genomics books

	Bioinformatics, Genomics, And Proteomics: Getting the Big Picture (Biotechnology in the 21st Century)
	By: Ann Finney Batiza Ph.D. ISBN: 0791085171 Publisher: Chelsea House Publications Release Date: September, 2005 Bioscience book rank: 1066384	If you don't know anything about Bioinformaticas, this book is very adeccuacy for your first time
	DNA Microarrays and Related Genomics Techniques: Design, Analysis, and Interpretation of Experiments (Biostatistics)
	By: David B. Allison, Grier P. Page, T. Mark Beasley, Jode W. Edwards ISBN: 0824754611 Publisher: Chapman & Hall/CRC Release Date: 14 November, 2005 Bioscience book rank: 863231	An expansive tour of existing statistical methodologies used in microarray data analysis from contributed experts. What it does is deeply explore what people are using nowadays, cites references in each chapter beautifully, and gives the reader a solid footing as to the pros and cons of each technique presented. Each chapter delves deep enough, and by citing references extensively, one can go seek further detail from the source. <br /> <br />IMHO, this is probably one of the most professionally done books out there. By that I mean there is no fluff, just high quality content across the board. The intended audience is those having some computational background, particularly in statistics. However, each chapter begins with an introductory paragraph serving as a review so that anyone could pretty much gather what is going to be discussed. <br /> <br />A really nice feature of this compilation is that not only does it provide insight into the current methods, it outlines where further developments are needed and how they may help in filling in the gaps. With so many developments having been made in microarray data analysis recently, its nice to know that this book exists to help one gain a solid foundation on how to proceed with some sort of clarity. A five star rating for this one hands down. :)
	Principles of Genome Analysis and Genomics
	By: Sandy B. Primrose, Richard Twyman ISBN: 1405101202 Publisher: Wiley-Blackwell Release Date: 30 December, 2002 Bioscience book rank: 1016148	Presents material in a succinct manner. A good read for an introduction to the subject.
	Genomic Regulatory Systems: Development and Evolution
	By: Eric H. Davidson ISBN: 0122053516 Publisher: Academic Press Release Date: 15 February, 2001 Bioscience book rank: 734505	This is a very intersting book on an amazing topic which is straightforward enough for an interested educted layman to understand. But unfortunately it is a wierd mix of chatty remarks and pointlessly obstruse passages that read like letters to Nature. <br /> <br />The very worst thing is the illustrations and blurbs. The design is so bad that it really is hilarious at times. Sometimes the blurbs are so long they are spread onto the next page. The contain three or four different fonts in the same sentence. The sources of the information are pointless mixed with non-technical information about the content... <br /> <br />There is no logic in the way "subillustrations" are combined to illustrations. (Why do they insist on subillustrations at all? Why not make separate illustration?) They are just slapped together any old way. Sometime there are additional frams, sometimes not. Even the numbering convention varies. The order that the subillustration appear in the illustrations is also random. <br /> <br />The book is almost impossible to read. It needs to go back to the publisher and be totally reorganized for readability. <br /> <br />What a pity. The content is actually fascinating. This book is complementary too, but on a more advanced level than Sean Carroll's From DNA To Diversity, which I strongly recommend as a great intro book to evo-devo. Davidson's book is tough going in places, which is why I gave it one star off, but the material is in fairness quite complex. He emphasizes the role of cis-regulatory sequences in genes and the structure of the systems that regulate gene expression in development and evolution in some detail. It becomes clear how minor mutations in the regulatory part of a gene can transform how it is expressed, and why the importance for evolution in mutations in gene expression is clearly much greater than for mutations in the protein coding sequence. His explanation for what is responsible for the incredible homologies in, for example, the pax 6 gene that regulates eye development across phyla is very illuminating. A must read for anybody interested in the molecular basis for development and evolution. Genomic Regulatory Systems : development and evolution, by<br>Eric Davidson<p>The book is about how the genome actually works in [embryo?] development.<br>It is a beautiful book with many attractive illustrations.<br>The book's introductory material and<br>that of each chapter is clear and interesting.<br>I enjoyed about 3 valuable hours with this book<br>before getting lost because of my inadequate background (nonbio major).<br>He gives 4 reasons why this field has been so exciting over the past decade:<br>(1) We can now bring regulatory hard wiring at<br>the DNA nucleotide level into concise functional focus,<br>(2) We now have the full DNA sequence,<br>(3) Good minds from evolution and from development have converged,<br>(4) A lot of confusion in molecular phylogeny has been cleared up.<p>The book is mostly about bilaterians.<br>The size of the genome within a clade [some very similar critters]<br>can vary by a factor of ten whereas<br>the variation in protein coding (mRNA) is much smaller.<br>Amniotes [embryo in sac] have 4 hox clusters on 4 chromosomes.<br>There are remarkable examples of diverse usage of similar genes<br>of diverse organisms.<br>I don't think he defines the difference between cis- regulatory elements<br>[within the chromosome] and trans- [across chromosomes] so I needed<br>to do some guessing or find some other references.<br>Next time I take another look at this book,<br>I'll probably restart back about page 9.<br>I noticed on page 110 on the morphogenesis of heart parts<br>that different genes were identified for right and left sides<br>of the heart -- a matter of interest to me as my apparantly healthy 25 year old son ...died suddenly and unexpectedly<br>of natural causes,*many tears*, presumably a heart attack.<br>Perhaps the next decade or two will bring life-saving diagnostics.
	Introduction to Ecological Genomics
	By: Nico M. van Straalen, Dick Roelofs ISBN: 0198566719 Publisher: Oxford University Press, USA Release Date: 11 May, 2006 Bioscience book rank: 445497	This book is intended for use in beginning graduate level coursework, and of course to the working researcher with a need for more knowledge in this field. It presumes a basic level of knowledge in the biological sciences at the bachelor of science level. Some knowledge of ecology, evolutionary biology, microbiology, plant physiology, animal physiology, genetics, and molecular biology will be needed. The concentration in this book is to ecology and evolutionary biology with emphasis placed on aspects that should be particularly new to the student. The book is based on research published primarily in the last five years. <br /> <br />The book focuses on three fundamental ecological questions: <br /> <br />1. What is the relationship between community structure and ecological function in ecosystems? <br /> <br />2. How can the variation in life-history patterns among species be explained from interaction between the genome and the environment? <br /> <br />3. To what extent can the limits of the ecological niche be understood from molecular stress responses? <br /> <br />Before this book was written, journal articles comprised the only literature on ecological genomics. They were widely scattered, difficult to find and do not present a unified approach.
	The Genus Yersinia: From Genomics to Function (Advances in Experimental Medicine and Biology) (Advances in Experimental Medicine and Biology)
	By: Robert D. Perry, Jacqueline D. Fetherston ISBN: 0387721231 Publisher: Springer Release Date: 25 September, 2007 Bioscience book rank: 1167861
	Gene Regulation and Metabolism: Post-Genomic Computational Approaches (Computational Molecular Biology)
	By: Julio Collado-Vides, Ralf Hofestädt ISBN: 0262532689 Publisher: The MIT Press Release Date: 01 September, 2004 Bioscience book rank: 1049481	The determination of the genome of organisms is quite an achievement, and one that is taking place with incredible rapidity at the present time. But in order to completely understand the life processes of an organism one needs to understand how the genes are expressed and the consequent effects on the metabolism. As is pointed out in this book, even for the bacterial organism Escherichia coli, whose genome is the most understood in the biosphere, only about six hundred promoters have been determined experimentally. If genome determination is to have practical applications to human and animal health, it will become necessary to have a much better understanding of how the metabolism of an organism is regulated by its genes. This is an enormously difficult undertaking due to the magnitude of the information involved. It is therefore no surprise that computing machines and algorithms have been used to sort through and organize this information. Whether it goes by the name of computational biology or computational genomics, the use of these machines has assisted greatly in the understanding of the life processes. This book outlines a few of the approaches that have been taken. It is directed towards experts, but it could be read by anyone who has an interest in genetic and metabolic engineering from an information-theoretic, computational perspective. The book was first published four years ago, and so it is somewhat out of date, due to the increases in CPU processing speeds and new algorithms that have been developed since then. <br /> <br />Of particular interest is the article by Collado-Vides et al and which concerns the use of software to translate a DNA sequence into all possible proteins so as to compare them against a database of proteins that were determined by experiment. The authors discuss how this can be done for the case of E. coli and for a database called RegulonDB, which can be accessed on the Web, and which contains information on transcription initiation and operon organization in the K-12 strain of E. coli. The goal of the authors is to understand the structure of gene regulatory networks, both from a purely computational point of view and using experimentally determined transcription profiles. The article is broken down into four parts, with the first one concentrating on the prediction of gene regulatory networks using sequence information, followed by one discussing the use of Bayesian networks to assist in these predictions. The third part gives examples on how to use the database information to analyze transcription experiments and the last puts all of this analysis in the context of evolutionary origins of transcriptional regulation. <br /> <br />The authors are very interested in the process of transcription, particularly the initiation phase. As is well known, gene transcription is catalyzed by the RNA polymerase (RNAP) proteins. In particular, the RNAP `holoenzyme' contains the `sigma factor' that guides RNAP to specific sequences on the genomic DNA (the promoter). The RNAP holoenzyme with the sigma factor thus recognizes the precise site where transcription is initiated. Having located a promoter and binding to it, the RNAP holoenzyme and the bound DNA then undergo a series of conformational changes that allow RNA synthesis to be initiated. For the case of E. coli, the study of the formation of RNAP contacts at these specific sites on the promoter DNA has been the subject of intense experimental investigation, the challenge being the measurement of the formation of these contacts in real time. In this context the author's goal is find computational schemes that will predict the promoters and other protein-binding sites. This has traditionally been done with the use of weight matrices, but as the authors point out this method (and others) results in a large number of false positives. To improve on this method, they first obtain a population of potential candidates using a low enough threshold that weaker sites can be identified. The next step is to select a collection of promoters by comparing them with all candidates within the regulatory region. The candidates are split into groups separated by the distance to the beginning of the gene, and each group contributes one best candidate. This method, the authors claim, leads to one true promoter out of six candidates on the average. <br /> <br />The authors though do not end the analysis here, as they believe that the prediction of promoters is not reliable enough to search for sites for operator sites for specific transcriptional regulators (the information content of the promoter sites is too low). They therefore make use of a `dyad-detector' algorithm that has the ability to identify oligonucleotides up to seven bases long that are overrepresented in a given family of upstream regions. The dyad-detector can also find words with internal symmetry, such as palindromes. Also of interest to the authors is the identification of transcriptional activators and repressors that affect transcription initiation. Their goal is to identify which protein binds to which set of sites, assuming that a collection of protein-binding motifs has been identified and that the number in this collection is equal to the number of transcriptional regulators.
	Parasite Genomics Protocols (Methods in Molecular Biology)
	By: Sara E. Melville ISBN: 158829062X Publisher: Humana Press Release Date: 17 May, 2004 Bioscience book rank: 1201695
	Genomics, Proteomics and Vaccines
	By: Guido Grandi ISBN: 0470856165 Publisher: Wiley Release Date: 19 March, 2004 Bioscience book rank: 1165173
	Essentials of Genomics and PowerPoint CD Package
	By: Philip Benfey ISBN: 0131686410 Publisher: Benjamin Cummings Release Date: 09 December, 2004 Bioscience book rank: 1030811