Computational Systems Bioinformatics : Proceedings of the Conference CSB 2006.
Title:
Computational Systems Bioinformatics : Proceedings of the Conference CSB 2006.
Author:
Markstein, Peter.
ISBN:
9781860947575
Personal Author:
Physical Description:
1 online resource (416 pages)
Series:
Series on Advances in Bioinformatics and Computational Biology ; v.4
Series on Advances in Bioinformatics and Computational Biology
Contents:
CONTENTS -- Committees -- Referees -- Preface -- Keynote Addresses -- Exploring the Ocean's Microbes: Sequencing the Seven Seas -- Don't Know Much About Philosophy: The Confusion Over Bio-Ontologies -- Invited Talks -- Biomedical Informatics Research Network (BIRN): Building a National Collaboratory for BioMedical and Brain Research -- Protein Network Comparative Genomics -- Systems Biology in Two Dimensions: Understanding and Engineering Membranes as Dynamical Systems -- Bioinformatics at Microsoft Research -- Movie Crunching in Biological Dynamic Imaging -- Engineering Nucleic Acid-Based Molecular Sensors for Probing and Programming Cellular Systems -- Reactome: A Knowledgebase of Biological Pathways -- Structural Bioinformatics -- Effective Optimization Algorithms for Fragment-Assembly based Protein Structure Prediction -- Transmembrane Helix and Topology Prediction Using Hierarchical SVM Classifiers and an Alternating Geometric Scoring Function -- Protein Fold Recognition Using the Gradient Boost Algorithm -- A Graph-Based Automated NMR Backbone Resonance Sequential Assignment -- A Data-Driven Systematic Search Algorithm for Structure Determination of Denatured or Disordered Proteins -- Multiple Structure Alignment by Optimal RMSD Implies that the Average Structure is a Consensus -- Identification of a-Helices from Low Resolution Protein Density Maps -- Efficient Annotation of Non-Coding RNA Structures Including Pseudoknots via Automated Filters -- Thermodynamic Matchers: Strengthening the Significance of RNA Folding Energies -- Microarray Data Analysis and Applications.
PEM: A General Statistical Approach for Identifying Differentially Expressed Genes in Time-Course CDNA Microarray Experiment without Replicate -- Efficient Generalized Matrix Approximations for Biomarker Discovery and Visualization in Gene Expression Data -- Computational Genomics and Genetics -- Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes) -- Sorting Genomes by Translocations and Deletions -- Turning Repeats to Advantage: Scaffolding Genomic Contigs Using LTR Retrotransposons -- Whole Genome Composition Distance for HIV-1 Genotyping -- Efficient Recursive Linking Algorithm for Computing the Likelihood of an Order of a Large Number of Genetic Markers -- Optimal Imperfect Phylogeny Reconstruction and Haplotyping (IPPH) -- Toward an Algebraic Understanding of Haplotype Inference by Pure Parsimony -- Global Correlation Analysis Between Redundant Probe Sets Using a Large Collection of Arabidopsis ATH1 Expression Profiling Data -- Motif Sequence identification -- Distance-Based Identification of Structure Motifs in Proteins Using Constrained Frequent Subgraph Mining -- An Improved Gibbs Sampling Method for Motif Discovery via Sequence Weighting -- Detection of Cleavage Sites for HIV-1 Protease in Native Proteins -- A Methodology for Motif Discovery Employing Iterated Cluster Re-Assignment -- Biological Pathways and Systems -- Identifying Biological Pathways via Phase Decomposition and Profile Extraction -- Expectation-Maximization Algorithms for Fuzzy Assignment of Genes to Cellular Pathways -- Classification of Drosophila Embryonic Developmental Stage Range Based on Gene Expression Pattern Images.
Evolution versus "Intelligent Design": Comparing the Topology of Protein-Protein Interaction Networks to the Internet -- Protein Functions and Computational Proteomics -- Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction -- Protein Subcellular Localization Prediction Based on Compartment-Specific Biological Features -- Predicting the Binding Affinity of MHC Class II Peptides -- Codon-Based Detection of Positive Selection Can be Biased by Heterogeneous Distribution of Polar Amino Acids Along Protein Sequences -- Bayesian Data Integration: A Functional Perspective -- An Iterative Algorithm to Quantify the Factors Influencing Peptide Fragmentation for MS/MS Spectrum -- Complexity and Scoring Function of MS/MS Peptide De Novo Sequencing -- Biomedical Applications -- Expectation-Maximization Method for Reconstructing Tumor Phylogenies from Single-Cell Data -- Simulating In Vitro Epithelial Morphogenesis in Multiple Environments -- A Combined Data Mining Approach for Infrequent Events: Analyzing HIV Mutation Changes Based on Treatment History -- A Systems Biology Case Study of Ovarian Cancer Drug Resistance -- Author index.
Abstract:
This volume contains about 40 papers covering many of the latest developments in the fast-growing field of bioinformatics. The contributions span a wide range of topics, including computational genomics and genetics, protein function and computational proteomics, the transcriptome, structural bioinformatics, microarray data analysis, motif identification, biological pathways and systems, and biomedical applications. There are also abstracts from the keynote addresses and invited talks. The papers cover not only theoretical aspects of bioinformatics but also delve into the application of new methods, with input from computation, engineering and biology disciplines. This multidisciplinary approach to bioinformatics gives these proceedings a unique viewpoint of the field. Sample Chapter(s). Chapter 1: Exploring the Ocean's Microbes: Sequencing the Seven Seas (122 KB). Contents: Exploring the Ocean's Microbes: Sequencing the Seven Seas (M E Frazier et al.); Protein Network Comparative Genomics (T Ideker); Bioinformatics at Microsoft Research (S Mercer); Protein Fold Recognition Using Gradient Boost Algorithm (F Jiao et al.); Efficient Annotation of Non-Coding RNA Structures Including Pseudoknots via Automated Filters (C Liu et al.); Efficient Generalized Matrix Approximations for Biomarker Discovery and Visualization in Gene Expression Data (W Li et al.); Sorting Genomes by Translocations and Deletions (X Qi et al.); Detection of Cleavage Sites for HIV-1 Protease in Native Proteins (L You); Identifying Biological Pathways via Phase Decomposition and Profile Extraction (Y Zhang & Z Deng); Complexity and Scoring Function of MS/MS Peptide De Novo Sequencing (C Xu & B Ma); Simulating In Vitro Epithelial Morphogenesis in Multiple Environments (M R Grant et al.); and other papers. Readership: Research and application community in bioinformatics, systems
biology, medicine, pharmacology and biotechnology. A useful reference for graduate researchers in bioinformatics and computational biology.
Local Note:
Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2017. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.
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