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检索条件"任意字段=2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005"

共 100 条记录，以下是21-30 订阅

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An information fusion approach to controlling complexity in bioinformatics research

An information fusion approach to controlling complexity in ...

引用

2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Olsson, Björn Nilsson, Patrie Gawronska, Barbara Persson, Anne Ziemke, Tom Andler, Sten F. School of Humanities and Informatics University of Skövde SE-54128 Skövde Sweden School of Life Sciences University of Skövde SE-54128 Skövde Sweden School of Technology and Society University of Skövde SE-54128 Skövde Sweden

ISBN: (纸本)0769524427

Information Fusion (IF) is about combining, or fusing, information from different sources in order to facilitate our understanding of a complex system and thereby provide insights that could not be gained from any of the individual data sources in isolation. We argue in this paper that there is a need for applying an IF approach in bioinformatics research, since the aim of bioinformatics is to understand complex biological systems using many different data sources providing complementary views of the system. We illustrate this argument with two application examples, where IF-based bioinformatics is applied to the study of stem cell differentiation and lipid digestion, respectively. We also discuss the use of automated information extraction from text sources, which is an essential component of a bioinformatics IF approach, given the abundant literature. © 2005 ieee.

关键词： Sensor data fusion

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Ontologies for Biologists - A Community Model for the Annotation of Genomic Data

Ontologies for Biologists - A Community Model for the Annota...

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Proceedings of the ieee computational systems bioinformatics conference, csb

作者： M. Ashburner Department of Genetics University of Cambridge Cambridge UK

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The National Alliance for Medical Imaging Computing (NA-MIC)

The National Alliance for Medical Imaging Computing (NA-MIC)

引用

Proceedings of the ieee computational systems bioinformatics conference, csb

作者： R. Kikinis Brigham and Womens Hospital Harvard Medical School USA

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Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions

Improved pairwise alignment of proteins in the Twilight Zone...

引用

2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Huang, Yao-Ming Bystroff, Christopher Center for Bioinformatics Dept. of Biology Rensselaer Polytechnic Institute Troy NY 12180 United States

ISBN: (纸本)0769524427

Recent advances in the ability to discriminate between homologous and non-homologous proteins in the "Twilight Zone" of sequence similarity, must be accompanied by accurate alignments if they are to be of value to molecular modelers. Pairwise alignments require a measure of evolutionary distance, traditionally modeled using global amino acid substitution matrices. But real differences in the likelihood of substitutions may exist for different structural contexts within proteins, since structure contributes to the selective pressure. HMMSUM (HMMSTR-based Substitution Matrices) is a new model for structure-dependent amino acid substitution probabilities consisting of a set of 281 matrices, one for each of the sequence-structure contexts defined in HMMSTR (a Hidden Markov Model for protein STRucture). HMMSUM does not require the structure of the protein to be known, using HMMSTR predictions instead, Alignments using the HMMSUM compare favorably BLOSUM50 alignments when validated against curated remote homolog alignments from BAUBASE. © 2005 ieee.

关键词： Proteins

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Oscillatory dynamics in the mitogen-activated protein kinase cascade

Oscillatory dynamics in the mitogen-activated protein kinase...

引用

2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Chiam, K.-H. Bhargava, Vipul Rajagopal, Gunaretnam Bioinformatics Institute 30 Biopolis Street #07-01 Singapore 138671 Singapore

ISBN: (纸本)0769524427

We have used quantitative modeling of signaling networks to show that the mitogen-activated protein kinase cascade - a highly-conserved signaling network in eukaryotes - can functions as a low-pass filter by amplifying low-frequency oscillations and attenuating high-frequency oscillations. This filtering function of the kinase cascade is in addition to other known functions such as being an ultrasensitive switch. We show how this low-pass filtering regulates downstream cellular functions and cellular physiology. We also show how the presence of scaffold proteins in the kinase cascade modifies the properties of the low-pass filter. In particular, we find that the presence of scaffold proteins destroys the properties of the low-pass filtering, and instead attenuate all oscillations. In particular, the higher the scaffold concentration, the greater the attenuation. © 2005 ieee.

关键词： Proteins

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Creating a protein ontology resource

Creating a protein ontology resource

引用

2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Sidhu, Amandeep S. Dillon, Tharam S. Chang, Elizabeth IEEE Faculty of Information Technology University of Technology Sydney Australia School of Information Systems Curtin University of Technology Perth Australia

ISBN: (纸本)0769524427

Protein Data Integration approaches at the moment considers data sources as data repositories, but not as applications;which in turn may embody complex interactions with other data sources. Current approaches do not provide methods both for generic mapping protein data representation, depicting interactions in data it describes and for interfacing existing data. The proposed Protein Ontology shows the value of hierarchy and relationships present in proteomics data. The creation of a Protein Ontology provides understanding of diverse types of data like: (1) Protein Entry Details, (2) 3D Structural Representations of Proteins, (3) Structural Folds and domains conserved in proteins, (4) Functional Domains and Families created based on Physiological and Pathological Functions of Proteins, and (5) Various Constraints like Genetic Defects and Chemical Properties of Cell that affect Final Stable Molecular Structure of Protein. Protein Ontology describes the concepts of interest in protein complex mechanisms and proteomics process. © 2005 ieee.

关键词： Proteins

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TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree

TreeRefiner: a tool for refining a multiple alignment on a p...

引用

Proceedings of the ieee computational systems bioinformatics conference, csb

作者： A. Manohar S. Batzoglou Department of Computer Science University of Stanford Stanford CA USA

We present TreeRefiner, a tool for refining multiple alignments of biological sequences. Given a multiple alignment, a phylogenetic tree, and scoring parameters as input, TreeRefiner optimizes the sum-of-pairs function in a restricted three-dimensional space around the alignment. At each internal node of the unrooted tree, the multiple alignment is projected to the sub-alignments corresponding to the three neighboring nodes, and three-dimensional dynamic programming is performed within a user-specified radius r around the original alignment. We test TreeRefiner on simulated sequences aligned by several popular tools, and demonstrate substantial improvements in the percentage of correctly aligned positions.

关键词： Phylogeny bioinformatics Genomics Proteins Iterative methods Testing Computer science Biology Dynamic programming Biological system modeling

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Enhanced MVDR beamforming implementation with arbitrary linear arrays on DS/CDMA

Enhanced MVDR beamforming implementation with arbitrary line...

引用

2005 ieee/ACES International conference on Wireless Communications and Applied computational Electromagnetics

作者： Kim, KyungSeok Choi, Yong-Seok Kim, Chang-Joo Choi, Ik-Guen Division of Bionics and Bioinformatics Chonbuk National University Korea Republic of

ISBN: (纸本)0780390687

The efficient scheme for enhancing the performance of the MVDR beamforming for DS/CDMA systems is proposed. The main focus of the proposed scheme is to enhance the practical estimation of an array response vector for the MVDR beamforming on the arbitrary geometry structure of antenna arrays. Thus, the proposed scheme used the real Toeplitz-plus-Hankel Approximation (RTHA) scheme to obtain the covariance matrix having the theoretical property of an overall noise-free signal. Computer simulation results are presented to show the effectiveness of the proposed scheme. © 2005 ieee.

关键词： Antenna arrays

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An efficient algorithm for perfect phylogeny haplotyping

An efficient algorithm for perfect phylogeny haplotyping

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Proceedings of the ieee computational systems bioinformatics conference, csb

作者： R. VijayaSatya A. Mukherjee School of Computer Science University of Central Florida USA

The Perfect Phylogeny Haplotyping (PPH) problem is one of the many computational approaches to the Haplotype Inference (HI) problem. Though there are many O(nm/sup 2/) solutions to the PPH problem, the complexity of the PPH problem itself has remained an open question. In this paper, we introduce the FlexTree data structure that represents all the solutions for a PPH instance. We also introduce row ordering that arranges the genotypes in a more manageable fashion. The column ordering, the FlexTree data structure and the row ordering together make the O(nm) OPPH algorithm possible. We also present some results on simulated data, which demonstrate that the OPPH algorithm performs quiet impressively when compared to the earlier O(nm/sup 2/) algorithms.

关键词： Phylogeny Humans Genomics bioinformatics Biological cells Inference algorithms Data structures History Computer science Diseases

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Multi-scale hierarchical structure prediction of helical transmembrane proteins

Multi-scale hierarchical structure prediction of helical tra...

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Proceedings of the ieee computational systems bioinformatics conference, csb

作者： Z. Chen Y. Xu Department of Biochemistry and Molecular Biology University of Georgia Athens GA USA

ISBN: (纸本)0769523447

As the first step toward a multi-scale, hierarchical computational approach for membrane protein structure prediction, the packing of transmembrane helices was modeled at the residual and atomistic levels, respectively. For predictions at the residual level, the helix-helix and helix-lipid interactions were described by a set of knowledge-based energy functions. For predictions at the atomistic level, CHARMM19 force field was employed. To facilitate the system to overcome energy barriers, Wang-Landau sampling was carried out by performing a random walk in the energy and conformational spaces. Native-like structures were predicted at both levels for 2- and 7-helix systems. Interestingly, consistent results were obtained from simulations at residual and atomistic levels for the same system, strongly suggesting the feasibility of a hierarchical approach for membrane structure prediction.

关键词： Proteins Biomembranes Sampling methods Energy states Biochemistry Predictive models bioinformatics Space exploration Biology computing Biological system modeling

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