Pacific Symposium on Biocomputing 2003 Kauai, Hawaii, 3-7 January 2003 (World Scientific, 2002)
Includes bibliographical references
Gene regulation. Session introduction / S. Batzoglou and L. Pachter -- Multiclass cancer classification using gene expression profiling and probabilistic neural networks / D.P. Berrar, C.S. Downes, and W. Dubitzky -- Inferring gene regulatory networks from time-ordered gene expression data of bacillus subtilis using differential equations / M.J.L. de Hoon ... [et al.] -- Genome-wide analysis of bacterial promoter regions / E. Eskin ... [et al.] -- MOPAC: motif finding by preprocessing and agglomerative clustering from microarrays / R. Ganesh, D.A. Siegele, and T.R. Ioerger -- Improved gene selection for classification of microarrays / J. Jaeger, R. Sengupta, and W.L. Ruzzo -- Kernel Cox regression models for linking gene expression profiles to censored survival data / H. Li and Y. Luan -- Extracting conserved gene expression motifs from gene expression data / T.M. Murali and S. Kasif -- Decomposing gene expression into cellular processes / E. Segal, A. Battle, and D. Roller --
- Genome, pathway, and interaction bioinformatics. Session Introduction / P. Karp ... [et al.] -- Suitability and utility of computational analysis tools: characterization of erythrocyte parameter variation / R.E. Altenbaugh, K.J. Kauffman, and J.S. Edwards -- Foundations of a query and simulation system for the modeling of biochemical and biological processes / M. Antoniotti ... [et al.] -- Incorporating biological knowledge into evaluation of causal regulatory hypotheses / L. Chrisman ... [et al.] -- Assessment of the reliability of protein-protein interactions and protein function prediction / M. Deng, F. Sun, and T. Chen -- Boundary formation by notch signaling in drosophila multicellular systems: experimental observations and gene network modeling by genomic object net / H. Matsuno ... [et al.] -- Influence of network topology and data collection on network inference / V.A. Smith, E.D. Jarvis, and A.J. Hartemink --
- Informatics approaches in structural genomics. Session introduction / S.D. Mooney and P.C. Babbit -- Simultaneous sequence alignment and tree construction using hidden Markov models / R.C. Edgar and K. Sjölander -- Towards discovering structural signatures of protein folds based on logical hidden Markov models / K. Kersting ... [et al.] -- Automated construction of structural motifs for predicting functional sites on protein structures / M.P. Liang, D.L. Brutlag, and R.B. Altman -- Prediction of boundaries between intrinsically ordered and disordered protein regions / P. Radivojac ... [et al.] -- Identifying structural motifs in proteins / R. Singh and M. Saha -- A path planning-based study of protein folding with a case study of hairpin formation in protein G and L / G. Song ... [et al.] -- Profile-profile alignment: a powerful tool for protein structure prediction / N. von Öhsen, I. Sommer, and R. Zimmer -- Protein threading by linear programming / J. Xu ... [et al.]
Genome-wide analysis and comparative genomics. Session introduction / L. Wei, I. Dubchak, and V. Solovyev -- Towards identifying lateral gene transfer events / L. Addario-Berry, M. Hallett, and J. Lagergren -- Whole genome human/mouse phylogenetic footprinting of potential transcription regulatory signals / E. Cheremushkin and A. Kel -- MAP: searching large genome databases / T. Kahveci and A. Singh -- Towards the development of computational tools for evaluating phylogenetic network reconstruction methods / L. Nakhleh ... [et al.] -- Identification of regulatory binding sites using minimum spanning trees / V. Olman, D. Xu, and Y. Xu -- Intrasplicing -- analysis of long intron sequences / S. Ott ... [et al.] -- Trajectory clustering: a non-parametric method for grouping gene expression time courses, with applications to mammary development / T.L. Phang ... [et al.] -- Algorithms for multiple genome rearrangement by signed reversals / S. Wu and X. Gu --