i.e. standard problems).
A little dry.
The book is a little dry at times. Also, I didn't get a very clear idea of how to select kernel functions, which seems pretty important.

Not even close to an intro...
Oh Puhleeeezzzzz... How is your vector math??? Remember your linear algebra well?Do you have a background in SVM's? Intuitively able to suck out of thin air the meaning of the Gamma co-efficient as applied to svm's?? You've read all the background papers and remember your formal logic???? No?? too bad..your out of luck..
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Subjects:  1. Algorithms    2. Algorithms (Computer Programming)    3. Artificial Intelligence - General    4. Computer Books: General    5. Computers    6. Computers - General Information    7. General    8. Kernel functions    9. Machine Learning    10. Programming - General    11. Computers / Bioinformatics    12. Data capture & analysis    13. Pattern recognition   

Subjects:  1. Bioinformatics    2. Biotechnology    3. Medical    4. Medical / Nursing    5. Medical informatics    6. Reference    7. Applications of Computing    8. Biomedial Informatics    9. Health Informatics    10. Medical / Administration    11. Medical Computing    12. Medical equipment & techniques   

Reviews (10)

Great introductory text
This is an excellent introduction to Bioinformatics. It does assume some very basic knowledge of biology- perhaps a couple of paragraphs could help the total newbies.
great beginner
In spite of the title (I don't know many dummies interested in multiple sequence alignments) this reference is written by experts in the field of bioinformatics and is very accessable for the beginner.I purchased this book as a beginning graduate student so that I could learn which programs to use to compare amino acid and nucleic acid sequences as well as prepare them for publication and this book was perfect for this end.This text doesn't delve into the algorithms or much theory (which is learned through practice and other sources), nevertheless, I recommend this for the researcher for a crash course or quick reference.This book really helped me get my feet wet in this area (and recently publish a nice alignment) and will certainly reduce my workload next semester for my bioinformatics course!

misleading title ....
The tile might be misleading.
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Subjects:  1. Bioinformatics    2. Biological Research    3. Biology    4. Biotechnology    5. Computer Books: Operating Systems    6. Data Processing - General    7. Databases    8. Internet resources    9. Life Sciences - Biology - General    10. Life Sciences - Genetics & Genomics    11. Research & Methodology    12. Science    13. Science/Mathematics    14. Computer Software Packages    15. DNA    16. Epidemiology & medical statistics    17. Medical / Biotechnology   

Reviews (5)

Nice introduction, but no more
Well, at first I was petrified to find a book that sounded like it deeply explores the subject of kernel methods. But all in all, it did not quite achieve what I hoped for. As a practical approach, when it comes to implementation, it serves nicely as a reference. The deeper mathematical roots of kernels (especially when it comes to measure theory and functional analysis) are not dealt with at all or just scratched at the very surface. The notation is sometimes awkward, mentioning for example the representation of an object in a given vector space with respect to the basis. And: Too much copied and pasted from the former book about SVMs. Basically, reading papers of Carmeli, Aronszajn and others will give you a much deeper insight into the subject.

coherent and accessible reference, ready-to-use algorithms
This work presents a coherent overview of an important field in machine learning. The unifying framework of kernel methods has proven state of the art results and the community has been waiting for a book like this to make both theory and practice of kernel methods accesssible for readers of all different backgrounds (researchers, students, practioners from both academia and industry, ...).
A Useful Reference on Kernel Methods
The book is divided into 3 parts. The theory is all in part I,
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Subjects:  1. Algorithms    2. Computer Books: Languages    3. Computers    4. Data processing    5. General    6. Kernel functions    7. Machine learning    8. Mathematics    9. Pattern perception    10. Programming - Systems Analysis & Design    11. Computer Software Packages    12. Computers / Bioinformatics    13. Pattern recognition   

Reviews (1)

Book contains many chapters to help get you started
I purchased this book to learn specific details and look at applications for the functions present in bioconductor.I have had trouble applying some of the chapters to custom data because they are written for specific microarray/data formats.Overall, this book is a good value because it contains examples of how bioconductor can be used to aid in hypothesis testing, but I struggle to apply what I have read to the different types of data I have.The section on Statistical analysis for genomic experiments and the section on gaphs and networks should be the reason you purchase this book. They are very helpful and interesting. The case studies were not very helpful in my opinion. ... Read more

Subjects:  1. Biostatistics    2. Life Sciences - Biology - General    3. Life Sciences - Zoology - General    4. Medical / Nursing    5. Science    6. Science/Mathematics    7. Biology, Life Sciences    8. Computing and Information Technology    9. Medical / Biostatistics   

Reviews (13)

Somewhat more than an out-of-date catalog of tools
The book is a collection of chapters by different authors addressing software tools for various problems: database search, multiple sequence alignment, gene prediction, protein structure prediction, etc.A big flaw is that all of the authors assume a different level of prior background and have rather different emphases. A survey for tool users
Like any survey, it seems to touch the major features only. And, as others have pointed out, the tools change but the book doesn't.
Bioinformatic for the beginner...
I guess that everybody interrested by this kind of book knows already a little about bioinformatic and wants to improve his bioinformatician skill. So forget about this book:Read more

Subjects:  1. Base Sequence    2. Bioinformatics    3. Computational Biology    4. Life Sciences - Biochemistry    5. Life Sciences - Biology - Molecular Biology    6. Science    7. Science/Mathematics    8. Sequence Analysis    9. methods    10. Genetics (non-medical)    11. Science / Molecular Biology   

Reviews (1)

A great review of network reconstructions
While this may not be an all encompassing review of what systems biology is, it provides an insightful view on network reconstruction. I've found this book very helpful and well written (being a first edition, it does have a few typos, but this is normal). It has a very logical flow, but it is written on the level of a professional or graduate student interested in entering the field of systems biology. ... Read more

Subjects:  1. Bioinformatics    2. Computational biology    3. Genomics    4. Life Sciences - Biology - General    5. Research & Methodology    6. Science    7. Science/Mathematics    8. System Theory    9. Biology, Life Sciences    10. Science / Genetics   

Subjects:  1. Bioinformatics    2. Genetics    3. Life Sciences - Biochemistry    4. Life Sciences - Evolution    5. Life Sciences - Genetics & Genomics    6. Science    7. Science/Mathematics    8. Biochemistry    9. Genetics (non-medical)    10. Science / Biochemistry   

Reviews (1)

Most Elegant Account of Bioinformatics
I was impressed with the 1st edition of this book for its
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Subjects:  1. Bioinformatics    2. Biostatistics    3. Life Sciences - Biology - General    4. Medical    5. Medical / Nursing    6. Statistical methods    7. BLAST    8. Medical / Biostatistics    9. computational biology   

Subjects:  1. Computer Books: General    2. Computer Science    3. Computers    4. Computers - Languages / Programming    5. Information Technology    6. Programming - Software Development    7. Computers / Programming / Software Development    8. General Theory of Computing    9. bioinformatics    10. cluster computing    11. computational mathematics    12. computational science    13. distributed systems    14. high-performance communication    15. high-performance computing    16. image processing    17. information systems    18. internet computing security    19. numerical computing    20. parallel computing    21. supercomputing    22. visualization   

Reviews (1)

"Computational genome analysis: An Introduction" Deonier R., Tavare S., Waterman M. Springer-Verlag New York, Inc., Secaucus, NJ
This textbook was based on the authors' instructional experiences in undergraduate Computational Biology courses for Bachelor seniors, first-year Master's, and Ph.D. students at the University of Southern California.Readers could also includeinvestigators in medical schools, computer scientists, biologists, applied mathematicians,biochemists, and persons working in the biotechnology industry.
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Subjects:  1. Bioinformatics    2. Biostatistics    3. Computer Science    4. Genetics    5. Life Sciences - Biochemistry    6. Life Sciences - Biology - Molecular Biology    7. Life Sciences - Genetics & Genomics    8. Mathematics    9. Science    10. Science/Mathematics    11. DNA    12. Medical / Biostatistics    13. Probability & statistics   

Editorial Review

Biology, it seems, is a good showcase for the talents of Perl. Newcomers to Perl who understand biological information will find James Tisdall's Read more

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Reviews (23)

Mostly for the Biologist
People come to Bioinformatics from either the bio side or the CS side, with a few from various other disciplines. This book is best for the bio person who is getting into programming, not the programmer who is getting into bio.
Beginning Perl for BioInformatics
Excellent book.The perl programming language is the most versitile and powerful software tool available today.This book was written for Biologists to learn this incredible programming language.Examples are pulled from real problems Biologists face and explained in terms they can understand.The book is clearly written.

excellent introduction...
i find this book is an excellent intoudction for one of the most intersting topic..The book is so easy to read if you know the elementary of molecular biology and begining introudction about perl.I do recommed this book to start with if you interested about programming for bioinformatics.You will be able to build simple bioinformatics programmes after reading this book as well as you will be able to understand easily how the commerically avaliable bioinformatics programs are working. ... Read more

Subjects:  1. Bioinformatics    2. Computer Books: General    3. Computer Science    4. Computers    5. Computers - Languages / Programming    6. Data processing    7. Life sciences    8. Perl (Computer language)    9. Perl (Computer program languag    10. Perl (Computer program language)    11. Programming Languages - Perl    12. Biology, Life Sciences    13. Computers / Languages / Programming    14. Computers / Programming Languages / CGI, JavaScript, Perl, VBScript    15. Computers / Programming Languages / Perl    16. Computers/Bioinformatics    17. Programming languages    18. biological data analysis, GenBank    19. Science    20. Molecular Biology    21. Data mining   

Reviews (2)

Simply fascinating
The sheer number of books in the area of bioinformatics is growing rapidly, and each author takes a different approach to the topic: Bergeron's Bioinformatics Computing uses concepts from Information Theory, while Pervzner's Computational Molecular Biology uses Graph Theory and Durbin et. al. Biological Sequence Analysis use Statistics and hard core mathematical analysis to get the point across.Campbell and Heyer, the authors of Discovering Genomics, Proteomics, & Bioinformatics use concepts from Electrical Engineering and Control Engineering to prescribe some of the details of genomics and proteomics.As an instructor you need to choose the right book to meet the needs and understanding level of your target audience.For biology students that have little mathematics or statistics knowledge but have taken Physics II (E&M), this would be the perfect book.The authors are a little heaving on the biological terminologies, so a sophomore level Computer Science major with little or no biology background would have a difficult time coming up to speed at the beginning, but the glossary of terms at the end of the book is comprehensive enough that can aid the learning process.
A novel approach!
Abstract: great and innovative book. I have seen many books, but none like this. It is still concise in this first edition, yet could become the "Lewin" of genomics.Read more

Subjects:  1. Bioinformatics    2. Biotechnology    3. Genetic Code    4. Genomics    5. Life Sciences - Biochemistry    6. Life Sciences - Biology - General    7. Life Sciences - Biology - Molecular Biology    8. Life Sciences - Genetics & Genomics    9. Proteins    10. Proteomics    11. Science    12. Science/Mathematics    13. Genetics (non-medical)    14. Science / Molecular Biology   

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Reviews (30)

horrible
This book is the worst I've ever purchased. It has been no help whatsoever.It had a couple examples of PERL programming...big deal. Good introduction, somewhat uneven
This book is a good introduction to Bioinformatics and to what it takes to get started in the field. Some reviewers deride it as too superficial or as too Unix-centric, but I think those are two of its strengths. The authors lay no claim to having written the definitive work on the subject of Bioinformatics, and they freely admit that they come in with a certain bias. If you are serious about Bioinformatics this won't be your last book anyway, but it'll get you started. Useful only for a reference book
We are all well aware that it is impossible to write a book on bioinformatics satisfying all types of readers. That is the reason why we are spending much time on finding a book that we can say "This book is just for me!"Read more

Subjects:  1. Bioinformatics    2. Computer Books: General    3. Computers    4. Data processing    5. Life Sciences - Biology - General    6. Life sciences    7. Perl (Computer program language)    8. Programming - General    9. Science    10. Applications of Computing    11. Computational Biology    12. Computers / Bioinformatics    13. Computers / General    14. Genetics (non-medical)    15. Science/Life Sciences - Biology - General    16. data mining, bioinformatics    17. Data mining    18. Perl (Computer program languag   

Reviews (3)

Highly Recommended
"...an intriguing work targeted toward biologists wanting to solve problems...provides a compendium of many biological insights and breakthroughs and will be a useful resource...highly recommended." (Choice, Vol. 41, No. 7, March 2004)

Excellent for bioinformatics from a user's perspective
Unlike the previous review, I found the user perspective, rather than the mathematical perspective refreshing.I have been teaching bioinformatics to CS students for several years and all too often the students are great at algorithms and theory but do not understand the user they are designing for.This book teaches just that -- how to use bioinformatics from a user or researcher's viewpoint.Medical students and biologists will find it useful for direct applicability to their work, but I also reccomend it for bioinformatics students who need to complement their theoretical background with practical use.All too often, CS students of bioinformatics can design a great database with powerful access tools, but with a horrible interface because they don't have this perspective. Bioinformatics for computational dummies
A genious attempt to present bioinformatics as if it is a discipline without any computational content. Perfect for students who lost any hope to understand what is the engine drivingbioinformatics tools but want simply to memorize how to use them instead. Must be a very comfortable reading for biologists but is as exciting as a long carefully designed restaurant menu for a mathematician. If the author wants to raise a new generation of biologists with this book then biology and *real* bioinformatics will be divorced forever. ... Read more

Subjects:  1. Bioinformatics    2. Data processing    3. Genetics    4. Genomics    5. Life Sciences - Biochemistry    6. Life Sciences - Biology - Molecular Biology    7. Proteomics    8. Science    9. Science/Mathematics    10. Biotechnology    11. DNA    12. Medicine: General Issues    13. Science / Molecular Biology   

Reviews (2)

A great textbook and reference book for both students and researchers.
Bioinformatics is a burgeoning interdisciplinary field that holds great promise in handling large scale biomedical data by computational approaches. The book "Fundamental Concepts of Bioinformatics" is a very important textbook and reference book for both biology and computer science students and researchers, as well as for those professionals in medical science, and the pharmaceutical industry. It goes with saying that many laboratory approaches are expensive and time consuming, and cannot hope to keep up with the rapid growth of available data, making computational approaches indispensable.While a number of books dealing with bioinformatics, most of them are generally limited in scope, and very few of them provide a comprehensive but easy understandable treatment from both computer science and biomedical principles.This book is unique and is well-organized, and provides a systematic but straightforward treatment of the various techniques used for bioinformatics. One of the attractive features of the book is the comprehensive coverage of the various types of data use in bioinformatics analysis, followed by computational approaches that are most suited to the particular data type. This book also helps researchers entering bioinformatics. The reader can quickly identify the chapters that are most relevant to their own interest. It could also be used as a textbook for a senior undergraduate or a graduate level bioinformatics course. It is a valuable resource to both students and researchers, no matter whether they perform experimental research or computer science studies. Computer scientists, mathematicians, and statisticians seeking to discover how bioinformatics is related to well-defined paradigms in computer science could also benefit greatly from this book. Professors Michael L. Raymer and Dan E. Kranehave authored many research articles in both computer science and biological science. I highly recommend this book as a great textbook and reference book for both students and researchers.

good undergrad/opening text
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Subjects:  1. Science/Mathematics    2. Biotechnology    3. Life Sciences - Biology - Molecular Biology    4. Science / Molecular Biology    5. Life Sciences - Biology - General    6. Science    7. Bioinformatics   

Reviews (6)

Perhaps the CGI could have been omitted?
This is the sequel to his earlier beginner's book on Perl. Now, he goes further into usages of Perl. While experienced programmers will not find these terribly challenging, they are not the intended audience.
Good Companion text
This first half of the book focuses entirely on Object-Oriented(OO) Perl. The second half follows up with a general survey of various perl implementations of particular programming issues involving databasing, cgi, graphics, modules, etc, and BioPerl.
Great book, leads to others for true mastery
Published in late 2003, this clearly-written book picks up where "Beginning Perl for Bioinformatics" leaves off.Perl is very commonly used in the field of bioinformatics, and this book does a good job of surveying the more advanced topics in perl from the bioinformatics point-of-view.For a more thorough treatment of each of these topics though, the student will need to explore more specialized titles.
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Subjects:  1. Bioinformatics    2. Computer Books: Operating Systems    3. Computers    4. Computers - Languages / Programming    5. Operating Systems - General    6. Perl (Computer program languag    7. Perl (Computer program language)    8. Programming Languages - Perl    9. Bioinformatics, Perl, bioperl    10. Computers / Languages / Programming    11. Computers / Programming Languages / CGI, JavaScript, Perl, VBScript    12. Computers / Programming Languages / Perl    13. Computers/Bioinformatics    14. Programming languages   

Reviews (1)

Very good approach to modern biology.
This book gives a very good overview of cell and molecular biology. The information provided is not complete but enough to get a solid knowledge about biological processes. That means you do not have to read hundreds of papes to come to the point you are interested in. Moreover, it provides you a good knowledge about different types of proteins and their role in biological processes. This is important because somehow they are all connected with each other in a complex way.
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Subjects:  1. Bioinformatics    2. Biology (General)    3. Biomedical engineering    4. Cytology    5. Life Sciences - Biology - General    6. Life Sciences - Biophysics    7. Molecular biology    8. Science    9. Science/Mathematics    10. Biology, Life Sciences    11. Biotechnology    12. Science / Biophysics