Table of contents for Genomics and proteomics engineering in medicine and biology / edited by Metin Akay.


Bibliographic record and links to related information available from the Library of Congress catalog
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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



Library of Congress subject headings for this publication: Proteomics, Genomics