What is included with this book?
Preface | |
Session Introduction | p. 3 |
Multiclass Cancer Classification Using Gene Expression Profiling and Probabilistic Neural Networks | p. 5 |
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus subtilis Using Differential Equations | p. 17 |
Genome-Wide Analysis of Bacterial Promoter Regions | p. 29 |
MOPAC: Motif Finding by Preprocessing and Agglomerative Clustering from Microarrays | p. 41 |
Improved Gene Selection for Classification of Microarrays | p. 53 |
Kernel Cox Regression Models for Linking Gene Expression Profiles to Censored Survival Data | p. 65 |
Extracting Conserved Gene Expression Motifs from Gene Expression Data | p. 77 |
Decomposing Gene Expression into Cellular Processes | p. 89 |
Session Introduction | p. 101 |
Suitability and Utility of Computational Analysis Tools: Characterization of Erythrocyte Parameter Variation | p. 104 |
Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes | p. 116 |
Incorporating Biological Knowledge into Evaluation of Causal Regulatory Hypotheses | p. 128 |
Assessment of the Reliability of Protein-Protein Interactions and Protein Function Prediction | p. 140 |
Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object Net | p. 152 |
Influence of Network Topology and Data Collection on Network Inference | p. 164 |
Session Introduction | p. 176 |
Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models | p. 180 |
Towards Discovering Structural Signatures of Protein Folds Based on Logical Hidden Markov Models | p. 192 |
Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structures | p. 204 |
Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions | p. 216 |
Identifying Structural Motifs in Proteins | p. 228 |
A Path Planning-Based Study of Protein Folding with a Case Study of Hairpin Formation in Protein G and L | p. 240 |
Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction | p. 252 |
Protein Threading by Linear Programming | p. 264 |
Session Introduction | p. 276 |
Towards Identifying Lateral Gene Transfer Events | p. 279 |
Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals | p. 291 |
MAP: Searching Large Genome Databases | p. 303 |
Towards the Development of Computational Tool for Evaluating Phylogenetic Network Reconstruction Methods | p. 315 |
Identification of Regulatory Binding Sites Using Minimum Spanning Trees | p. 327 |
Intrasplicing - Analysis of Long Intron Sequences | p. 339 |
Trajectory Clustering: A Non-Parametric Method for Grouping Gene Expression Time Courses, with Applications to Mammary Development | p. 351 |
Algorithms for Multiple Genome Rearrangement by Signed Reversals | p. 363 |
DIGIT: A Novel Gene Finding Program by Combining Gene-Finders | p. 375 |
Session Introduction | p. 388 |
Evaluation of the Vector Space Representation in Text-Based Gene Clustering | p. 391 |
Playing Biology's Name Game: Identifying Protein Names in Scientific Text | p. 403 |
Mining Terminological Knowledge in Large Biomedical Corpora | p. 415 |
A Biological Named Entity Recognizer | p. 427 |
Linking Biomedical Language Information and Knowledge Resources: GO and UMLS | p. 439 |
A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical Text | p. 451 |
Session Introduction | p. 463 |
Selection of Minimum Subsets of Single Nucleotide Polymorphisms to Capture Haplotype Block Diversity | p. 466 |
On the Power to Detect SNP/Phenotype Association in Candidate Quantitative Trait Loci Genomic Regions: A Simulation Study | p. 478 |
Errors and Linkage Disequilibrium Interact Multiplicatively when Computing Sample Sizes for Genetic Case-Control Association Studies | p. 490 |
An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block Boundaries | p. 502 |
PyPop: A Software Framework for Population Genomics: Analyzing Large-Scale Multi-Locus Genotype Data | p. 514 |
Joint Bayesian Estimation of Mutation Location and Age Using Linkage Disequilibrium | p. 526 |
SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project | p. 535 |
Methods for Analysis and Visualization of SNP Genotype Data for Complex Diseases | p. 548 |
Session Introduction | p. 562 |
Functional Discrimination of Gene Expression Patterns in Terms of the Gene Ontology | p. 565 |
Towards a Broad-Coverage Biomedical Ontology Based on Description Logics | p. 577 |
Evaluation of Ontology Merging Tools in Bioinformatics | p. 589 |
Semantic Similarity Measures as Tools for Exploring the Gene Ontology | p. 601 |
Linking Molecular Imaging Terminology to the Gene Ontology (GO) | p. 613 |
A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using DAML + OIL | p. 624 |
Development Under Extreme Conditions: Forensic Bioinformatics in the Wake of the World Trade Center Disaster | p. 638 |
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