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2009 IEEE International Conference on Bioinformatics and Biomedicine

1-4 Nov. 2009

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Displaying Results 1 - 25 of 90
  • [Front cover]

    Publication Year: 2009, Page(s): C1
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  • [Title page i]

    Publication Year: 2009, Page(s): i
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  • [Title page iii]

    Publication Year: 2009, Page(s): iii
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  • [Copyright notice]

    Publication Year: 2009, Page(s): iv
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  • Table of contents

    Publication Year: 2009, Page(s):v - xi
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  • Preface

    Publication Year: 2009, Page(s):xii - xiii
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  • Conference Committees

    Publication Year: 2009, Page(s):xiv - xv
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  • Program Committee

    Publication Year: 2009, Page(s):xvi - xix
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  • Additional referees

    Publication Year: 2009, Page(s): xx
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  • Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines

    Publication Year: 2009, Page(s):3 - 8
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (327 KB) | HTML iconHTML

    Predicting protein folding rate is useful for understanding protein folding process and guiding protein design. Most previous methods of predicting folding rate require the tertiary structure of a protein as an input. And most methods do not distinguish the different kinetic natures (two-state folding and multi-state folding) of the proteins. Here we developed a method, SeqRate, to predict both pr... View full abstract»

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  • Bioinformatics Pipeline for Identification of Binding Motifs of Flexible Protein Tethers

    Publication Year: 2009, Page(s):9 - 14
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1273 KB) | HTML iconHTML

    Proteins use conserved binding motifs associated with relatively unconserved flexible amino acid sequences as mobile tethers for interacting molecules, as exemplified by C-terminal tether sequences of bacterial chemotaxis receptors. We describe here a bioinformatics pipeline to discover new instances of flexible tethers and their binding motifs. C-terminal regions of all proteins in subsets of bac... View full abstract»

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  • Extremal Optimization for the Protein Structure Alignment

    Publication Year: 2009, Page(s):15 - 19
    Cited by:  Papers (6)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (353 KB) | HTML iconHTML

    This paper proposes a combinational optimization algorithm extremal optimization (EO) for protein structure alignment based on the contact map overlap (CMO) model. EO is a meta-heuristic algorithm, as genetic algorithm and simulated annealing, but with a local fitness introduced to guide the improvement of the optimization. By exploiting similarity matrix between two contact maps, the results demo... View full abstract»

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  • Biological Feature Incorporated Alignment for Cross Species Analysis on Carbohydrate Binding Modules

    Publication Year: 2009, Page(s):20 - 25
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2164 KB) | HTML iconHTML

    Multiple sequence alignment is widely applied to discover core conserved regions among query sequences. However, the major deficiency is that alignment accuracy is extremely sensitive to primary sequence identity, which causes alignment of low identity sequences difficult. We propose a feature-integrated model called feature-incorporated alignment (FIA) which integrates relevant biological charact... View full abstract»

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  • Accurate Prediction of Stability Changes in Bacteriophage T4 Lysozyme upon Single Amino Acid Replacements

    Publication Year: 2009, Page(s):26 - 30
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1126 KB) | HTML iconHTML

    A computational mutagenesis methodology utilizing a four-body, knowledge-based, statistical contact potential is applied toward quantifying sequence-structure compatibility changes in bacteriophage T4 lysozyme upon single amino acid replacements. We show that these scalar scores correlate with experimentally measured stability changes to the protein due to the mutations. For each mutant, the appro... View full abstract»

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  • High Throughput Short Read Alignment via Bi-directional BWT

    Publication Year: 2009, Page(s):31 - 36
    Cited by:  Papers (11)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (169 KB) | HTML iconHTML

    The advancement of sequencing technologies has made it feasible for researchers to consider many high-throughput biological applications. A core step of these applications is to align an enormous amount of short reads to a reference genome. For example, to resequence a human genome, billions of reads of 35 bp are produced in 1-2 weeks, putting a lot of pressure of faster software for alignment. Ba... View full abstract»

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  • Neural Grammar Networks in QSAR Chemistry

    Publication Year: 2009, Page(s):37 - 42
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (276 KB) | HTML iconHTML

    In this paper, we describe the neural grammar network (NGN) and its application to quantitative structure-activity relationship (QSAR) in computational chemistry. The NGN is a novel machine learning device that applies the generic function approximation capability of a dynamic recursive neural network to the syntactic structure of a parsed string. In our QSAR task, we represent each molecule by a ... View full abstract»

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  • Predicting Yeast Synthetic Lethal Genetic Interactions Using Protein Domains

    Publication Year: 2009, Page(s):43 - 47
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (250 KB) | HTML iconHTML

    Synthetic lethal genetic interactions are of interest as they can be used to predict function of unknown proteins and find drug target or drug combinations. In this study, we applied support vector machine (SVM) classifier to predict synthetic lethal genetic interactions in Saccharomyces cerevisiae based on domain information in proteins. We found that our method can predict synthetic lethal genet... View full abstract»

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  • Detection of Gene Orthology Based on Protein-Protein Interaction Networks

    Publication Year: 2009, Page(s):48 - 53
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (388 KB) | HTML iconHTML

    Ortholog detection methods present a powerful approach for finding genes that participate in similar biological processes across different organisms, extending our understanding of interactions between genes across different pathways, and understanding the evolution of gene families. We exploit features derived from the alignment of protein-protein interaction networks to reconstruct KEGG ortholog... View full abstract»

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  • Assessment of Gene Annotation Accuracy by Inferring Transcripts from RNA-Seq

    Publication Year: 2009, Page(s):54 - 59
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (466 KB) | HTML iconHTML

    Next generation sequencing is quickly changing long standing paradigms of genomics in terms of what is feasible to accomplish within a ldquoresearch life timerdquo and what is supposed to remain beyond limits of reliable experimental analysis. Sequencing and mapping of a prokaryote transcriptome can provide experimental validation for computationally predicted genes annotated in a prokaryotic geno... View full abstract»

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  • An Algorithm for the Discovery of Phenotype Related Metabolic Pathways

    Publication Year: 2009, Page(s):60 - 65
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (208 KB) | HTML iconHTML

    Microorganisms are being increasingly used in industrial processes due to certain beneficial phenotypes they exhibit. Improving the ability of microorganisms to exhibit these phenotypes has driven interest in identifying the genes that are responsible for a given phenotype. Some of these phenotypes are the result of various chemical compounds being modified by a series of metabolic reactions, or m... View full abstract»

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  • Protein Long Disordered Region Prediction Based on Profile-Level Disorder Propensities and Position-Specific Scoring Matrixes

    Publication Year: 2009, Page(s):66 - 69
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (259 KB) | HTML iconHTML

    Identification of long disordered regions in protein sequence is important for understanding protein function. In this work, a class of novel propensities at profile level is presented, namely, the order profile disorder propensities, which use the evolutionary information of profile for protein long disorder prediction. These propensities, combined with position-specific scoring matrices, are inp... View full abstract»

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  • ChemAlign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties

    Publication Year: 2009, Page(s):70 - 73
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (847 KB) | HTML iconHTML

    We present a new algorithm, ChemAlign, that uses physicochemical properties and secondary structure elements to create biologically relevant multiple sequence alignments (MSAs). Additionally, we introduce the physicochemical property difference (PPD) score for the evaluation of MSAs. This score is the normalized difference of physicochemical property values between a calculated and a reference ali... View full abstract»

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  • 3D Rotation Invariant Features for the Characterization of Molecular Density Maps

    Publication Year: 2009, Page(s):74 - 78
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1835 KB) | HTML iconHTML

    Cryo electron microscopy produces 3D density maps of large macromolecular structures. An important task lies in the efficient identification of structural similarities between different molecular density maps. Here we construct and test three different types of 3D rotation invariant features for template free similarity detection in molecular density maps. The density map comparison is based on fe... View full abstract»

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  • Fast Motif Selection for Biological Sequences

    Publication Year: 2009, Page(s):79 - 82
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (231 KB) | HTML iconHTML

    We consider the problem of identifying motifs, recurring or conserved patterns, in the sets of biological sequences. To solve this task, we present new deterministic and exact algorithms for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. The proposed algorithms (1) improve search efficiency compared to existing exact algorithms by focusing sea... View full abstract»

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  • Inexact Local Alignment Search over Suffix Arrays

    Publication Year: 2009, Page(s):83 - 87
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (290 KB) | HTML iconHTML

    We describe an algorithm for finding approximate seeds for DNA homology searches. In contrast to previous algorithms that use exact or spaced seeds, our approximate seeds may contain insertions and deletions. We present a generalized heuristic for finding such seeds efficiently and prove that the heuristic does not affect sensitivity. We show how to adapt this algorithm to work over the memory eff... View full abstract»

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