Book Review: Bioinformatics and Genome Analysis. Edited by Hans-Werner Mewes, Bertram Weiss, and Henrik Seidel
Post on 06-Jun-2016
Embed Size (px)
Bioinformatics and GenomeAnalysis
Edited by Hans-Werner Mewes,Bertram Weiss,and Henrik Seidel.Springer-Verlag,Heidelberg 2002.296 pp., hard-cover E 80.20.ISBN 3-540-42893-3
As a compilation of articles by theinvited speakers at a workshop withthe same title (Ernst Schering Founda-tion Workshop No. 38, Berlin 2001), thisbook is not intended to be a textbookquite a few of those have also recentlyappeared on the market, if that is whatyou are looking for. Instead, the editorsare addressing scientists and research-ers working in bioinformatics andgenome analysis world-wide with thisvolume, and it is packed full with reallyhot topics.
The editors have brought together aremarkably diverse set of recognizedresearchers from different specialistareas, ranging from purely wet-experi-mental functional genomics to theatleast at presentextremely theoreticalrealm of systems biology (which couldbe very roughly described as theendeavor to extend kinetic modeling toentire organisms). The biological/bio-medical context of the articles in thebook ranges from identifying cancergenes to determining protein interac-tions and to drug discovery. The editorsare to be complimented for lookingahead and thus not missing out onsome of the currently less wellresearched topics, such as membranes,
metabolic networks, and glycosylation.Probably because of the present lack ofa clear concept of how these areas couldbe investigated experimentally on alarge enough scale to feed the datainto our post-genomic big picture, theyare often overlooked in compendia ofthis kind. Scarcity of data also meansthat the reliability of predictive bioin-formatic approaches cannot be easilyassessedall the more reason to raiseawareness of these next challenges.The editors2 aim towards diversity in theselection of speakers for the workshop isreflected in the different backgrounds ofthe authors, who include biologists ofvarious kinds, computer scientists, math-ematicians/statisticians, and all flavors inbetween.
As I mentioned above, the book onthe whole is not for beginners. However,some of the chapters are very instructiveoverviews in which the authors address abroad audience and describe the specialfeatures of their respective fields. Chap-ter 1 by A. Reis, which explains posi-tional cloning in a simple way, appealsespecially in this regard. Other topics onwhich the reader will gain a good over-view are membrane proteins and cur-rent methodology for predicting trans-membrane protein features fromsequence (Chap. 2, G. van Heijne), therole of gene promoter sequences andmethodology for predicting these(Chap. 4, T. Werner), and considerationspertaining to protein glycosylation(Chap. 13, R. Gupta, L. J. Jensen, S.Brunak). The overview about effortstowards representing, and querying,metabolic pathways by graphical theo-retical means (Chap. 12, J. van Helden,L. Wernisch, D. Gilbert, S. J. Wodak) isdifferent in that the topic discussed isvery narrow, new, and still in progress,but here also there is a clear attempt tokeep a wider audience interested.Finally, the outline of how proteinmodeling can assist at different stagesof the drug discovery process (Chap. 8,L. Brive, R. Abagyan) seems to pay alittle less attention than the aforemen-tioned chapters to reviewing methods ofothers besides those of the authors.However, this is understandable giventhe breadth of scope the authors havechosen for their contribution, and thischapter too belongs in the category ofeasily accessible overview articles
albeit with a potentially confusing title(Computational Structural Proteo-mics).
It is symptomatic of the differencesin terminology (or misunderstandings?)between scientific disciplinesespe-cially where buzz-words are involvedthat the word proteomics is used withno less than three different meanings inChapters 8 10. In one case it is aderivative of the classic experimentaldefinition of the proteome as thecomplement of expressed proteins in acell under particular conditions (Chap.9). Secondly it is extended to includeany protein whose expression can beinduced in vitro, disregarding its naturalsubcellular location and potentially mis-predicted gene termini, in the case ofeukaryotes (Chap. 10). Thirdly (Chap. 8)it represents the entirety of predictedproteins in a genome (a priori, withoutexperimental verification of whether theputative gene sequences in question areever really expressed). Only the authorsof Chapter 9 took the time to explicitlydefine their use of the term, which isunfortunate since this would haveseemed a good forum to clarify issueslike the precise usage of common terms.
A few other chapters in the book canbe categorized as specialist reviews ofcurrent research in specific areas ortechniques. These articles will be veryvaluable to experts in the respectivefields, but require advanced knowledgeand understanding of technical languagein one or several fields. The thoroughreview of the latest developments inexperimental proteomics technology byM. Gentzel, T. KBcher, and M. Wilm(Chap. 9) should come as a welcomebreak to non-bioinformaticians, sincethis is the only chapter in which thereis no reliance, in one way or another, oncomputational interpretation or predic-tiononly solid experimental techni-ques. Unfortunately, the technical lan-guage used might pose a problem for themany bioinformaticians who wouldgreatly benefit from understanding thistechnology in more detail whenattempting to analyze the data emergingfrom it. Two further chapters applyinteresting combinations of wet-experi-mental and theoretical perspectives.One of them (Chap. 6, N. Friedman, N.Kaminski) describes methods used toextract information from recent micro-
3715Angew. Chem. Int. Ed. 2003, 42, 3715 3717 www.angewandte.org ' 2003 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
array studies (including the associateddifficulties) and is specifically focusedon cancer research. The other onereviews current experimental strategiesfor investigating on a large scalewhether two proteins interact witheach other, and includes a discussion ofprediction methodology (Chap. 10, V.SchFchter).
The remaining chapters in the bookshould be read as research articles inwhich the authors describe and discussnovel computational/theoretical meth-ods of their own. In some cases thetechniques seem to be quite well estab-lished, and some validation is included;others contain interesting proposals andideas for future work. A novice readershould be aware that much research intothe practical value and applicability ofthese methods still remains to be done,but for the specialist these chaptersmake interesting reading and startingpoints for discussion amongst collea-gues. The problems addressed rangefrom finding functionally connectedgenes from sequence (Chap. 3, G. Kole-sov, H.-W. Mewes, D. Frishman) or fromgene expression data (Chap. 5, R.Sharan, R. Elkon, R. Shamir; a partic-ularly well-structured chapter discussingthe authors2 clustering method), to com-paring protein structures (Chap. 7, W. R.Taylor), and to modeling entire cells(Chap. 11, H. V. Westerhoff, W. M.Getz, H. W. van Verseveld, J.-H. S. Hof-meyr, J. L. Snoep).
With such a colorful variety of topicsand authors, holding the contributors tostricter guidelines with respect to thebreadth, style, and extent of specialisttechnical language used in their articleswould most certainly have opened upthis book to a broader audience. Viewedas an entity, this collection of articlesclearly lacks coherence in these aspects.Admittedly, this is probably paintingquite a realistic portrait of one of thegreatest challenges (besides the scien-tific ones) that must be overcome tomake interface research more effective:communication difficulties. All in all,however, experienced readers whocome from within the multidisciplinaryscene or are familiar with it will thor-oughly enjoy the articles as individualpieces (I did). The workshop itself musthave been a delight for speakers andother participants alike, featuring such
variety in such an active scientific area.These are exciting times for all of us,with teams of scientists from all fieldsand affiliations joining up to tacklewhole genomes/organisms and (hope-fully one day) to understand what isgoing on inside.
Dietlind L. GerloffInstitute of Cell & Molecular BiologyUniversity of Edinburgh (UK)
Chemistry, Prop-erties, Applica-tions. Edited byKlaus Hunger.Wiley-VCH, Wein-heim 2003. 660pp., hardcoverE 199.00.ISBN3-527-30426-6
Comprehensive surveys of industriallyimportant dyes appear only rarely.With-out such up-to-date surveys one hasusually had to rely on Ullmann tofind information about importantclasses of dyes arranged under keyheadings. Therefore the publication ofa monograph on dyes of technologicalimportance is very welcome. The aim ofthis book is to give an up-to-date over-view of the subject and to provideconvenient access to the patent litera-ture, which is often difficult to find one2sway around. Here the editor, KlausHunger, who is best known as one ofthe authors of Industrial Organic Pig-ments, has set out, together with 18co-authors who are mainly industrialdye chemists, to give a survey of thecurrent state of knowledge in colorchemistry from an industrial standpoint.The result is a substantial book of 660pages divided into eight chapters.
Chapter 1 consists of a short over-view describing the classification ofdyes, their economic importance(although unfortunately without suffi-ciently up-to-date numerical data), andaspects of their production (which aretreated too briefly and unspecifically).
In Chapter 2, which amounts to about100 pages, the various authors in theteam describe the most important typesof chromophores in turn. This form oftreatment is appropriate, because itgives a thorough picture of how theenormous variety of commercially inter-esting dyes all depend on a limitednumber of basic chromophores. How-ever, the different authors do not allcover their subjects with the samedegree of success. In some of the con-tributions the variety is simply cata-logued in full and the reader is over-loaded with too many details. Also theclassification of the chromophores ispuzzling in some cases; for example,cationic dye chromophores and arylme-thane dyes are treated as two differentclasses of chromophores, which inevita-bly results in some overlapping.
In Chapter 3 the most importantclasses of dyes are described, groupedaccording to their applications andmodes of use: reactive dyes, dispersedyes, acid dyes, direct dyes, and sulfurdyes. The chemistry relating to eachtype is explained, including syntheticroutes, and also the most importantcommercial dyes of that type are listedwith their structures and CI numbers,which is very useful. This enables thereader to find the desired informationvery quickly, including details of com-mercially available dyes for particularareas of application. Unfortunately,however, the above classification is notalways followed consistently. As well asthe classification of dyes according totheir uses, the same chapter alsoincludes articles relating to particularchromophores, for example, groupingtogether dyes based on anthraquinone,metal complex, or naphthoquinonechromophores. This leads to someunnecessary overlapping and repetition;for example, anthraquinone dispersedyes are covered twice. Vat dyes arenot treated in a separate article but areincluded along with anthraquinone dyes.The technology of using textile dyes isdescribed in a separate chapter, and thusthe chemistry of these dyes and their useare treated in different places. Oneconsequence of splitting the discussionin this way is that the relationshipsbetween the structures of the dyes andtheir technological properties cannot bebrought out as clearly as they should be.
3716 ' 2003 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim www.angewandte.org Angew. Chem. Int. Ed. 2003, 42, 3715 3717