Part I Computational Methods for Microarray, Gene Expression
Analysis, and Gene Regulatory Networks
1 A Technical Platform for Generating Reproducible
Expression Data from Streptomyces coelicolor Batch
Cultivations ................................................. 3
F. Battke, A. Herbig, A. Wentzel, Ø.M. Jakobsen, M. Bonin,
D.A. Hodgson, W. Wohlleben, Т.Е. Ellingsen, the STREAM
Consortium, and K. Nieselt
2 MiRNA Recognition with the yasMiR System: The Quest
for Further Improvements .................................... 17
Daniel Pasailă, Andrei Sucilă, Irina Mohorianu, Ştefan
Pantiru, and Liviu Ciortuz
3 Top Scoring Pair Decision Tree for Gene Expression
Data Analysis ............................................... 27
Marcin Czajkowski and Marek Krętowski
4 Predictive Minimum Description Length Principle
Approach to Inferring Gene Regulatory Networks .............. 37
Vijender Chaitankar, Chaoyang Zhang, Preetam Ghosh, Ping
Gong, Edward J. Perkins, and Youping Deng
5 Parsimonious Selection of Useful Genes in Microarray
Gene Expression Data ........................................ 45
Felix F. Gonzaáz-Navarro and Lluis A. Belanche-Muñoz
6 Hierarchical Signature Clustering for Time Series
Microarray Data ............................................. 57
Lars Koenig and Eunseog Youn
7 Microarray Database Mining and Cell Differentiation
Defects in Schizophrenia .................................... 67
Aurelian Radu, Gabriela Hristescu, Pavel Katsel, Vahram
Haroutunian, and Kenneth L. Davis
8 miRNA Prediction Using Computational Approach ............... 75
A.K. Mishra and D.K. Lobiyal
9 Improving the Accuracy of Gene Expression Profile
Classification with Lorenz Curves and Gini Ratios ........... 83
Quoc-Nam Tran
10 Feature Selection in Gene Expression Data Using
Principal Component Analysis and Rough Set Theory ........... 91
Debahuti Mishra, Rajashree Dash, Amiya Kumar Rath, and
Milu Acharya
11 Dramatically Reduced Precision in Microarray Analysis
Retains Quantitative Properties and Provides Additional
Benefits ................................................... 101
William C. Ray
12 Algebraic Model Checking for Boolean Gene Regulatory
Networks ................................................... 113
Quoc-Nam Tran
13 Comparative Advantages of Novel Algorithms Using MSR
Threshold and MSR Difference Threshold for Biclustering
Gene Expression Data ....................................... 123
Shyama Das and Sumam Mary Idicula
14 Performance Comparison of SLFN Training Algorithms
for DNA Microarray Classification .......................... 135
Hieu Trung Huynh, Jung-Ja Kim, and Yonggwan Won
15 Clustering Microarray Data to Determine Normalization
Method ..................................................... 145
Marie Vendettuoli, Erin Doyle, and Heike Hofmann
Part II Bioinformatics Databases, Data Mining, and Pattern
Discovery Techniques
16 Estimation, Modeling, and Simulation of Patterned Growth
in Extreme Environments .................................... 157
B. Strader, K.E. Schubert, M. Quintana, E. Gomez,
J. Curnutt, and P. Boston
17 Performance of Univariate Forecasting on Seasonal
Diseases: The Case of Tuberculosis ..........................
Adhistya Erna Permanasari, Dayang Rohaya Awang Rambli,
and P. Dhanapal Durai Dominic
18 Predicting Individual Affect of Health Interventions
to Reduce HPV Prevalence ................................... 181
Courtney D. Corley, Rada Mihalcea, Armin R. Mikler, and
Antonio P. Sanfilippo
19 Decision Tree and Ensemble Learning Algorithms with Their
Applications in Bioinformatics ............................. 191
Dongsheng Che, Qi Liu, Khaled Rasheed, and Xiuping Tao
20 Pattern Recognition of Surface EMG Biological Signals
by Means of Hilbert Spectrum and Fuzzy Clustering .......... 201
Ruben-Dario Pinzon-Morales, Katherine-Andrea Baquero-
Duarte, Alvaro-Angel Orozco-Gutierrez, and Victor-Hugo
Grisales-Palacio
21 Rotation of Random Forests for Genomic and Proteomic
Classification Problems .................................... 211
Gregor Stiglic, Juan J. Rodriguez, and Peter Kokol
22 Improved Prediction of MHC Class I Binders/
Non-Binders Peptides Through Artificial Neural Network
Using Variable Learning Rate: SARS Corona Virus,
a Case Study ............................................... 223
Sudhir Singh Soam, Bharat Bhasker, and Bhartendu Nath
Mishra
Part III Protein Classification and Structure Prediction, and
Computational Structural Biology
23 Fast Three-Dimensional Noise Reduction for Real-Time
Electron Tomography ........................................ 233
José Antonio Martínez and Jose Jesus Fernández
24 Prediction of Chemical-Protein Binding Activity Using
Contrast Graph Patterns .................................... 243
Andrzej Dominik, Zbigniew Walczak, and Jacek Wojciechowski
25 Topological Constraint in High-Density Cells' Tracking
of Image Sequences ......................................... 255
Chunming Tang, Ling Ma, and Dongbin Xu
26 STRIKE: A Protein-Protein Interaction Classification
Approach ................................................... 263
Nazar Zaki, Wassim El-Hajj, Hesham M. Kamel, and Fadi Sibai
27 Cooperativity of Protein Binding to Vesicles ............... 271
Francisco Torrens and Gloria Castellano
28 The Role of Independent Test Set in Modeling of Protein
Folding Kinetics ........................................... 279
Nikola Štambuk and Paško Konjevoda
Part IV Comparative Sequence, Genome Analysis, Genome
Assembly, and Genome Scale Computational Methods
29 Branch-and-Bound Approach for Parsimonious Inference
of a Species Tree from a Set of Gene Family Trees .......... 287
Jean-Philippe Doyon and Cedric Chauve
30 Sequence-Specific Sequence Comparison Using Pairwise
Statistical Significance ................................... 297
Ankit Agrawal, Alok Choudhary, and Xiaoqiu Huang
31 Modelling Short Time Series in Metabolomics: A Functional
Data Analysis Approach ..................................... 307
Giovanni Montana, Maurice Berk, and Tim Ebbels
32 Modeling of Gene Therapy for Regenerative Cells Using
Intelligent Agents ......................................... 317
Aya Sedky Adly, Amal Elsayed Aboutabl, and M. Shaarawy
Ibrahim
33 Biomarkers Discovery in Medical Genomics Data .............. 327
A. Benis and M. Courtine
34 Computer Simulation on Disease Vector Population
Replacement Driven by the Maternal Effect Dominant
Embryonic Arrest ........................................... 335
Mauricio Guevara-Souza and Edgar E. Vallejo
35 Leukocytes Segmentation Using Markov Random Fields ......... 345
C. Reta, L. Altamirano, J.A. Gonzalez, R. Diaz, and
J.S. Guichard
Part V Experimental Medicine and Analysis Tools
36 Ontology-Based Knowledge Discovery in Pharmacogenomics ..... 357
Adrien Coulet, Malika SmaYl-Tabbone, Amedeo Napoli, and
Marie-Dominique Devignes
37 Enabling Heterogeneous Data Integration and Biomedical
Event Prediction Through ICT: The Test Case of Cancer
Reoccurrence ............................................... 367
Marco Picone, Sebastian Steger, Konstantinos Exarchos,
Marco De Fazio, Yorgos Goletsis, Dimitrios I. Fotiadis,
Elena Martinelli, and Diego Ardigò
38 Complexity and High-End Computing in Biology and Medicine .. 377
Dimitri Perrin
39 Molecular Modeling Study of Interaction of Anthracenedione
Class of Drug Mitoxantrone and Its Analogs with DNA
Tetrameric Sequences ....................................... 385
Pamita Awasthi, Shilpa Dogra, Lalit K. Awasthi, and Ritu
Barthwal
40 A Monte Carlo Analysis of Peritoneal Antimicrobial
Pharmacokinetics ........................................... 401
Sanjukta Hota, Philip Crooke, and John Hotchkiss
Part VI Computational Methods for Filtering, Noise
Cancellation, and Signal and Image Processing
41 Histopathology Tissue Segmentation by Combining Fuzzy
Clustering with Multiphase Vector Level Sets ............... 413
Filiz Bunyak, Adel Hafiane, and Kannappan Palaniappan
42 A Dynamically Masked Gaussian Can Efficiently Approximate
a Distance Calculation for Image Segmentation .............. 425
Shareef M. Dabdoub, Sheryl S. Justice, and William C. Ray
43 Automatic and Robust System for Correcting Microarray
Images' Rotations and Isolating Spots ...................... 433
Anlei Wang, Naima Kaabouch, and Wen-Chen Hu
44 Multimodality Medical Image Registration and Fusion
Techniques Using Mutual Information and Genetic Algorithm-
Based Approaches ........................................... 441
Mahua Bhattacharya and Arpita Das
45 Microcalcifications Detection Using Fisher's Linear
Discriminant and Breast Density ............................ 451
G.A. Rodriguez, J.A. Gonzalez, L. Altamirano,
J.S. Guichard, and R. Diaz
46 Enhanced Optical Flow Field of Left Ventricular Motion
Using Quasi-Gaussian DCT Filter ............................ 461
Slamet Riyadi, Mohd. Marzuki Mustafa, Aini Hussain, Oteh
Maskon, and Ika Faizura Mohd. Nor
47 An Efficient Algorithm for Denoising MR and CT Images
Using Digital Curvelet Transform ........................... 471
S. Hyder Ali and R. Sukanesh
48 On the Use of Collinear and Triangle Equation for
Automatic Segmentation and Boundary Detection of Cardiac
Cavity Images .............................................. 481
Riyanto Sigit, Mohd. Marzuki Mustafa, Aini Hussain, Oteh
Maskon, and Ika Faizura Mohd. Nor
49 The Electromagnetic-Trait Imaging Computation of Traveling
Wave Method in Breast Tumor Microwave Sensor System ........ 489
Zhi-fu Tao, Zhong-ling Han, and Meng Yao
50 Medical Image Processing Using Novel Wavelet Filters Based
on Atomic Functions: Optimal Medical Image Compression ..... 497
Cristina Juarez Landin, Magally Martinez Reyes, Anabelem
Soberanes Martin, Rosa Maria Valdovinos Rosas, Jose Luis
Sanchez Ramirez, Volodymyr Ponomaryov, and Maria Dolores
Torres Soto
51 Cancellation of Artifacts in ECG Signals Using Block
Adaptive Filtering Techniques .............................. 505
Mohammad Zia Ur Rahman, Rafi Ahamed Shaik, and D.V. Rama
Koti Reddy
52 Segmentation of Medical Image Sequence by Parallel Active
Contour .................................................... 515
Abdelkader Fekir and Nacera Benamrane
53 Computerized Decision Support System for Mass
Identification in Breast Using Digital Mammogram: A Study
on GA-Based Neuro-Fuzzy Approaches ......................... 523
Arpita Das and Mahua Bhattacharya
Part VII Computer-Based Medical Systems
54 Optimization-Based Technique for Separation and Detection
of Saccadic Movements and Eye-Blinking in
Electrooculography Biosignals .............................. 537
Robert Krupiński and Przemysław Mazurek
55 A Framework for Lipoprotein Ontology ....................... 547
Meifania Chen and Maja Hadzic
56 Verbal Decision Analysis Applied on the Optimization of
Alzheimer's Disease Diagnosis: A Case Study Based on
Neuroimaging ............................................... 555
Isabelle Tamanini, Ana Karoline de Castro, Plácido Rogério
Pinheiro, and Mirian Calíope Dantas Pinheiro
57 Asynchronous Brain Machine Interface-Based Control
of a Wheelchair ............................................ 565
C.R. Hema, M.R Paulraj, Sazali Yaacob, Abdul Hamid Adom,
and R. Nagarajan
58 Toward an Application to Psychological Disorders
Diagnosis .................................................. 573
Luciano Comin Nunes, Plácido Rogério Pinheiro, Tarcísio
Cavalcante Pequeno, and Mirian Calíope Dantas Pinheiro
59 Enhancing Medical Research Efficiency by Using Concept
Maps ....................................................... 581
Varadraj P. Gurupur, Amit S. Kamdi, Tolga Tuncer, Murat
M. Tanik, and Murat N. Tanju
60 Analysis of Neural Sources of P300 Event-Related Potential
in Normal and Schizophrenic Participants ................... 589
Malihe Sabeti, Ehsan Moradi, and Serajeddin Katebi
61 Design and Development of a Tele-Healthcare Information
System Based on Web Services and HL7 Standards ............. 599
Ean-Wen Huang, Rui-Suan Hung, Shwu-Fen Chiou, Fei-Ying
Liu, and Der-Ming Liou
62 Fuzzy Logic Based Expert System for the Treatment of
Mobile Tooth ............................................... 607
Vrjay Kumar Mago, Anjali Mago, Poonam Sharma, and
Jagmohan Mago
63 A Microcomputer FES System for Wrist Moving Control ........ 615
Li Cao, Jin-Sheng Yang, Zhi-Long Geng, and Gang Cao
64 Computer-Aided Decision System for the Clubfeet
Deformities ................................................ 623
Tien Tuan Dao, Frédéric Marin, Henri Bensahel, and Marie
Christine Ho Ba Tho
65 A Framework for Specifying Safe Behavior of the CID?
Medical System ............................................. 637
Seyed Morteza Babamir
Part VIII Software Packages and Other Computational Topics
in Bioinformatics
66 Lotka-Volterra System with Volterra Multiplier ............. 647
Klaus Gürlebeck and Xinhua Ji
67 A Biological Compression Model and Its Applications ........ 657
Minh Due Cao, Trevor I. Dix, and Lloyd Allison
68 Open Source Clinical Portals: A Model for Healthcare
Information Systems to Support Care Processes and Feed
Clinical Research .......................................... 667
Paolo Locatelli, Emanuele Baj, Nicola Restifo, Gianni
Origgi, and Silvia Bragagia
69 Analysis and Clustering of MicroRNA Array: A New
Efficient and Reliable Computational Method ................ 679
Luca Sterpone, Federica Collino, Giovanni Camussi, and
Claudio Loconsole
70 Stochastic Simulations of Mixed-Lipid Compartments: From
Self-Assembling Vesicles to Self-Producing Protocells ...... 689
Kepa Ruiz-Mirazo, Gabriel Piedrafita, Fulvio Ciriaco, and
Fabio Mavelli
71 A New Genetic Algorithm for Polygonal Approximation ........ 697
Cecilia Di Ruberto and Andrea Morgera
72 Challenges When Using Real-World Bio-data to Calibrate
Simulation Systems ......................................... 709
Elaine M. Blount, Stacie I. Ringleb, and Andreas Tolk
73 Credibility of Digital Content in a Healthcare
Collaborative Community .................................... 717
Wail M. Omar, Dinesh K. Saini, and Mustafa Hasan
74 Using Standardized Numerical Scores for the Display and
Interpretation of Biomedical Data .......................... 725
Robert A. Warner
75 ImagCell: A Computer Tool for Cell Culture Image
Processing Applications in Bioimpedance Measurements ....... 733
Alberto Yúfera, Estefania Gallego, and Javier Molina
76 From Ontology Selection and Semantic Web to an Integrated
Information System for Food-borne Diseases and Food
Safety ..................................................... 741
Xianghe Yan, Yun Peng, Jianghong Meng, Juliana Ruzante,
Pina M. Fratamico, Lihan Huang, Vijay Juneja, and David
S. Needleman
77 Algebraic Analysis of Social Networks for
Bio-surveillance: The Cases of SARS-Beijing-2003 and
AH1N1 Influenza-México-2009 ................................ 751
Doracelly Hincapie and Juan Ospina
Index ......................................................... 763
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