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| Detection of Monosaccharide Types from Coordinates | p. 3 |
| Mining Super-Secondary Structure Motifs from 3D Protein Structures: A Sequence Order Independent Approach | p. 15 |
| FragQA: Predicting Local Fragment Quality of a Sequence-Structure Alignment | p. 27 |
| Predicting B Cell Epitope Residues with Network Topology Based Amino Acid Indices | p. 40 |
| Comparative Pair-Wise Domain-Combinations for Screening the Clade Specific Domain-Architectures in Metazoan Genomes | p. 50 |
| A Conservative Parametric Approach to Motif Significance Analysis | p. 61 |
| Recognition of Polyadenylation Sites from Arabidopsis Genomic Sequences | p. 73 |
| Computational Analysis and Modeling of Genome-Scale Avidity Distribution of Transcription Factor Binding Sites in ChIP-PET Experiments | p. 83 |
| Linear-Time Reconstruction of Zero-Recombinant Mendelian Inheritance on Pedigrees without Mating Loops | p. 95 |
| Computed Protonation Properties: Unique Capabilities for Protein Functional Site Prediction | p. 107 |
| An Accurate and Efficient Algorithm for Peptide and PTM Identification by Tandem Mass Spectrometry | p. 119 |
| The Comparative Genomics of Protein Interactions | p. 131 |
| Weighted Lasso in Graphical Gaussian Modeling for Large Gene Network Estimation Based on Microarray Data | p. 142 |
| GO Based Tissue Specific Functions of Mouse using Countable Gene Expression Profiles | p. 154 |
| Functional Centrality: Detecting Lethality of Proteins in Protein Interaction Networks | p. 166 |
| The in silico Prediction of Promoters in Bacterial Genomes | p. 178 |
| Discovering Biomolecular Mechanisms with Protein Sequence Studies: The Annotator Software Suite | p. 193 |
| The p53 Pathway | p. 194 |
| Regulation of Gene Expression by Small Non-Coding RNAs | p. 195 |
| Mapping the Transcriptional Network in Stem Cells Regulated by REST | p. 196 |
| Computational Dissection of Mammalian Regulation Networks | p. 197 |
| Author Index | p. 199 |
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