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Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05)

Date 19-21 Oct. 2005

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Displaying Results 1 - 25 of 56
  • Fifth IEEE Symposium on Bioinformatics and Bioengineering - Cover

    Publication Year: 2005, Page(s): c1
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  • Fifth IEEE Symposium on Bioinformatics and Bioengineering - Title Page

    Publication Year: 2005, Page(s):i - iii
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  • Fifth IEEE Symposium on Bioinformatics and Bioengineering - Copyright Page

    Publication Year: 2005, Page(s): iv
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  • Fifth IEEE Symposium on Bioinformatics and Bioengineering - Table of contents

    Publication Year: 2005, Page(s):v - viii
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  • Chairs Forward

    Publication Year: 2005, Page(s): ix
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  • Committees

    Publication Year: 2005, Page(s):x - xi
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  • A model-free and stable gene selection in microarray data analysis

    Publication Year: 2005, Page(s):3 - 10
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (240 KB) | HTML iconHTML

    Microarray data analysis is notorious for involving a huge number of genes compared to a relatively small number of samples. Detecting the most significantly differentially expressed genes under different conditions, or gene selection, has been a central focus for researchers. The gene selection problem becomes more difficult when the numbers of samples under different conditions vary significantl... View full abstract»

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  • An efficient algorithm for the extended (l,d)-motif problem with unknown number of binding sites

    Publication Year: 2005, Page(s):11 - 18
    Cited by:  Papers (5)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (176 KB) | HTML iconHTML

    Finding common patterns, or motifs, from a set of DNA sequences is an important problem in molecular biology. Most motif-discovering algorithms/software require the length of the motif as input. Motivated by the fact that the motifs length is usually unknown in practice, Styczynski et al. introduced the extended (l,d)-motif problem (EMP), where the motifs length is not an input parameter. Unfortun... View full abstract»

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  • Improved phylogenetic motif detection using parsimony

    Publication Year: 2005, Page(s):19 - 26
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (424 KB) | HTML iconHTML

    We have recently demonstrated (La et al, Proteins, 58:2005) that sequence fragments approximating the overall familial phylogeny, called phylogenetic motifs (PMs), represent a promising protein functional site prediction strategy. Previous results across a structurally and functionally diverse dataset indicate that phylogenetic motifs correspond to a wide variety of known functional characteristic... View full abstract»

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  • Highly scalable and accurate seeds for subsequence alignment

    Publication Year: 2005, Page(s):27 - 31
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (192 KB) | HTML iconHTML

    We propose a method for finding seeds for the local alignment of two nucleotide sequences. Our method uses randomized algorithms to find approximate seeds. We present a dynamic index to store the fingerprints of k-grams and a highly scalable and accurate (HSA) algorithm to incorporate randomization into process of seed generation. Experimental results show that our method produces better quality s... View full abstract»

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  • A novel quartet-based method for phylogenetic inference

    Publication Year: 2005, Page(s):32 - 39
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (272 KB) | HTML iconHTML

    In this paper we introduce a new quartet-based method. This method makes use of the Bayes (or quartet) weights of quartets as those used in the quartet puzzling. However, all the weights from the related quartets are accumulated to form a global quartet weight matrix. This matrix provides integrated information and can lead us to recursively merge small sub-trees to larger ones until the final sin... View full abstract»

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  • GOMIT: a generic and adaptive annotation algorithm based on gene ontology term distributions

    Publication Year: 2005, Page(s):40 - 48
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (248 KB) | HTML iconHTML

    We address the issue of providing highly informative annotations using information revealed by the structured vocabularies of gene ontology (GO). For a target, a set of candidate terms used to infer the target's property is collected and forms a unique distribution on the GO directed acyclic graph (DAG). We propose a generic and adaptive algorithm - GOMIT, which bases on term distributions and GO ... View full abstract»

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  • Classification of biomedical data through model-based spatial averaging

    Publication Year: 2005, Page(s):49 - 56
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (280 KB) | HTML iconHTML

    Ensemble learning is frequently used to reduce classification error. The more popular techniques draw multiple samples from the training data and employ a voting procedure to aggregate the decisions of the classifiers constructed from those samples. In practice, such ensemble methods have been shown to work well and improve accuracy. Here we present a meta-learning strategy that combines the decis... View full abstract»

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  • A multi-level approach to SCOP fold recognition

    Publication Year: 2005, Page(s):57 - 64
    Cited by:  Papers (10)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (352 KB) | HTML iconHTML

    The classification of proteins based on their structure can play an important role in the deduction or discovery of protein function. However, the relatively low number of solved protein structures and the unknown relationship between structure and sequence requires an alternative method of representation for classification to be effective. Furthermore, the large number of potential folds causes p... View full abstract»

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  • A wrapper induction application with knowledge base support: a use case for initiation and maintenance of wrappers

    Publication Year: 2005, Page(s):65 - 72
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (248 KB) | HTML iconHTML

    Integrating life science Web databases, while important and necessary, is a challenge for current integration systems mainly due to the large number of these databases, their heterogeneity and the fact that their interfaces may change often. BACIIS, a biological and chemical information integration system, is a tightly coupled federated database system that uses the mediator wrapper method in orde... View full abstract»

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  • Predicting human papilloma virus prevalence and vaccine policy effectiveness in demographic strata

    Publication Year: 2005, Page(s):73 - 80
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (328 KB) | HTML iconHTML

    Human Papilloma Virus (HPV) is a sexually transmitted virus, which can lead to cervical cancer. HPV DNA is found in cervical cancers with types 16, 18, 31 and 45 accounting for more than 75% of cervical cancers. Candidate vaccines have entered phase III testing with the Food and Drug Administration and several drug companies are in licensing arbitration. Once this vaccine becomes available, an eff... View full abstract»

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  • Approximate global alignment of sequences

    Publication Year: 2005, Page(s):81 - 88
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (168 KB) | HTML iconHTML

    We propose two novel dynamic programming (DP) methods that solve the approximate bounded and unbounded global alignment problems for biological sequences. Our first method solves the bounded alignment problem. It computes the distribution of the edit distance between the remaining suffixes. For a given bound k and approximation p%, it uses this distribution to prune the entries of the DP matrix th... View full abstract»

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  • Multi-class biclustering and classification based on modeling of gene regulatory networks

    Publication Year: 2005, Page(s):89 - 96
    Cited by:  Papers (3)  |  Patents (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (448 KB) | HTML iconHTML

    The attempt to elucidate biological pathways and classify genes has led to the development of numerous clustering approaches to gene expression. All these approaches use a single metric to identify genes with similar expression levels. Until now, the correlation between the expression levels of such genes has been based on phenomenological and heuristic correlation functions, rather than on biolog... View full abstract»

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  • DSIM: A distance-based indexing method for genomic sequences

    Publication Year: 2005, Page(s):97 - 104
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (232 KB) | HTML iconHTML

    In this paper, we propose a Distance-based Sequence Indexing Method (DSIM) for indexing and searching genome databases. Borrowing the idea of video compression, we compress the genomic sequence database around a set of automatically selected reference words, formed from high-frequency data substrings and substrings in past queries. The compression captures the distance of each non-reference word i... View full abstract»

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  • Discovery of repetitive patterns in DNA with accurate boundaries

    Publication Year: 2005, Page(s):105 - 112
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (224 KB) | HTML iconHTML

    The accurate identification of repeats remains a challenging open problem in bioinformatics. Most existing methods of repeat identification either depend on annotated repeat databases or restrict repeats to pairs of similar sequences that are maximal in length. The fundamental flaw in most of the available methods is the lack of a definition that correctly balances the importance of the length and... View full abstract»

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  • Prediction of outer membrane proteins by support vector machines using combinations of gapped amino acid pair compositions

    Publication Year: 2005, Page(s):113 - 120
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (152 KB) | HTML iconHTML

    Discriminating outer membrane proteins from proteins with other subcellular localizations and with other folding classes are both important to predict farther their functions and structures. In this paper, we propose a method for discriminating outer membrane proteins from other proteins by support vector machines using combinations of gapped amino acid pair compositions. Using 5-fold cross-valida... View full abstract»

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  • Discovery of gene expression patterns across multiple cancer types

    Publication Year: 2005, Page(s):121 - 128
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (200 KB) | HTML iconHTML

    In this paper, we investigate the underlying common gene expression signatures in related cancer types. Shared expression signatures are investigated in breast and ovarian cancers specifically through the definition of four progressively more difficult classification problems. SHEBA, a stochastic Bayesian inference approach, is introduced to identify highly predictive gene sets in the defined clas... View full abstract»

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  • Effective pre-processing strategies for functional clustering of a protein-protein interactions network

    Publication Year: 2005, Page(s):129 - 136
    Cited by:  Papers (4)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (264 KB) | HTML iconHTML

    In this article we present novel preprocessing techniques, based on typological measures of the network, to identify clusters of proteins from protein-protein interaction (PPI) networks wherein each cluster corresponds to a group of functionally similar proteins. The two main problems with analyzing protein-protein interaction networks are their scale-free property and the large number of false po... View full abstract»

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  • Improving genome rearrangement phylogeny using sequence-style parsimony

    Publication Year: 2005, Page(s):137 - 144
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1064 KB)

    The study of genome rearrangements, the evolutionary events that change the order and strandedness of genes within genomes, presents new opportunities for discoveries about deep evolutionary events. The best software so far, GRAPPA, solves breakpoint and inversion phylogenies by scoring each tree topology through iterative improvements of internal node gene orders. We find that the greedy hill-cli... View full abstract»

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  • Haplotype phasing using semidefinite programming

    Publication Year: 2005, Page(s):145 - 152
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (152 KB) | HTML iconHTML

    Diploid organisms, such as humans, inherit one copy of each chromosome (haplotype) from each parent. The conflation of inherited haplotypes is called the genotype of the organism. In many disease association studies, the haplotype data is more informative than the genotype data. Unfortunately, getting haplotype data experimentally is both expensive and difficult. The haplotype inference with pure ... View full abstract»

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