Book Description

This book evolved from an interdisciplinary graduate course entitled Molecular Modeling developed at New York University. Its primary goal is to stimulate excitement for molecular modeling research while introducing readers to the wide range of biomolecular problems being solved by computational techniques and to those computational tools. The book is intended for beginning graduate students in medical schools and scientific fields such as biology, chemistry, physics, mathematics, and computer science. Other scientists who wish to enter, or become familiar, with the field of biomolecular modeling and simulation may also benefit from the broad coverage of problems and approaches.

The book surveys three broad areas: biomolecular structure and modeling: current problems and state of computations; molecular mechanics: force field origin, composition, and evaluation techniques; and simulation methods: geometry optimization, Monte Carlo, and molecular dynamics approaches. Appendices featuring homework assignments, reading lists, and other information useful for teaching molecular modeling complement the material in the main text. Extensive use of world wide web resources is encouraged, and additional course and text information may be found on a supplementary website.

Some praise for Tamar Schlick's "Molecular Modeling and Simulation: An Interdisciplinary Guide":||"The interdisciplinary structural biology community has waited long for a book of this kind which provides an excellent introduction to molecular modeling."|-Harold A. Scheraga, Cornell University||"A uniquely valuable introduction to the modeling of biomolecular structure and dynamics. A rigorous and up-to-date treatment of the foundations, enlivened by engaging anecdotes and historical notes."|-J. Andrew McCammon, Howard Hughes Medical Institute, University of California at San Diego||"I am often asked by physicists, mathematicians and engineers to recommend a book that would be useful to get them started in computational molecular biology. I am also often approached by my colleagues in computational biology to recommend a solid textbook for a graduate course in the area. Tamar Schlick has written the book that I will be recommending to both groups. Tamar has done an amazing job in writing a book that is both suitably accessible for beginners, and suitably rigorous for experts."|-J.J. Collins, Boston University

FROM THE REVIEWS:

BIOTECH INTERNATIONAL [BTI]: " . . . The text emphasises that the field is changing very rapidly and that it is full of exciting discoveries. Many of these findings have lead to medical and technological breakthroughs. This book stimulates this excitement, while still providing students many computational details . . . It should appeal to beginning graduate students in medical schools, and in many scientific departments such as biology, chemistry, physics, mathematics, and computer science. ... Read more

Reviews (10)

Excellent book for both students and researchers
This book covers state-of-arts technologies used in today's hot field: molecular modeling. The book is easy to understand and it is suitable for graduate students in both theoretic majors and experimental majors. The homeworks in the book are practical for students to learn basic molecular modeling computer skills very fast.

Dr. Schlick is an expert in this field and her group has published tons of molecular modeling research papers. Her expertise also makes this book valuable for computational scientific researchers. I highly recommend it.

A long expected book in molecular modeling is finally here
I highly recommend Professor T. Schlick's book. It is beautifully written with many examples and great illustrations. The book is truly interdisciplinary; it covers, in good depth, both the biological and mathematical aspects of computational structural biology. Most chapters start with an amenable introduction and finish with "hands-on" recommendations and future challenges. I was particularly pleased with the level of detail in each chapter (in particular those that show the reader the advantages and pitfalls of the different methods presented). My colleague Mariel Vazquez and I used this book in the design and preparation of our "Special topics in Mathematics" course at the UC Berkeley Mathematics Department during the Spring of 2003.

This upper-level undergraduate/lower-level graduate course was centered on mathematical and computational models of the three dimensional structure of DNA, and DNA topology. We found Professor T. Schlick's book very useful in our class preparation. In particular we covered chapter 5 (DNA structure) completely, sections 3 and 4 from chapter 7 (basic principles and formulation of atomic interactions in molecular mechanics), and several sections or subsections from chapters 8 and 9 (force terms used in molecular dynamics simulations). We also covered most of the material in chapter 10 (Multivariate Minimization), and gave a brief introduction to chapter 11 (Monte-Carlo techniques) and chapter 12 (Molecular Dynamics algorithms).

Chapter 5 starts with a very amenable and brief introduction that relates DNA with other biological processes and describes some of the challenges in studying DNA structure. It continues describing the basic building blocks of DNA. The author wisely spends some time defining the nomenclature for each of the atoms, angles and bonds that form these basic blocks. The following sections teach the reader what parameters are relevant for describing a DNA double helix and how they characterize the A, B and Z- forms of DNA. Illustrations in this chapter are particularly helpful.

Although our course's approach to DNA supercoiling was different that the one in the book I found particularly useful some illustrations in chapter 6 and movies (to be found in her webpage) that Prof. Schlick's group has developed over the years. In brief, chapter 6 is a study of more complex structures and behavior of DNA (such as structural role of the DNA sequence, DNA-protein interactions, and higher order organization of DNA -i.e. DNA supercoiling and histone-DNA interactions). This chapter can be a good source for short research projects (e.g. final projects).

Chapters 7, 8 and 9 describe the basic concepts in molecular mechanics. From sections 7.3 and 7.4 I found of interest how the author addresses the problem of the system size (i.e. number of interacting molecules) and some of the details that the author gives for modeling the geometry of atomic interactions. At the end of the chapter (section 7.4.3) interested readers can find some of the limitations of current approaches. Chapters 8 and 9 describe in depth the force fields and how to implement them. Chapter 9 also illustrates with clarity how to implement periodic boundary conditions and the advantages of using different lattice models.

Chapter 10 describes a number of familiar methods for energy minimization (i.e. steepest descent, conjugate gradient, etc....). We used sections 10.1 to 10.4 and section 10.5.2 (conjugate gradient). I found the Hessian patterns shown in figures 10.4 and 10.5 and the minimization trajectories shown in 10.10 very pedagogical. As in previous chapters the author finishes with practical recommendations and future challenges.

We left chapter 11 (Monte Carlo methods) for last in the course and discussed chapter 12 (molecular dynamics) first. As in previous chapters the author gives a very nice introduction (section 12.1 and 12.2) and covers the basics on simulation protocols in sections 12.3 and 12.4. Section 12.4 describes the basic integration algorithms such as leap-frog, verlet, etc... Figure 12.3 was revealing for the students as it compares the time scales in biological systems.

Chapter 11 (Monte-Carlo methods) provides a very comprehensive introduction to Monte-Carlo methods. We found particularly useful some of the subsections of random number generation and the treatment of Importance sampling and Markov chains in section 11.5.

As mentioned earlier we were particularly delighted with the amount of details given in each topic. For example chapters 7 and 8 provide all the formalism needed for the problems of molecular mechanics. In section 8.4 (bond angle potential) the author highlights the differences (both formally and by figures-see figure 8.4) between different formulations of the problem (see also figure 8.6). In Chapter 10 the author describes minimization algorithms in detail and shows some of the patterns that one observes in the Hessian associated to minimization functions of biological structures (see figs. 10.4, 10.5 and 10.11). She also makes very detailed comparisons between the different minimization methods (see figs 10. 2, 10.10). In chapter 12 she compares the different methods and initial conditions for the algorithms discussed (figs 12.3, 12.4, 12.6).

Overall we found that Prof. T. Schlick's book is very adequate for a broad spectrum of levels and very accessible to both graduate and undergraduate students interested in mathematical modeling and computational biology. It is also very well organized facilitating the option of selecting parts of the material for the classroom or for use in one's research.

Outstanding introduction
... not only to molecular modeling, but to some of the subtleties of DNA and protein behavior and geometry, too.

This book's focus is generally on interactions with large molecules, DNA and proteins, although it does discuss small molecules (drugs, a few dozen to a few hundred atoms) too. That means that it skips most of the quantum mechanical modeling of more advanced computational chemistry texts.

Nothing is lost, because Schlick covers her chosen topic (molecular modeling and dynamics) in such detail. She starts with a very clear discussion of the structure of large biomolecules, with emphasis on the features that need quantitative description for modeling. That covers protein structure at ever level. It also covers DNA/RNA structure in the best detail I've ever seen. The double-helix is the just the starting point. There are alternative helix forms, non-standard binding between nucleotides, and asymmetries caused by nucleotide composition. The next chapters describe the geometric model and, briefly, the forces acting between atoms.

The second half of the book gets down to the nuts and bolts of modeling. This includes numerical techniques, minimization, sampling and Monte Carlo techniques, and the start of dynamics. Schlick attacks some of the nasty points of the calculations, such as modeling of forces that act on very different time scales. As with the simpler material, the development is clear, descriptive, and free of pointless theorems. The meticulous reader should come away able to implement most or all of the techniques described. The level of presentation is consistent and approachable. I think freshman physics should be enough preparation for most students to get most of the value out of the discussion.

The book is written with clarity as a top priority. The glossary is in the front, making sure that the reader knows it's a first-class part of the text. After that, every chapter starts with a list of the mathematical symbols and variables used and a one-line description of each. These are small things, but they increase the book's readability immensely. The illustrations are generally informative enough. On the whole, though, they don't seem quite up to the level of the textual and mathematical presentations.

I needed a crash course in the mathematical techniques used for describing molecular structure and behavior. I should have read this book first - its clarity and thoroughness would have saved me a lot of time. After this one, I can now go back and reread the more complex texts with more hops of understanding. Do yourself a favor and read this one first.

Beautifully written!
As a person with no expertise in molecular modeling who wanted to learn about this field, this book is right on! I find the author's lively text to be as well-written and clear as any science textbook I have ever read. I especially enjoyed the first two chapters for their historical perspective and their practical illustrations of applications of genetics in the world today. These chapters can be understood by non-scientists, whereas the rest of the book is clearly designed for graduate students in any one of the science disciplines.

The interesting information sprinkled throughout the book, including the boxes and figures, help keep the reader stimulated and yearning for greater knowledge of this exciting field. The color graphics also complement the book nicely. Although the subject covered in the book is extremely broad, the author managed to convey the perspectives of multiple scientific disciplines (e.g., biology, chemistry, computer science, math) very well. The combination of breadth and depth in a readable style is remarkable.

Overall, I highly recommend this book to readers interested in the area.

Never short of something exciting
It contains many many exiting problems and stimulate to go through the world of art of biology and mathematics. This book can guide the way where to go when you lost in the world of biomathematics, specifically molecular modeling. It looks like a well-organized dictionary with analysis. So it is good for a beginner and also deep-thinker in computational biology field. ... Read more

Book Description

The application of computational methods to DNA and protein science is a new and exciting development in biology. Bioinformatics: Sequence and Genome Analysis is a comprehensive introduction to this emerging field of study. The book has many unique and valuable features:

It is written for any biologist who wants to understand methods of sequence and structure analysis and how the necessary computer programs work

Sequence alignment, structure prediction, phylogenetic and gene prediction, database searching, and genome analysis are clearly explained and amply illustrated

Underlying algorithms and assumptions are clearly explained for the non-specialist

Examples are presented in simple numerical terms rather than complex formulas and notation

Theoretical underpinnings are linked to biological problems and their solutions

Extensive tables provide descriptions and Web sources for a broad range of publicly available software

Based on the author's extensive experience as a molecular geneticist and bioinformaticist at the University of Arizona, this is a uniquely educational book, ideal as a laboratory reference for investigators and also as teaching reference for graduate and undergraduate students studying this fast-changing discipline. ... Read more

Reviews (14)

good for computational biologist
If you are a biologist and just want to know some background information of how to apply bioinformatics to your research, do not read this book. My recommendation for you is "developing bioinformatics computer skills" and some other books like that.
If you are a student or scientist who study bioinformatics, this book is an excellent book and really worthy to read. This books gives very detailed information on algorithm to help us understand how the software such as BLAST and FASTA are designed. The illustrations are easy to understand compared with other books I have read, especially for the statistics part of any algorithm.
One weak point is that the book focus on nucleic acid sequence analysis while talk little about protein.

Horrible. A lot better books should be available nowadays
In short, the author does not have enough writing skill to write this text book.

I purchased this book a while ago. At that time, the book was really difficult to read. I thought that it is because I do not have enough knowledge to understand the material. So I stopped reading this book and studied bioinformatics by other means.

After gaining enough knowledge in bioinformatics, I re-opened this book, and it is funny to find that I still have the same amount of difficulty in understanding what the author wrote about topics that I have already built good understanding. Reading this book will only deteriorate one's understanding.

Several years ago, only just a few books were available on the market, so one needed to purchase this book. These days, there are lots of varieties to choose, and any choice is likely to be better than this book.

Horrible
While this book may, and I stress the word may, contain useful information, it is so badly written that it is incomprehensible. Dr. Mount seems to believe that ten words are better than one, making "Bioinformatics" very tedious to read. After awhile I felt like I was reading a Victorian novel.
Despite being wordy, the explanations are too brief and not clear. If you don't know what he is talking about before hand, you will never understand what he is explaining. He uses an excess of words, and rarely provides a clear, concise example of what he is referring to (or if he does it is in another chapter in the book).
It also appears that the book was never edited. For example, when trying to define "ortholog" and "homolog," he writes two opposing definitions for ortholog and none for homolog. Clearly this is a mistake and Dr. Mount accidentally used the word ortholog twice while meaning to use ortholog once and homolog the other time (pg 56). While it can be argued that this mistake is unimportant and the reader can look up the definitions, it makes me wonder what else in the book is wrong that I have no way of detecting (until I waste a bunch of time doing something incorrectly).

Strong foundation builder
This book will give you very strong foundations in
the basics of computation in the bio world. Though
this book does not give details of the computation
methods, it does give a very clear picture of math-
ematics and the science involved.

This book has a good coverage of FASTA and
BLAST. (Though a little bit short)

The programming techniques coverd are bare. Though
concepts like searching sequences using dynamic p-
rogramming are covered, you are better off reading
something like Proteome Research by wilkins et al.

I am yet to find a good book that deals only with
the technical and programming aspects of bio informatics
if you do find some thing interesting lemme know.

On the whole this book helped me understand a lot
about sequencing, alignment and prediction. The illustrations
and pictures provided are good and the text to the point.

If you are reading this review pls understand that I am
primarily a programmer trying to get into the
bio informatics business. I do not have any schooling
or degree or even experience in the bio informatics world.

Hope this helps

Santy

whatever
Decent qualitative overview. Some discussions of algorithms are so superficial that they are misleading. Slick presentation. Used at Stanford's intro to methods course - a good recommendation.

So far, the best there is for a survey course - but for depth and accuracy in sequence analysis algorithms, go to Durbin et al or Gussfield. ... Read more

Book Description

Pharmaceutical companies continue to face a growing need for scientists trained in the basics of pharmacology. At GlaxoSmithKline, a pharmaceuticals world-leader, Terry Kenakin regularly teaches this course and has drawn on his valuable experience to write A Pharmacology Primer. This guide has been designed especially for scientists trained in molecular biology and related fields who now need to know the basic theories, principles and practical applications of pharmacology.

Important chapters cover: Drug Receptor Theory; Drug Antagonism; The Drug Discovery Process; Pharmacological Assay Formats; Statistics & Experimental Design; and many more!

A Pharmacology Primer is stocked with helpful resources -- derivations of all formulae in every chapter, a glossary and appendices, scores of full-color illustrations -- that further enhance the value and utility of this book.

*185 illustrations and figures, four-color throughout
*Bulleted lists at the end of each section sum up main topics
*Glossary of Pharmacological Terms included for quick reference ... Read more

Reviews (1)

A very well written pharmacology primer.
Dr. Kenakin's book is a well written primer for scientists who already have some familiarity with the topic at hand. It reviews the essentials of pharmacology starting with the basics such as potency, affinity and efficacy and continues with discussions of partial agonists, receptor theory and expression of recombinant receptors in heterologous systems. Each chapter has a short summary and has the derivations of the key equations for those so interested. Excellent resource! ... Read more

Book Description

"PCR: the basics" is the ideal practical introduction to PCR practices in the laboratory. By providing basic theory, background material and suggestions for suitable protocols, it enables a novice to become a proficient user of many PCR techniques. Coverage includes: * Experimental aspects * Analyzing and manipulating PCR products * Genome analysis * Gene cloning and manipulation * Gene expression and medical diagnosis "PCR: the basics" is invaluable for undergraduates, graduates, or experienced researchers who are about to undertake PCR for the first time. ... Read more

Reviews (4)

PCR for beginners: A must-have !
This book explains really good all the basics of the PCR.
For the beginning PhD student, or even before, all you need to know and even more is inside. Some applications are more complicated, but the book is never too difficult to understand.
A must-have!!

Great Book on PCR
This book is a great practical introduction to PCR. It truly does cover the full spectrum of PCR topics from background to benchtop (real-world) applications. It is very clearly written and easy to understand. I own about 10 books on basic and advanced PCR methods, and this one is by far the best. If you want a clear, concise, comprehensive introduction to PCR, this book is it.

PCR is Good
PCR by McPherson and Moeller, is a great great little book that addresses the practical and theoretical aspects of the polymerase chain reaction. The fundamental aspects of PCR, ranging from reagents and instrumentation, to PCR optimization, to the analysis of genomes, are outlined in each of 10 chapters with companion protocols for each application. Each technique is explained with clarity and numerous illustrations greatly aid in the understanding. I tried personally the "SOEing" method to generate a deletion mutants and it worked to perfection. Another great feature of this book is that it explains many of the potential pitfalls associated with PCR technology in a very comprehensive manner, and gives simple solutions to remedy these problems. PCR has been around for some 15 years, and the many applications of this revolutionary technique have often been overlooked due to the sheer number; PCR takes many of these new applications and makes them simple for the reader, and in that it constitutes one of the more comprehensive educational books on the subject. PCR will surely simplify the task of students and veteran molecular biologists alike, and for these reasons I highly recommend it.

Attention All Molecular Biologists
This book is ideal for both students and experienced researchers. In addition to covering the basic and theoretical aspects of PCR, the book also describes cutting-edge PCR methods and applications. It's nice to have such a comprehensive, up-to-date book on PCR. The clarity of the text made for enjoyable reading. This is a must for students and any molecular biology laboratory. Happy Reading! ... Read more

Book Description

Blackwell’s Underground Clinical Vignettes: Biochemistry, third edition is your primary source for clinically relevant, case-based material essential for Step 1 review.Each Clinical Vignette presents approximately 100 cases with over 1000 classic buzzwords in Hx, PE, lab, imaging, pathology and treatment.

The revised editions contain: · High-yield updates to nearly every case· Links to Basic Science and Clinical Science Color Atlas · New Cases on commonly tested USMLE topics ... Read more

Reviews (15)

Clinical case scenarios of OB/Gyn
This book gives you 53 major cases of Obstetrics and Gynecology as one of the Underground Clinical Vignettes series. Obviously, this book alone is not enough to prepare for USMLE Step 2, but the great thing about this book is that it really focus on the disease and keywords that actually appear in the exam (e.g. vaginitis, OCP, amenorrhea, eclampsia etc). You pick up this book, see any of the scenario and if you cannot guess the diagnosis by reading through the history and findings, or any of the highlighted keywords on the scenario is unfamiliar to you, you need to buy this book. If you can, forget about this series, and work on simulated tests.

Not useful
In my experience, this book was not helpful for Step 1 preparation. Partly because Behavioral Sciences is not heavily tested in the exam and clinical vignettes are time consuming. Also, I felt that by studying a standard review book alone, I was able to remember the distinguishing aspects of each disease. However I am sure there are many people who would find this book useful.

Don't bother
This is the worst book of the series and is a waste of time. Pharmacology cannot be taught by clinical vignettes and the author himself recognizes this. In the book review section of First Aid, Dr. Bhushan admits that it is not an ideal review source. The problem is that within two lines of the clinical vignette, the drug is revealed, so there is no chance to guess the answer. There are less time consuming ways to learn the side effects of drugs.

Excellent for USMLE prep
All three of the PathoPysiology books of the Clinical Vignettes series are excellent review books for pre-clinical students taking Step 1. Many questions on the exam are asked from a clinical standpoint. For IMGs who have clinical experience before taking Step 1, these books are less useful. However, they are still good to review unusual diseases. Since Pathology is so heavily tested in Step 1, these books are a good investment for anyone preparing for Step 1.

One of the best of the series
I found this book very helpful in forming a clinical picture in my mind for all those confusing biochemical diseases. I felt this was one of the best books of this series. It is good to use after reviewing the subject. This book is not sufficient on its own and should be used as an adjunct to a standard review book. ... Read more

Reviews (17)

It is the clearest Biochemistry book and it is a must for ev
I found the 2e of "Principles of Biochemistry" by A. Lehninger, one of the most exciting books written in the field of Biochemistry. The book should be a treasure, especially, for undergradute students who have interest in the field. I have already adopted it as the main text book for the Biochemistry, a 300 level, course that I teach. Concepts are clearly and cleverly presented.

It is the clearest Biochemistry book and it is a must
I found the 2e of "Principles of Biochemistry" by A. Lehninger, one of the most exciting books written in the field of Biochemistry. The book should be a treasure, especially, for undergradute students who have interest in the field. I have already adopted it as the main text book for the Biochemistry, a 300 level, course that I teach. Concepts are clearly and cleverly presented.

It continues being the best one.
The fourth edition of Lehninger Principles of Biochemistry is the best book is the subjet. Like in the third edition the treatment of the topics is very goog. The first chapthers of the past edition were simplified in one single chapter. Also new is an innovative graphical style for depicting enzyme reaction mechanisms. Introduces the human genome. Biochemical insights derived from the human genome are integrated throughout the text.
Tracking the emergence of genomics and proteomics, this chapter establishes DNA technology as a core topic and a path to understanding metabolism, signaling, and other topics covered in the middle chapters of this edition. Includes up-to-date coverage of microarrays, protein chips, comparative genomics, and techniques in cloning and analysis.

The best Biochemistry book ever so far!
This is the best Biochemistry book (recent edition 4 th edition published April 2004)from the collection of books I have (Stryer, Voet, Garett, Norton,Mathews, please add any other!)The book is very easy to understand specially if you don't have an intimate relation with Biochemistry. Nice illustrations, summary, and a lot more. Do not miss it!

Good book, bad price.
I intend to major in Biochem, so this book might not be enough, but so far it's suit me quite well. Sometimes I feel like the book doesn't go deep enough into some areas, but in the other hand it covers a wide range of things... ... Read more

Book Description

Genomes 2 covers modern molecular genetics from the genomics perspective, incorporating major advances made in the past three years, including the sequencing of the human genome, characterization of genome expression
and replication processes, and transcriptomics and proteomics. The text is richly illustrated with clear, easy-to-follow, full-color diagrams, which are downloadable from the book's website (www.wiley.com/brown).
... Read more

Reviews (14)

Where's the genome?
On the basis of a favorable "Nature Genetics" review, I bought the first edition of this book--and I was quite disappointed with what I found. Basically, it is just another text on molecular & cell biology but with lousy graphics. (The author explicitly states that the figures and other visualizations somehow limit one's learning & thinking.) I am hoping the recent crops of explicit genomics-oriented texts will be better. But I'd steer clear of this one.

Excellent General Overview of Genomics
I found that "Genomes" provides the reader with a thorough yet gentle introduction to the field -- ample illustrations, well-written text, frequent sidebars describing relevant techniques or developments. I've found the book to be a good reference to have on the shelf, and have purchased copies for people when they join my lab group in order to introduce them to or refamiliarize themselves with the technologies underlying the generation of sequence data. I can very easily see this book being used to supplement lectures in an introductory course on genomics and biotechnology.

Useful Text
"...probably the most up-to-date textbook on molecular biology...a useful text...and reference..." (Annals of Pharmacotherapy, September 2003)

Marvelous Text
"...a marvelous text...plenty of definitions and excellent illustrations essential for an introductory textbook...the reader is...guided wonderfully through the text...this text is an essential cornerstone of information..." (Pharmaceutical Research, Vol. 19, No. 12, December 2002)

User Friendly
"...a second edition to incorporate new developments in genome science and to make the book more 'user friendly'...the book substantially exceeds that modest objective; this is a text suitable for anyone who does not specialize in genome science." (Clinical Chemistry, Vol. 48, No. 12) ... Read more

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. ... Read more

Reviews (3)

Informative, but not information I can use
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
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!!!
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 :-) . ... Read more

Book Description

''Considerably augmented for [the] second edition...[contains] a vast amount of information....it will surely be much used.'' --Ultramicroscopy This newly updated second edition details the latest instrumentation and applications of the confocal microscope. This edition features 21 new chapters and includes information on preparing living specimens for the confocal microscope. ... Read more

Reviews (1)

A must have if you want to know about confocal microscopy
This is a great reference book. A great place to start if you want to learn about confocal microscopes. The chapters are written by experts in their specific field of confocal microscopy. The book is also well referenced so that you can easliy continue your search for knowledge on confocal microscopy. I also found the appendix interesting, they list most of the existing confocal systems and there specs. This is useful if you plan on purchasing one. This book is also useful if you plan on building your own. ... Read more

Book Description

'Provides comprehensive detail on the various aspects of particular molecules involved in the phases of injury and repair and thecellular movements and processes....This is an excellent referencebook for libraries serving biology and health science clientele andfor workers in this field of research.' --AmericanScientist, from a review of the First Edition All chapters of thissecond edition have been completely revised and expanded--especially the chapters on growth factors and extracellular matrix molecules. New chapters discuss provisional matrix proteins, extracellular matrix receptors, and scarring versus nonscarring wound healing. ... Read more

Book Description

A timely overview of this rapidly-expanding topic, covering the most important classes of compounds and incorporating the latest literature. With its application-oriented approach, this book is the first to emphasize current and potential applications, extending to such fields as materials science, bioorganic chemistry, medicinal chemistry, and organic synthesis. In the biological context in particular, the book clarifies which receptor systems work well in water or better under physiological conditions.

From the contents:

• Amino Acid, Peptid and Protein Receptors
• Carbohydrate Receptors
• Ammonium, Amidinium and Guanidinium Receptors
• Anion Receptors
• Molecular Capsules and Self Assembly
• Dynamic Combinatorial Libraries based on Molecular Recognition
• Molecular Machines
• Self-Replication

Book Description

Wiley is proud to announce the publication of the first ever broad-based textbook introduction to Bioinformatics and Functional Genomics by a trained biologist, experienced researcher, and award-winning instructor. In this new text, author Jonathan Pevsner, winner of the 2001 Johns Hopkins University "Teacher of the Year" award, explains problem-solving using bioinformatic approaches using real examples such as breast cancer, HIV-1, and retinal-binding protein throughout. His book includes 375 figures and over 170 tables. Each chapter includes: Problems, discussion of Pitfalls, Boxes explaining key techniques and math/stats principles, Summary, Recommended Reading list, and URLs for freely available software. The text is suitable for professionals and students at every level, including those with little to no background in computer science. ... Read more

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.

Now, for the book itself. It is easy to read and covers all aspects of bioinformatics from a sequence perspective (information retrieval, BLAST, gene expression and microarrays, proteomics and protein bioinformatics, genomes and disease). The coverage of databases and URLs is thourough and the text is easy to read, yet useful. The book is comprehensive with one area seemingly missing -- it would have been useful to include a chapter on systems biology and/or cellular modeling and the tools available (i.e. E-Cell). The book is especially useful to a researcher who is trying to explore all aspects of a particular gene, protein, disease, or pathway using bioinformatics tools.

The book is in stark contrast to the other Pevser (that is Pevzner) who wrote a bioinformatics book that surveyed algorithm theory underlying bioinformatics.

This book is also useful for less technical professionals in industry -- the managers, lawyers and venture capitalists that pervade the biotech landscape all need to communicate effectively and they can surely learn that here, provided they have some background in cell biology first.

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 driving bioinformatics 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

Book Description

The first two editions of this manual have been mainstays of molecular biology for nearly twenty years, with an unrivalled reputation for reliability, accuracy, and clarity.

In this new edition, authors Joe Sambrook and David Russell have completely updated the book, revising every protocol and adding a mass of new material, to broaden its scope and maintain its unbeatable value for studies in genetics, molecular cell biology, developmental biology, microbiology, neuroscience, and immunology.

Handsomely redesigned and presented in new bindings of proven durability, this three-volume work is essential for everyone using today’s biomolecular techniques.

The opening chapters describe essential techniques, some well-established, some new, that are used every day in the best laboratories for isolating, analyzing and cloning DNA molecules, both large and small.

These are followed by chapters on cDNA cloning and exon trapping, amplification of DNA, generation and use of nucleic acid probes, mutagenesis, and DNA sequencing.

The concluding chapters deal with methods to screen expression libraries, express cloned genes in both prokaryotes and eukaryotic cells, analyze transcripts and proteins, and detect protein-protein interactions.

The Appendix is a compendium of reagents, vectors, media, technical suppliers, kits, electronic resources and other essential information.

As in earlier editions, this is the only manual that explains how to achieve success in cloning and provides a wealth of information about why techniques work, how they were first developed, and how they have evolved. ... Read more

Reviews (13)

Comprehensive guide to do-it-yourself cloning
When Bobs first recieved this set as a gift I thought it would make a lovely doorstop. My last pregnancy, however, was a triple birth that Bobs and our live-in next-door neighbor, Chompson, cooked up in a petrie dish down in the basement. I thought that this cloning business was all a bunch of hogwash, but as the years pass I've come to realize that two of the babies are exact clones of Chompson! (the third appears to be a clone of Bobs' favorite TV goddess, Farrah Fawcett-Majors) While I think that Bobs was remiss in his choice of subjects, you have to respect the science that makes miracles like this possible.

the BIBLE of every biologist
So few and so much to say about this bible of Biology at the bench...
You'll really find everything you want in it, including the composition of all the buffers and solutions, the new protocols for high-tech biology (FLIM-FRET), some paragraphs about bioinformatics and more.Incredibly precise, this book is consequently a big book (3 huge volumes), so better know exactly wath you're looking for before opening it!
The must have of every lab!

the BIBLE of every biologist
So few and so much to say about this bible of Biology at the bench...
You'll really find everything you want in it, including the composition of all the buffers and solutions, the new protocols for high-tech biology (FLIM-FRET), some paragraphs about bioinformatics and more.Incredibly precise, this book is consequently a big book (3 huge volumes), so better know exactly wath you're looking for before opening it!
The must have of every lab!

Excellent reference for all
In this 3 volume set of books the authors summarize the most important laboratory protocols for DNA analysis and cloning. As someone involved in computational biology and mathematical gene sequence analysis, I was needing such a summary to get an idea of just how genetic engineering is actually practiced in the laboratory. The book is definitely written for those readers that are very experienced in these "wet" techniques, but it still could be perused profitably by anyone who is curious about genetic engineering. There is also an excellent website that owners of the books can go to and search for protocols and obtain updates and additions to the protocols.

At the beginning of each chapter, the authors give an introduction to the protocols and this is of an enormous help to those readers with only rudimentary acquaintance with the laboratory procedures. Typically, this introduction contains an historical summary of the procedures as they were developed or discovered. One can only marvel at the ingenuity of the discoverers of these techniques. These introductions are fairly straightforward to read, even for those that are not experts in biochemistry.

At the end of each chapter, the authors include an "information panel" that gives a more in-depth view of the biochemistry or genetics behind the procedures. These are summaries and are highly specialized, and are again meant for experienced readers. A very lengthy list of references is also included at the end of each chapter.

Becuase of the size of this collection, space here does not permit a detailed review, so I will list some of the areas that I thought were particularly interesting or well-written (these coming from the introduction or the information panels only): 1. The DNA synthesis at the colE1 replicon and the interaction between RNAI and RNAII. 2. The discussion of electroporation and the physics behind this technique to introduce DNA into eukaryotic cells. 3. The discussion on the discovery of bacteriophage lambda. 4. The discussion (with diagram), of the assembly pathway of bacteriophage lambda. 5. The summary of the early analysis of DNA using electrophoresis and the different pulsed-field configurations used. 6. The anecdote on the discovery of the polymerase chain reaction. 7. The short discussion on computer-assisted design of oligonucleotide primers. 8. The discussion of oligonucleotide synthesis. 9. The flowchart detailing the preparing and screening of a cDNA library. 10. The history of the development of the methods to synthesize and clone cDNAs. 11. The detailed discussion of the molecular cloning of double-stranded cDNA. 12. The discussion on the methods to validate clones of cDNA. 13. The discussion on magnetic beads for affinity purification. 14. The discussion on the history of DNA sequencing and the different techniques to accomplish it, particularly the information panel on automated DNA sequencing. 15. The discussion of the different types of mutagenesis and the different methods for accomplishing it. 18. The fascinating discussion of how to introduce cloned genes into mammalian cells. 19. The discussion on the steps involved in DNA footprinting. 20 The discussion on green flourescent protein and its use as a fusion tag. 21. The discussion on the use of surface plasmon resonance spectroscopy.

A must for molecular biologists
I love this book, however some areas are better covered in Current Protocols in Molecular Biology, and vice versa. So I would recommend having both. ... Read more

Book Description

A personal adventure, a fascinating study of anthropology and ethnopharmacology, and, most important, a revolutionary look at how intelligence and consciousness come into being.

This adventure in science and imagination, which the Medical Tribune said might herald "a Copernican revolution for the life sciences," leads the reader through unexplored jungles and uncharted aspects of mind to the heart of knowledge.

In a first-person narrative of scientific discovery that opens new perspectives on biology, anthropology, and the limits of rationalism, The Cosmic Serpent reveals how startlingly different the world around us appears when we open our minds to it.

"The Cosmic Serpent is a spellbinding, scholarly tour de force that may presage a major paradigm shift in the Western view of reality." --Michael Harner, Ph.D., president, Foundation for Shamanic Studies, and author of The Way of the Shaman ... Read more

Reviews (37)

Good questions, but inconclusive
Jeremy Narby's argument is that when shaman's drink hallucinogenic brews, their consciousness sinks to the molecular level, and literally communicates with DNA, the basic building block of life. DNA appears to shamans, and others who drink these magic brews, as serpents. This is why, Narby claims, serpents loom large in ancient cultures around the world. It is also how shamans get their expert knowledge of plants. When shamans say that the spirit in the plants tell them how to concoct life-saving remedies, they mean what they say. In hallucinogenic trances, the plants speak. Narby goes onto to speculate that the world is one vast communication network among strands of DNA. You don't have to buy the DNA-communication theory to enjoy this book. It is written in an engaging, personal, first person narrative style. It shows how science works, how "eureka moments" occur when one is relaxed and thinking about other things. Maybe his theory is totally off-base, but even so, big ideas like this one often spur research in different, interesting directions. We are only as good as our questions, and Narby's question is a great one: What if the shamans are right?

An insightful book that leads us back to the planet.
I found this to be one of the most exciting books I have ever read. Not because of the science or the shaman perspective but because it leads us out of the clouds and back to the planet we live on to learn fundamental truths about life. The appreciation and love of our planet and all its species is crucial to our continued existence and Dr. Narby certainly whets our interest with his fascinating hypotheses. Perhaps, if God created everything and God is in us and all around us, God and DNA may be synonymous. And how wonderful it would be for us to feel that God actually has such a close physical association with us instead of being a separate being living in a far off realm. This book brings a number of important ideas and concepts together to attempt the creation of a whole meaning. Wonderful read!!!

Cosmic Serpent: DNA And The Origins of Knowledge
I have always been conflicted with the theory of evolution. It seems rational, but speciously so. It ignores consciousness, which is senior to science. Surely, any theory that purports to map out the arrow of life must account for our ability to know that we know. Without bringing theology or Creationism, God forbid (pun intended) into the equation, Narby explains a viewpoint that puts sentinent life onto center stage. Weaving together intuition and rationlism, Narby allowed me to dispell my conflict and realize that LIFE is consciousness and is the driving force behind "evolutionary" progress. Sounds corny, I know, but read it with an open mind and see if your views don't change, even a bit.

Incredible Ruminations
This book takes you on a wild ride of DNA, mythology, and culture and somehow integrates them. The only problem is you have to be somewhat of a believer in the first place to allow Mr. Narby to buckle you in and hit the thrusts. Really though, it is a fascinating cultural study that never claims to be true or untrue, it just reports what was said and seen. There is a power to ayahuasca and hallucinogenic drugs of which we still don't know the full extent. This book is far-fetched but in today¡¯s rapidly changing world it¡¯s not impossible that we (from the modern world) will not soon agree with them (from the 'primitive' world).

The best part of the book is the way it personalizes and characterizes DNA. After reading it it¡¯s all you will think about: how much is DNA effecting everything we do.

It¡¯s a fascinating read. It points out simple similarities like the fact that the double helix is shaped like a snake but then goes into detail that I can't do justice to here. If you have any interest in DNA or anthopological studies then this book is a must.

Weird
This book develops a hypothesis that DNA expresses information about itself to humans through consumption of hallucinogenic plant substances. As support for his idea, Narby notes that many cultures worldwide worshiped serpents or used serpent symbols in some form or another. Narby attributes this to the serpentine nature of the form of DNA which is expressing knowledge of itself to people. According to Narby, people from less-developed cultures, especially religious people, are more likely to be receptive to the messages from DNA because training in rational thought processes doesn't get in the way of transmission of the messages. For me, the most valuable observation that Narby makes is that through meditation, one may connect with new ideas and ways to look at problems that the unconscious mind has discovered while the rational mind was chasing down facts. Unlike Narby, however, I think I personally would look for a few more pieces of hard evidence to support the wild ideas of the unconscious mind before publishing them. The book includes extensive references; in fact, there are 60 pages of endnotes and 20 pages of bibliography in the 246 page text. ... Read more

Book Description

Extensively revised and updated, the new edition of the highly regarded Handbook of Proteolytic Enzymes is an essential reference for biochemists, biotechnologists and molecular biologists. Edited by world-renowned experts in the field, this comprehensive work provides detailed information on all known proteolytic enzymes to date. This two-volume set unveils new developments on proteolytic enzymes which are being investigatedin pharmaceutical research for such diseases as HIV, Hepatitis C, and the common cold.

Volume I covers aspartic and metallo petidases while Volume II examines peptidases of cysteine, serine, threonine and unknown catalytic type. A CD-ROM accompanies the book containing fully searchable text, specialised scissile bond searches, 3-D color structures and much more.

* Presents practical information in terms of name, history, activity, specificity, structural chemistry, preparation, biological aspects, distinguishing features, and relevant references for each enzyme; representative assay conditions are also included
* Enzymes are further presented not only according to the Enzyme Commission system, but are further subdivided within each class to include clans and families, based on genetic relatedness
* Provides information and answers on how one peptidase can be distinguished from another and referred to ambiguously, and how a scientist can tell when they have discovered a novel peptidase
* Accompanying CD-ROM provides useful search facilities ... Read more

Book Description

This volume commemorates the 50th anniversary of the appearance in Volume 4 in 1948 of Dr. Jeffries Wyman's famous paper in which he "laid down" the foundations of linkage thermodynamics. Experts in this area contribute articles on the state-of-the-art of this important field and on new developments of the original theory. Among the topics covered in this volume are electrostatic contributions to molecular free energies in solution; site-specific analysis of mutational effects in proteins; allosteric transitions of the acetylcholine receptor; and deciphering the molecular code of hemoglobin allostery. ... Read more

Book Description

Discovering Genomics, Proteomics, and Bioinformatics combines integrated Web exercises with a problem-solving approach to train readers in basic hands-on genomic analysis. The authors present global problems, then provide the tools of genomic analysis to help readers dissect the answer, thus encouraging critical thinking skills. Short boxed readings called "Math Minutes" explain the math behind the biology.For anyone interested in genomics, proteomics, or bioinformatics. ... Read more

Reviews (1)

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.
Score: 9/10.

Recommended to students: yes, together with classic works like Brown.

Recommended to Central Library: yes.

1. The supplied CD-ROM is a nice teaching aid. Yet, it is difficult to "extract" pictures from it for teaching purposes. It would be much more useful if the pictures were individually supplied in standard high-quality graphic formats like TIFF, instead of PDF. The later is perfect for distributing text with pictures, but not to retrieve such pictures. Other publishers distribute the book artwork as individual TIFF files. That approach greatly enhances the book and boost sales. This is particularly useful for teachers. Actually, it is a must for us these days. Please, make sure that future versions of the CD-ROM or DVD-ROM are --as this one-- compatible with the open-source Unix-based Mac OS X platform. Thanks.

2. The associated web page "Instructor's Guide"3. The discovering questions are terrific. Please, expand them in future versions.

4. Math minutes are an excellent idea.

5. Boxes are welcome. Please, include more.

6. Also helpful are the boldface words on each chapter. Perhaps they could be also included in a keywords at the beginning of each chapter.

7. The index should be more comprehensive and should have all main entries in boldface. This is important to any index and very few books have it right.

8. The glossary is helpful. It should be more comprehensive,
including more terms.

9. The summaries and conclusions are great, yet should be expanded to include more relevant information. They should be like a "minichapter" an the end of each chapter or --better-- at the beginning. All partial summaries could be pooled into a larger summary that way.

10. Addendum sections could be included as separate notes or boxes.

11. The pronunciation tips for new words are also an excellent idea; mostly for non-English speakers.

12. The classified references are really useful. Well done. If they were commented or "annotated" they would be just perfect.

13. A list of abbreviations would be welcome. A list sorted by the full name would be very handy as well.

14. What about telomerase and aging? What about the fact that
unicellular organisms are immortal? Or stem cells? Or tumor cells? Death is a tax that multicellular organisms have to pay to nature in order to evolve. Yet we humans might change that soon.

15. It should be clearly indicated the organisms with genomes made of dsDNA, ssDNA, dsRNA and ssRNA.

16. Missing bioinformatics tools and step-by-step analysis of genes and mRNA (see next) and whole genomes.

17. It would be really helpful to explain clearly and analyze --even from a bioinformatics point of view-- the structure of genes, mRNA, CDS, introns, exons, promoters and terminators. It is not clear where do these elements start or end or how to recognize them. Diagrams and graphs would greatly help to explain these absolutely basic and fundamental concepts. In other words, imagine that you have cloned and sequenced a genomic gene as well as a full mRNA (cDNA). Now you want to publish your results and for that you do a comprehensive description of your gene (chromosome) and cDNA (mRNA). That is precisely the kind of information that is missing as a diagram and explanation. In this way, it should be indicated that you may encounter several ATG (or other) starting coding triplets in the mRNA, that if the 20 or so amino acid residues of the 5'-end of a peptide have a high percentage of hydrophobic residues, they are likely part of a leading peptide which would be further excised, that you may encounter several polyadenylation signals, etc. On the genome side, the promoter and terminator structures should be analyzed, as well as the intron-exon boundaries.

18. Likewise, it should be indicated the tools and current
possibilities to determine or predict the 3D structure of a protein (folding) from the primary structure of the peptide.

19. Does not mention Lasergene package of DNAStar20. Which genes are best to draw dendrograms? Differentiation between genes from the nucleus or organelles (mitochondrion or chloroplast). Likewise for DNA fingerprinting and molecular markers.

21. Differential display methodologies are missing (as well as other methodologies of gene expression like subtractive hybridization).

22. Large-scale sequencing is missing. For instance, sequencing of single-molecules will allow the sequencing of whole chromosomes or genomes.

23. Missing tables comparing different genomes with full details
(size, ploidy, percentage of genes, introns, exons, repetitive DNA, junk DNA, etc).

24. Reference to manufacturers is very useful. Please, include also links to web sites. Best if all manufacturers are included as an appendix.

25. All web sites (NCBI, etc) and web-based applications (BLAST, ORF Finder, etc) should be clearly indicted in an appendix.

26. It is not indicated that the PCR was in fact described with full details by Khorana et al 14 years before Mullis et al.

27. Please, include more drawings and pictures in the printed book and CD-ROM.

28. Suggestion: including chapters on eukaryotic-genomic DNA
libraries, cDNA libraries, subtractive libraries.

29. Suggestion: including chapters on plant and animal transformation.

30. Suggestion: including drawing of Maxam-Gilbert sequencing method and Sanger method (Applied Biosystems electropherograms,
electrofluorograms).

31. Prions, viroids and viruses could be also included.

32. A title index at the beginning of each chapter would be very
useful. Besides the goals for chapter, which are quite useful.

33. Bioinformatics could be significantly expanded.

34. QuickTime videos explaining some topics would be fantastic.
Please, make them in QuickTime (best quality, platform-independent).

35. All in all, a great novel approach. Keep up the great work! ... Read more