preface_Bioinformatics Trends and Methodologies......Page 1
Part 1 Bioinformatics in Biology......Page 15
Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective......Page 17
Part 2 Data Integration......Page 53
Data Integration in Bioinformatics: Current Efforts and Challenges......Page 55
Semantic Data Integration on Biomedical Data Using Semantic Web Technologies......Page 71
Part 3 Data Mining and Applications......Page 97
Vector Space Information Retrieval Techniques for Bioinformatics Data Mining......Page 99
Massively Parallelized DNA Motif Search on FPGA......Page 121
A Pattern Search Method for Discovering Conserved Motifs in Bioactive Peptide Families......Page 135
Database Mining: Defining the Pathogenesis of Inflammatory and Immunological Diseases......Page 157
Data Mining Pubmed Identifies Core Signalings and miRNA Regulatory Module in Glioma......Page 171
Part 4 Sequence Analysis and Evolution......Page 185
Significance Score of Motifs in Biological Sequences......Page 187
A Systematic and Thorough Search for Domains of the Scavenger Receptor Cysteine-Rich Group-B Family in the Human Genome......Page 209
Assessing Multiple Sequence Alignments Using Visual Tools......Page 225
Optimal Sequence Alignment and Its Relationship with Phylogeny......Page 257
Predicting Virus Evolution......Page 283
Part 5 Protein Structure Analysis......Page 301
A Bioinformatical Approach to Study the Endosomal Sorting Complex Required for Transport (ESCRT) Machinery in Protozoan Parasites: The Entamoeba histolytica Case......Page 303
Structural Bioinformatics Analysis of Acid Alpha-Glucosidase Mutants with Pharmacological Chaperones......Page 327
Bioinformatics Domain Structure Prediction and Homology Modeling of Human Ryanodine Receptor 2......Page 339
Identifying Enzyme Knockout Strategies on Multiple Enzyme Associations......Page 367
Part 6 Genome Analysis......Page 385
Using Bacterial Artificial Chromosomes to Refine Genome Assemblies and to Build Virtual Genomes......Page 387
Basidiomycetes Telomeres โ A Bioinformatics Approach......Page 407
SNPpattern: A Genetic Tool to Derive Haplotype Blocks and Measure Genomic Diversity in Populations Using SNP Genotypes......Page 439
Algorithms for CpG Islands Search: New Advantages and Old Problems......Page 463
Translational Oncogenomics and Human Cancer Interactomics: Advanced Techniques and Complex System Dynamic Approaches......Page 487
Part 7 Transcriptional Analysis......Page 525
In-silico Approaches for RNAi Post-Transcriptional Gene Regulation: Optimizing siRNA Design and Selection......Page 527
MicroRNA Targeting in Heart: A Theoretical Analysis......Page 553
Genome-Wide Identification of Estrogen Receptor Alpha Regulated miRNAs Using Transcription Factor Binding Data......Page 573
Part 8 Gene Expression and Systems Biology......Page 589
Quantification of Gene Expression Based on Microarray Experiment......Page 591
On-Chip Living-Cell Microarrays for Network Biology......Page 623
Novel Machine Learning Techniques for Micro-Array Data Classification......Page 645
Part 9 Next Generation Sequencing......Page 667
Deep Sequencing Data Analysis: Challenges and Solutions......Page 669
Whole Genome Annotation: In Silico Analysis......Page 693
Part 10 Drug Design......Page 719
Designing of Anti-Cancer Drug Targeted to Bcl-2 Associated Athanogene (BAG1) Protein......Page 721