scientific article; zbMATH DE number 2061770

Authors

Publication date 24 March 2004

bicomputing bioinformatics biomedical ontologies computational biology computational genomics genomic data analysis

Proceedings of conferences of miscellaneous specific interest (00B25) Proceedings, conferences, collections, etc. pertaining to computer science (68-06) Proceedings, conferences, collections, etc. pertaining to biology (92-06) Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40) Physiological, cellular and medical topics (92C99) Genetics and epigenetics (92D10)

Review text

This volume is grouped around five major topics: alternative splicing, computational tools for complex trait gene mapping, biomedical ontologies, joint learning from multiple types of genomic data, and informatics approaches to structural genomics, computational and symbolic systems biology. Seven contributions deal with various forms and techniques for tracing alternative splicing, such as its effects on transmembrane proteins in the mouse genome, the design of a high-throughput assay using polymerase colonies, genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs, the detection of novel splice forms as well as transcriptome and genome conservation of alternative splicing events in humans and mice, and search and data-base approaches to alternative splicing data sets. Six papers on computational tools for complex trait gene mapping are concerned with pedigree generation for analysis of genetic linkage and association, Markov chain approaches to the reconstruction of long haplotypes, the tradeoff between no-call reduction in genotyping error rate and loss of sample size for genetic case/control association studies, different strategies for computing confidence intervals of the linkage disequilibrium measure \(D'\), multiplexing schemes for generic SNP genotyping assays, as well as haplotype block definition and its application. The third chapter on biomedical ontologies contains eight contributions which cover part-of relations in anatomy ontologies (using RDFS and OWL formalizations), mouse phenotype ontologies, evidence knowledge for use in pathway/genome databases, terminological mappings for high through-put comparative biology of phenotypes, the consideration of the compositional structure of Gene Ontology terms, the role of defaults, context and implicit knowledge in biomedical ontologies, as well as the generation of lexical repositories for natural language processing from biological nomenclatures and the potential for ambiguity implied by this approach. The fourth part on joint learning from multiple types of genomic data has nine papers, e.g., on simultaneous searching of protein databases by sequence and structure, the prediction of the operon structure of the bacillus subtilis genome using operon length, intergene distance, and gene expression similarity information, the combination of text mining and sequence analysis to discover protein functional regions, kernel-based data fusion as applied to protein function prediction in yeast, the discovery of binding motif pairs from protein complex structural data and protein interaction sequence data, phylogenetic motif detection by expectation-maximization on evolutionary mixtures, the usage of protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks, motif discovery in heterogeneous sequence data and the role of negative information for motif discovery. Eight papers on informatics approaches in structural genomics focus on protein structure and fold prediction using a tree-augmented naive Bayesian classifier, the clustering of protein sequence and structure space with infinite Gaussian mixture models, accurate classification of protein structural families using coherent subgraph analysis, the identification of good predictions of RNA secondary structure, an exploration of bias in the Protein Data bank using contrast classifiers, geometric analysis of cross-linkability for protein fold discrimination, and protein fold recognition through application of residual dipolar coupling data. The final ten contributions on computational and symbolic systems biology introduce a mixed integer linear programming framework for inferring time delays in gene regulatory networks, strategies for robust identification of large genetic networks and for the reconstruction of chain functions in genetic networks, a molecular epistemics approach to inferring gene regulatory networks from raw data, a biopsi model for lymphocyte-endothelial interactions in inflamed brain venules, the modeling of cellular processes with a variational Bayesian cooperative vector quantizer, symbolic inference of xenobiotic metabolism, the determination of optimal models for small gene networks, pathway logic modeling of protein functional domains in signal transduction, and the modeling of gene expression from microarray expression data with state-space equations.

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