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43 篇 会议

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Pathway bioinformatics 2

Pathway bioinformatics

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2nd international computational systems bioinformatics conference

作者： Karp, P SRI Int Bioinformat Res Grp Menlo Pk CA 94025 USA

ISBN: (纸本)0769520006

Pathway bioinformatics is a subfield of bioinformatics that is concerned with pathway algorithms, ontologies, visualizations, and databases [4]. This talk will provide an overview of the pathway databases and software under development in the bioinformatics research group at SRI international, and will then discuss three pathway algorithms in detail. © 2003 ieee.

关键词： bioinformatics

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Proceedings of the 2003 ieee bioinformatics conference, csb 2003

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB ...

引用

2nd international ieee computer society computational systems bioinformatics conference, csb 2003

ISBN: (纸本)0769520006

The proceedings contain 134 papers. The topics discussed include: stepping up the pace of discovery: the genomes to life program;the role of algorithmic research in computational genomics;high performance computational biology - past progress and future promise;bridging paradigm gaps between biology and engineering;microbial functional genomics: pulling together a variety of approaches and concepts;the sea urchin endomesoderm gene regulatory network, an encoded logic map for early development;epitope prediction algorithms for peptide-based vaccine design;eulerian path methods for multiple sequence alignment;integrating bioinformatics advances into disease management systems to improve quality of care;motifs and modules in cellular signal processing: applications to microbial stress response pathways;and analysis of the genetic potential and gene expression of microbial communities involved in the in situ bioremediation of uranium and harvesting electrical energy from organic matter.

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Efficient constrained multiple sequence alignment with performance guarantee 2

Efficient constrained multiple sequence alignment with perfo...

引用

2nd international ieee computer society computational systems bioinformatics conference, csb 2003

作者： Chin, Francis Y.L. Ho, N.L. Lam, T.W. Wong, Prudence W.H. Chan, M.Y. Department of Computer Science and Information Systems University of Hong Kong Hong Kong Hong Kong

ISBN: (纸本)0769520006

The constrained multiple sequence alignment problem is to align a set of sequences subject to a given constrained sequence, which arises from some knowledge of the structure of the sequences. This paper presents new algorithms for this problem, which are more efficient in terms of time and space (memory) than the previous algorithms and with a worst-case guarantee on the quality of the alignment. Saving the space requirement by a quadratic factor is particularly significant as the previous O(n4)-space algorithm has limited application due to its huge memory requirement. Experiments on real data sets confirm that our new algorithms show improvements in both alignment quality and resource requirements. © 2003 ieee.

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Using easel for modeling and simulating the interactions of cells in order to better understand the basics of biological processes and to predict their likely behaviors 2

Using easel for modeling and simulating the interactions of ...

引用

2nd international computational systems bioinformatics conference

作者： Stojkovic, V Steele, G Lupton, W MSU Baltimore MD USA

ISBN: (纸本)0769520006

Modeling, simulation, visualization, and animation play a significant role in the study of bioinformatics. Research in this area is generally multidisciplinary in nature and collaboratively conducted by researchers with expertise in biology, bioinformatics, computer science, artificial intelligence, mathematics, and statistics. Easel programming language is used for modeling, simulation, visualization, and animation of interactions of cells in order to better understand the basics of biological processes and to predict their likely behaviors. This paper presents a computer science - modeling, simulation, visualization, and animation approach to such research. The paper provides a brief overview of the basic ideas in the "Message Passing" Easel program to demonstrate the transmission of signals between cells based on their physical proximity.

关键词： bioinformatics

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PTC: An interactive tool for phylogenetic tree construction 2

PTC: An interactive tool for phylogenetic tree construction

引用

2nd international computational systems bioinformatics conference

作者： Yang, C Khuri, S San Jose State Univ Dept Comp Sci San Jose CA 95192 USA

ISBN: (纸本)0769520006

A phylogenetic tree represents the evolutionary history of a group of organisms. In this work, we introduce a novel interactive tool for constructing phylogenetic trees, Phylogenetic Tree Construction package. The package supports four well-known algorithms, Unweighted Pair Group Method using Arithmetic average, Neighbor Joining, Fitch Margoliash, and Maximum Parsimony.

关键词： bioinformatics

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Development and assessment of bioinformatics tools for species conservation and habitat management 2

Development and assessment of bioinformatics tools for speci...

引用

2nd international computational systems bioinformatics conference

作者： Sutton, MA Deneke, L Eme, J Bennett, W Wray, F Univ W Florida Dept Biol Pensacola FL 32514 USA

ISBN: (纸本)0769520006

This project represents an interdisciplinary approach to integrating computational methods into the knowledge-discovery process associated with understanding biological systems impacted by the loss or destruction of sensitive habitats. We specifically developed bioinformatics tools for the study of (1) beach mouse communities and (2) marginal fish habitats. Data mining was used in these projects to intelligently query databases and to elucidate broad patterns that facilitate overall data interpretation. Visualization techniques that were developed present mined data in ways where context, perceptual cues, and spatial reasoning skills can be applied to uncover significant trends in behavioral patterns, habitat use, species diversity, and community composition.

关键词： Data visualization

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What makes IgG binding domain of protein L fold up to native state: A simulation study with physical oriented energy functions coupled to topology induced terms 2

What makes IgG binding domain of protein L fold up to native...

引用

2nd international ieee computer society computational systems bioinformatics conference, csb 2003

作者： Lee, Seung Yup Fujitsuka, Y. Takada, S. Kim, Do Hyun Department of Chemical and Biomolecular Engineering Center for Ultramicrochemical Process Systems Korea Advanced Institute of Science and Technology 373-1 Guseong-dong Yuseong-gu Daejeon305-701 Korea Republic of Graduate School of Science and Technology Kobe University Japan Japan Science and Technology Corporation Presto 21 Nada657-8501 Japan

ISBN: (纸本)0769520006

The folding pathways and mechanisms of IgG binding domain of protein L composed of 62 residues are simulated by an over-damped Langevin dynamics with a coarse-grained chain representation. Physical oriented effective energy functions (EEFs) are employed for sequence-specific interactions as well as topology induced energies to bias overall energies to native basin. We observed the preferential formation of N terminal hairpin and the break of structural symmetry during folding. In the free energy profile calculated from equilibrium sampling and histogram method, it clearly shows two state folding scenario with transition state (TS). In the TS regime, N terminal hairpin already forms whereas C terminal hairpin and alpha helix are not structured yet. The predicted results are fully consistent with experimental data. Moreover, we found that hydrophobicity and secondary local propensity among many physical interactions determine the overall folding routes significantly by reduced model studies. © 2003 ieee.

关键词： Proteins

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Two operative concepts for the post-genomic era: the "memoire vive" of the cell and a molecular algebra 2

Two operative concepts for the post-genomic era: the "memoir...

引用

2nd international computational systems bioinformatics conference

作者： Bentolila, S Univ Marne la Vallee IGM F-77454 Marne la Vallee 2 France

ISBN: (纸本)0769520006

The first successes in cloning experiments and stem cell "reprogramming" have already demonstrated the primordial role of cellular working-space memory and regulatory mechanisms, which use the knowledge stored in the DNA database in read mode. We present an analogy between living systems and informatics systems by considering: 1) the cell cytoplasm as a memory device accessible as read/write;2) the mechanisms of regulation as a programming language defined by a grammar, a molecular algebra;3) biological processes as volatile programs which are executed without being written;4) DNA as a database in read only mode. We also present applications to two biological algorithms: the immune response and glycogen metabolism.

关键词： Algebra

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Gene selection for cancer classification using bootstrapped genetic algorithms and support vector machines 2

Gene selection for cancer classification using bootstrapped ...

引用

2nd international computational systems bioinformatics conference

作者： Chen, XW Calif State Univ Northridge Dept Elect & Comp Engn Northridge CA 91330 USA

ISBN: (纸本)0769520006

The gene expression data obtained from microarrays have shown useful in cancer classification. DNA microarray data have extremely high dimensionality compared to the small number of available samples. In this paper, we propose a novel system for selecting a set of genes for cancer classification. This system is based on a linear support vector machine and a genetic algorithm. To overcome the problem of the small size of training samples, bootstrap methods are combined into genetic search. Two databases are considered: the colon cancer database and the leukemia database. Our experimental results show that the proposed method is capable of finding genes that discriminate between normal cells and cancer cells and generalizes well.

关键词： Database systems

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Automated protein NMR resonance assignments 2

Automated protein NMR resonance assignments

引用

2nd international computational systems bioinformatics conference

作者： Wan, X Xu, D Slupsky, CM Lin, GH Univ Alberta Dept Comp Sci Prot Engn Network Ctr Excellence Edmonton AB T6G 2E8 Canada

ISBN: (纸本)0769520006

NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents (1) a new scoring system for mapping spin systems to residues, (2) an automated adjacency information extraction procedure from NMR spectra, and (3) a very fast assignment algorithm based on our previous proposed greedy filtering method and a maximum matching algorithm to automate the assignment process. The computational tests on 70 instances of (pseudo) experimental NMR data of 14 proteins demonstrate that the new score scheme has much better discerning power with the aid of adjacency information between spin systems simulated across various NMR spectra. Typically, with automated extraction of adjacency information, our method achieves nearly complete assignments for most of the proteins. The experiment shows very promising perspective that the fast automated assignment algorithm together with the new score scheme and automated adjacency extraction may be ready for practical use.

关键词： Nuclear magnetic resonance

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