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1. Qualitative Knowledge Models in Functional Genomics d Proteomics MP Pc Irene 5 (Jabav ili, and Russ B. A/tanm 1 1. Introducion 1 1 2 Methods and ools 3 1.3. Modeing Approach and Resu lts 6 1. 1 Discussion 19 1.5 Conclusion 20 Reeirences 13 2. Interpreting Microarra) Data and Rlated pplications Using Nonlinear System Identifeation 25 lichael Korenber 2i1 Introducin 25 2.2. Background 25 .3. Parallel Cascade Identification 30 2.4. Construcing C lass Prdicors 3 2.5 Prediction Based on Gene Expression Proling 35 2 6 Comparing Diferent Predictor s Over the Same Data Set 46 2.7. Conclurding Remarks 48 Refrences 49 3 Gene Regulation Bioinformatics of Microarray Data 55 Ccit 1bps Iij nk De Si;t, Yves (letaut hn K a Marchel, and iBar De lioe 3.. Introductin 55 132. Inooduction to Tr anscoptional Regulation 57 .3. Measuring Gene1 xprecson Profiles 95 314 Preprocemssing of Data 61 3 5. Clustering of GCene Expression Pofiles 63 3.6 Cluster Va on 70 7 Sear-ching for Comion Bdiing Sites of Coregulited Genes k7 "3 "i. Si: le I tn egrated Analysis o Mic ir tay Data 87 3.9. 9 Fi nt lIntg rative Steps 3 10 7 clusio K.90 Se ere es 91 4. Robsr t enthods fot Mirorarray Analysis 99 (eora,r S. Bid'stm. Sht>;.S n M>'' ievin B; Knc'; k BrriaK ;iV. Wiic. ' ii i ; nri;; , A nt Avcon;, tr e hKi W crni r-W a o r 4.. Introdi uci 900 4.2. Micronrray Experiments andi Anailysis Methods 100 4.3. tnsuervis 4 e th ds 103 4.4. Snpervised Methods 117 4.5. Concusio n i27 5. In Sil%o Rdoion Onclogy: A Platform for Uinderst anding Canmcer Behavio aned Optimanhg Radiaion The rapy Trea mn t 131 .. "Pil'sopjhim' Tu mi'i,; s prinipiA uh rihi 3 Agri4hmic iciplf ofi- Siing 1B t I (Cancel n iCopte 1 5 Bief LA Ri 53a. viari of F urirnionsral Si ulatin of Tinmor C iowh S5.5. t T rens* 50 135 1Refereencei 50 6 1eno i ot Ir i entificatson Using a Dii onIi/ i odei 107 (.C niied I ree 16 6.4e Pa e Estimaton via 05a atio 1lgo 167') 7. Error Contr ol Codes ard the Genome 173 7 i'.1 E irro onol anwl Com inicat1: A N riw 173 7.2 Centil Dogmra as Communication System 180 7.. R rse Engineeting the Genetic Error Contol System 184 7.4 pApliations of Biologieal Coding Theory 20 Referenes 205 8. Complex life Science Multidatabase Queries 209 Zifia BcR1 Milecl Nianii ii! i, lot f iie He, Maci o 1i2(1 (41 nd O ir/i! ii1es 8.. Introduction 20 82. Architctrie 212 8.3 Qur y Exet ion Pla ns 214 8.4 Related Work 21C .5 Futurme rends 22 References 223 9. Computaional nalsis of Proteins 22 and C t Pd 12'liitkao' 9.1 intoduction: Defnition 27 9.2. Databass 229 9.3 Sequine Motifs and Do mains 23 9.4 Sequence Alignment 25 9.5. Modeling 241 9. Cilasificaon and Prediction 42 9. 7 Nauia i, anuage Processing 48 9. Future ITrends 52 Refetienes 252 . Conputational Anahysis of Interactions Between Tumorad Tumor Suppressor Proteins 257 E. Pi1 i, M. i14 ka/n md I. Cosic 0 1. IntrolucItion 7 10.. MethiOdology Resonant Rcoegnitian Model 2(1 10.3 Results and Dicussions S2 10.4. Conclrnson 284 Referenes 285