Systems Bioinformatics: An Engineering Case-Based Approach

Book Description

This trail-blazing work introduces a quantitative systems approach to bioinformatics research using powerful computational tools drawn from signal processing, circuit analysis, control systems, and communications. It presents the functionality of biological processes in an engineering context to facilitate the application of technical skills in solving the field's challenges, from the lab bench to data analysis and modeling, and to enable reverse engineering from biology in the development of synthetic biological devices.

This first-of-its-kind text explores how the knowledge bases of various technical disciplines relate to, and are observed, in biological systems. You learn fundamental signal processing techniques that are essential to biological data analysis, including biomedical imaging and image processing, feature extraction, classification, and estimation. You gain a thorough understanding of cellular regulatory systems and their similarities to traditional control systems, protein and gene networks, inference networks, and network dynamics. The book also addresses how biology-inspired molecular structures are being used to solve engineering challenges, and how one can mimic biology's designs in creating more robust technologies. Moreover, you discover the latest developments in proteomics, where these tools can make an immense impact due to the number, complexity, and interaction networks of proteins. A major addition under the evolving umbrella of systems biology and bioinformatics, this groundbreaking work points you to new frontiers in the convergence of engineering and biological research.

CD-ROM Included! Contains several fully working programs to save you time on the job, including Bayesian Discoverer (student version), VisANT, and OBOES, as well as full-color figures, PowerPoint lecture slides, Matlab Webinar, links to Web resources, and more.

Customer Reviews:

good shredder/slicer.......2007-05-14

It's handy. it's light. It works better than my heavy duty food processor. Would have loved some more "cutters" fo different shapes. Glad I bought it.

Microbial Proteomics: Functional Biology of Whole Organisms (Methods of Biochemical Analysis)

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Microbial Proteomics: Functional Biology of Whole Organisms (Methods of Biochemical Analysis)

Manufacturer: Wiley-Interscience
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471699756

Book Description

Discover important lessons learned about whole organism biology via microbial proteomics

This text provides an exhaustive analysis and presentation of current research in the field of microbial proteomics, with an emphasis on new developments and applications and future directions in research. The editors and authors show how and why the relative simplicity of microbes has made them attractive targets for extensive experimental manipulation in a quest for both improved disease prevention and treatment and an improved understanding of whole organism functional biology. In particular, the text demonstrates how microbial proteomic analyses can aid in drug discovery, including identification of new targets, novel diagnostic markers, and lead optimization.

Each chapter is written by one or more leading experts in the field and carefully edited to ensure a consistent and thorough approach throughout. Methods, technologies, and tools associated with the most promising approaches are stressed. Key topics covered include:

Microbial pathogenesis at the proteome level
Whole cell modeling
Structural proteomics and computational analysis
Biomolecular interactions
Physiological proteomics
Metabolic reconstruction using proteomics data

While presenting the practical utility of proteomics data, the text is also clear on the field's current limitations, pointing to areas where further investigation is needed.

Book Description

KEY BENEFIT: Discovering Genomics is the first genomics text that combines web activities and case studies with a problem-solving approach to teach upper-level undergraduates and first-year graduate students the fundamentals of genomic analysis. More of a workbook than a traditional text, Discovering Genomics, Second Edition allows students to work with real genomic data in solving problems and provides the user with an active learning experience. KEY TOPICS: Genomic Medicine Case Study: What’s wrong with my child? Genome Sequence Acquisition and Analysis, Comparative Genomics in Evolution and Medicine, Genome Variations, Genomic Medicine Case Study: Why Can’t I Just Take a Pill to Lose Weight? Basic Research with DNA Microarrays, Applied Research with DNA Microarrays, Proteomics, Genomic Medicine Case Study: Why Can’t We Cure More Diseases? Genomic Circuits in Single Genes, Integrated Genomic Circuits, Modeling Whole-Genome Circuits. MARKET: For all readers interested in genomics.

Customer Reviews:

Textbook + website = great new textbook.......2007-04-24

This was a great textbook. The website was very helpful and I liked how the author did not waste paper/printing/money on images and half of the information was on the web. It was nice not carrying around a heavy text all semester, even if half my reading/work was done in front of a computer. A lot of information packed into this book. One sentence sometimes requires a lot of knowledge (thank goodness for my professor who explained it all). I would have to say, without a lecture, I would walk away from this text thinking I knew something but not knowing much at all. For an amature like me, I definitely need a lecture to go along with this text. Although some mistakes were found, a lot less than the first edition (so I'm told).

Great New Format to get students out of a dull book.......2006-03-17

This book represents a breakthrough in textbook design. It starts with a 'case study' for a child visiting you the physician. You get the basic symptoms from the mother, then you are sent to the web to go attempt to establish a diagnosis. And you are not sent to some private web site, but to the Online Mendelian Inheitance in Man (OMIN) database of human diseases and genes, and to the National Center for Biotechnology Information. Immediately the student is exposed to a wealth of information far beyond what any book could provide. It's rare that you see a textbook that attempts to take the student into the real world.

Intermixed with the case studies is textual materials that provide the student with the basic background that they need. In addition there are almost random Math Minutes and Discovery Questions that direct the student into further depth of understanding.

If you are planning to teach this kind of class, you owe it to yourself to at least investigate this book before selecting a text.

Simply fascinating.......2004-12-08

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.

The approach to figuring out what, where and how genes are controlled using what are called circuits is simply fascinating. Genes are controlled in three ways: location of the gene, the time of control and the amount. These three metrics can easily be mapped to circuit diagram in Electrical Engineering using the concept of switches (transistors) and time varying influencers (control theory and feedback loops), the authors describe of genes are regulated. One can imagine that the process of mapping genes into circuits is a difficult task, and one would be right. In fact, only one gene, the Endo16, has been fully expressed in circuit diagrams and that task took years of research. Imagine the amount of man power and hours it would take to draw the circuit diagram for the entire human genome of over 35000 genes! Even the concepts of noise in the circuit and complex integrated circuits are explored in details. The authors make no hesitation in telling the readers what the unknowns are and what topics are under intense investigation. It is amazing to realize that we still a long way to go, and what we are seeing thus far is just the beginning on a very long journey.

In general, the book is very interactive filled with Discovery Questions, Math Minutes and a CD simply filled with tons and tons of pictures that are in PDF format that can be printed in need be. There is also a Web site that accompanies this book that explains various bioinformatics methods, and contains information required by some of the Discovery Questions. The text itself is divided into four units:
1) Genomic Sequences which talks about the whole picture of genomic analysis and its benefits. The question of why this field of study is so important and what we hope to gain from in the coming years and decades is also answered. The students are exposed to topics in the areas of biological weapons, antibiotics and how they work, the evolution and survival of DNA and ethical consequences of genetics and genetic engineering.
2) Genomic Expressions in which the how and where questions are answered in detail. How did we gather all of this information? DNA microarrays are discussed in detail including advanced research in the area and who is doing in. Proteins microarrays are also discussed, but not in as much details due to the fact that protein microarrays are very much in their infancies. The authors do make a number of predictions in terms of where the proteomics area of research is heading and what we need to get there.
3) Whole Genome Perspective. The bottom up approach takes the readers to the whole genome analysis, and that's where the authors discuss the notions of electronic circuits in describing the genome and proteins prescription.
4) Medical Case studies in the areas of drug discovery bring this book to an end. The authors tackle questions such as how a disease is discovered and researched, and go into some of the misconceptions of drug discovery and end the book with why discovering a new drug is such a difficult task.

A complete text with the entire information one would need to come up to speed with the area of life sciences. A good mix of biology, mathematics, statistics, engineering and computer science give the reader a comprehensive overview of the current problems, research areas and new developments in the field of bioinformatics.

I recommend this text for a bioinformatics course with students of biology with little mathematics and statistics background. The text is easy to read and follow. The accompanying CD-Rom is field with relevant pictures, graphs, etc, that can further the learning process.

A novel approach!.......2003-03-22

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 DNAStar 20. 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).

Book Description

Mass Spectrometry Data Analysis in Proteomics is an in-depth guide to the theory and practice of analyzing raw mass spectrometry (MS) data in proteomics. As MS is a high throughput technique, proteomic researchers must attend carefully to the associated field of data analysis, and this volume outlines available bioinformatics programs, algorithms, and databases available for MS data analysis. General guidelines for data analysis using search engines such as Mascot, Xtandem, and VEMS are provided, with specific attention to identifying poor quality data and optimizing search parameters. Several different types of MS data are discussed, followed by a description of optimal methods for conversion of raw data into peak lists for input to search engines. Choosing the most accurate and complete databases is emphasized, and a report of available sequence databases is included. Methods for assembling expressed sequence tags (ESTs) into assembled nonredundant databases are provided, along with protocols for further processing the sequences into a format suitable for MS data. Mass Spectrometry Data Analysis in Proteomics describes publicly available applications whenever possible.

Proteomics Today: Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis,and Microarray Technology (Wiley - Interscience Series on Mass Spectrometry)

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Proteomics Today: Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis,and Microarray Technology (Wiley - Interscience Series on Mass Spectrometry)
Mahmoud H. Hamdan , and Pier G. Righetti
Manufacturer: Wiley-Interscience
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471648175

Book Description

The last few years have seen an unprecedented drive toward the application of proteomics to resolving challenging biomedical and biochemical tasks. Separation techniques combined with modern mass spectrometry are playing a central role in this drive. This book discusses the increasingly important role of mass spectrometry in proteomic research, and emphasizes recent advances in the existing technology and describes the advantages and pitfalls as well.
* Provides a scientifically valid method for analyzing the approximatey 500,000 proteins that are encoded in the human genome
* Explains the hows and whys of using mass spectrometry in proteomic analysis
* Brings together the latest approaches combining separation techniques and mass spectrometry and their application in proteome analysis
* Comments on future challenges and how they may be addressed
* Includes sections on troubleshooting

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"The last few years have seen an unprecedented drive toward the application of proteomics to resolving challenging biomedical and biochemical tasks. Separation techniques combined with modern mass spectrometry are playing a central role in this drive. This book discusses the increasingly important role of mass spectrometry in proteomic research, and emphasizes recent advances in the existing technology and describes the advantages and pitfalls as well.

Provides a scientifically valid method for analyzing the approximatey 500,000 proteins that are encoded in the human genome
Explains the hows and whys of using mass spectrometry in proteomic analysis
Brings together the latest approaches combining separation techniques and mass spectrometry and their application in proteome analysis
Comments on future challenges and how they may be addressed
Includes sections on troubleshooting

Handbook of Genome Research: Genomics, Proteomics, Metabolomics, Bioinformatics, Ethical & Legal Issues

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Handbook of Genome Research: Genomics, Proteomics, Metabolomics, Bioinformatics, Ethical & Legal Issues

Manufacturer: Wiley
ProductGroup: Book
Binding: Hardcover

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Bioinformatics For Dummies (For Dummies (Math & Science))

ASIN: 3527313486

Book Description

In this unique presentation of a revolutionary field of science, the first section introduces the domains of application for genomics and bioinformatics, such as sequencing and the comparative sequence analysis of model organisms, investigating genetically influenced diseases, the development of new active substances, agri-food and environmental genomics.
There then follows an overview of current topics central to DNA technologies, proteomics, metabolomics and bioinformatics, including such hot topics as DNA chip fabrication, yeast two hybrid analysis, tools for gene expression studies, metabolic networks and systems biology.
The whole is rounded off by four chapters on the ethical, legal and social aspects of this sensitive topic.

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Highly Recommended
Excellent for bioinformatics from a user's perspective
Bioinformatics for computational dummies

Bioinformatics and Functional Genomics
Jonathan Pevsner
Manufacturer: Wiley-Liss
ProductGroup: Book
Binding: Paperback

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ASIN: 0471210048

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.

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Customer Reviews:

Highly Recommended.......2004-04-16

"...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.......2004-03-10

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.......2004-01-25

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.

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Proteomics for Biological Discovery
Timothy D. Veenstra , and John R. Yates
Manufacturer: Wiley-Liss
ProductGroup: Book
Binding: Paperback

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ASIN: 0471160059

Book Description

Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics.

Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications
Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications
Discusses higher level integrative aspects, including technical challenges and applications for drug discovery
Accessible to the novice while providing experienced investigators essential information

Book Description

A combined review, manual and reference for the successful analysis of proteins using the classical approach of 2-D gel electrophoresis, mass spectrometry and related sequence database inquiries.
The first section, written in a textbook style, introduces the entire technology, while the second section represents a comprehensive laboratory manual spanning the full range of methods from sample preparation to protein identification. Alternative methods and procedures are only suggested for those cases where the "default" procedure would fail to deliver adequate results. The third section is a unique troubleshooting guide, designed to answer many of the frequently asked questions regarding proteome analysis. The final section contains a thorough reference list to guide interested readers towards further detail.
Intended for all those wishing to go beyond the theoretical aspects of proteome analysis, this book is targeted at research groups within academia and industry, course instructors, research assistants and graduate students.
Special feature: Updates of recipes as well as animations illustrating crucial methodological steps are available on the Web at http://www.wiley-vch.de/books/info/3-527-30354-5

Proteins and Proteomics: A Laboratory Manual

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An OK book but reinvents the wheel
The "must have" book for the practicing proteomics lab .

Proteins and Proteomics: A Laboratory Manual

Manufacturer: Cold Spring Harbor Laboratory Press
ProductGroup: Book
Binding: Paperback

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ASIN: 0879695544

Book Description

Completion of sequencing of the human genome, as well as those of many other organisms, has now opened the door for exploration of the proteome, the many thousands of interacting proteins in a given organism. Critical to tackling the complexity of the proteome is a workable strategy using reliable and tested protocols for identifying, isolating, and quantifying proteins in cells and cell pathways and for performing functional assays. Proteins and Proteomics: A Laboratory Manual, authored by Richard Simpson of the Ludwig Institute for Cancer Research, Melbourne, provides the first authoritative and wide-ranging protocol-based approach to proteomics. Presented as a logical strategy for analyzing proteomes, Proteins and Proteomics provides information about protein structure and numerous methods for the preparation and analysis of protein samples ranging from electrophoresis and mass spectrometry to protein chips and informatics. Extensive background information and references are provided regarding the theoretic aspects of the techniques presented as well as their applications. This manual is an essential laboratory tool for genetics and molecular biology investigators moving from studies of genomics and genotype to those of proteomics and phenotype. It is invaluable for cell biologists, developmental biologists, and neuroscientists exploring the intricacies of the proteome. It will also be an excellent resource for protein chemists and biochemists.

Customer Reviews:

An OK book but reinvents the wheel.......2004-06-16

To be fair this is a good and useful book, but at a higher price than the already excellent published (2002) laboratory proteomics by Westermeier and Naven, save your dollars. The latter goes for half the price and serves the same purpose with excellent illustrations and protocols.

The "must have" book for the practicing proteomics lab ........2004-04-19

This is a outstanding book, covering all aspects of sample preparation and experimental techniques involved in protein and peptide analysis by gels, liquid chromatography and mass spectrometry. Each chapter gives detailed protocols complete with tips, reagent lists, short tutorials (printed in blue colored information panels) and references. The protocols will work for you just as they are written and will give you a place to start in customizing and adapting them to your own circumstances (and you certainly will do that!). As with any fast moving field an updated second edition will be welcome around 2006, but by then, I'll be happy to replace my dog-eared copy for a fresh one (or maybe not, I don't really think a book as good as this will ever be obsolete). I recommend you buy the paperback edition, it will serve you well and save you some $$$.

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