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

共 881 条记录，以下是551-560 订阅

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Bioinformatic insights from metagenomics through visualization

Bioinformatic insights from metagenomics through visualizati...

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ieee computational systems bioinformatics conference

作者： Havre, SL Webb-Robertson, BJ Shah, A Posse, C Gopalan, B Brockman, FJ Pacific NW Natl Lab Richland WA 99352 USA

ISBN: (纸本)0769523447

Cutting-edge biological and bioinformatics research seeks a systems perspective through the analysis of multiple types of high-throughput and other experimental data for the same sample. systems-level analysis requires the integration and fusion of such data, typically through advanced statistics and mathematics. Visualization is a complementary computational approach that supports integration and analysis of complex data or its derivatives. We present a bioinformatics visualization prototype, Juxter, which depicts categorical information derived from or assigned to these diverse data for the purpose of comparing patterns across categorizations. The visualization allows users to easily, discern correlated and anomalous patterns in the data. These patterns, which might not be detected automatically by, algorithms, may, reveal valuable information leading to insight and discovery. We describe the visualization and interaction capabilities and demonstrate its utility in a new field, metagenomics, which combines molecular biology and genetics to identify and characterize genetic material from multi-species microbial samples.

关键词： bioinformatics visualization metagenomics categorical nominal

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Key features of the UCSC genome site

Key features of the UCSC genome site

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2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Trumbower, Heather Jackson, Jennifer UCSC Genome Bioinformatics Group

ISBN: (纸本)0769524427

关键词： Genetic engineering

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Predicting a transcription start site: Case study with different genomes

Predicting a transcription start site: Case study with diffe...

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2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Loganantharaj, Raja Bioinformatics Research Lab. Center for Advanced Computer Studies University of Louisiana Lafayette

ISBN: (纸本)0769524427

Prediction of a transcription start site (TSS) is one of the many active research areas in bioinformatics. The main purpose of this paper is to study the ability of linear classifiers for predicting a TSS. Also we have focused on the relationship between the length of the subsequences surrounding TSS and their effectiveness. © 2005 ieee.

关键词： Genetic engineering

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On discriminating a TATA-box from putative TATA boxes: A case study using plant genome

On discriminating a TATA-box from putative TATA boxes: A cas...

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2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Loganantharaj, Raja Bioinformatics Research Lab. Center for Advanced Computer Studies University of Louisiana Lafayette

ISBN: (纸本)0769524427

Prediction of a promoter is one of the many active areas of bioinformatics. The outcome of a promoter detection algorithm is directly or indirectly influenced by the success of identifying the location of a TATA box in a promoter sequence. A profiling technique is very often used to find putative TATA boxes, but discriminating a TATA box from putative TATA boxes is still a challenging problem. In this work, we formulate the problem and provide solutions using both a linear and a non linear classifiers. © 2005 ieee.

关键词： Genes

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An information fusion approach to controlling complexity in bioinformatics research

An information fusion approach to controlling complexity in ...

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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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Oscillatory dynamics in the mitogen-activated protein kinase cascade

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

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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

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

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

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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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Gene teams with relaxed proximity constraint

Gene teams with relaxed proximity constraint

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2005 ieee computational systems bioinformatics conference, CSB 2005

作者： Kim, Sun Choi, Jeong-Hyeon Yang, Jiong School of Informatics Center for Genomics and Bioinformatics Indiana University IN 47408 United States School of Informatics Indiana University IN 47408 United States EECS Case Western Reserve Univ. OH 44106 United States

ISBN: (纸本)0769523447

Functionally related genes co-evolve, probably due to the strong selection pressure in evolution. Thus we expect that they are present in multiple genomes. Physical proximity among genes, known as gene team, is a very useful concept to discover functionally related genes in multiple genomes. However, there are also many gene sets that do not preserve physical proximity. In this paper, we generalized the gene team model, that looks for gene clusters in a physically clustered form, to multiple genome cases with relaxed constraint. We propose a novel hybrid pattern model that combines the set and the sequential pattern models. Our model searches for gene clusters with and/or without physical proximity constraint. This model is implemented and tested with 97 genomes (120 replicons). The result was analyzed to show the usefulness of our model. Especially, analysis of gene clusters that belong to B. subtilis and E. coli demonstrated that our model predicted many experimentally verified operons and functionally related clusters. Our program is fast enough to provide a sevice on the web at http://***/platcom/. Users can select any combination of 97 genomes to predict gene teams. © 2005 ieee.

关键词： Genes

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Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants

Structural genomics analysis of alternative splicing and its...

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2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Wang, Peng Yan, Bo Guo, Juntao Hicks, Chindo Xu, Ying Department of Biochemistry and Molecular Biology Institute of Bioinformatics University of Georgia Athens GA 30622 United States

ISBN: (纸本)0769524427

Alternative splicing is a sophisticated nuclear process that regulates gene expression [1] and is an important mean of enhancing protein diversity [2]. Alternatively spliced variants play important roles in development and defects in mRNA splicing are causes of many human diseases [3, 4, 5]. Information about alternatively spliced variants is mainly derived from primary transcripts and little knowledge exists regarding structures. Here we carry out a structural genomics analysis of known alternative splicing events and show that threading is a valid approach to model structures of alternatively spliced variants. We collect 3-D structures of proteins with know translated splicing products from PDB and further expand the dataset with high quality models generated with threading approach. Our analysis shows that splicing events have a strong preference for non-regular secondary structure elements and tend to avoid buried residues. Those observations suggest evolutionary constrains exist for locations of splicing in the context of 3-D environment. We then show that majority of substitutions in splicing events share high structural similarity and splicing events also tend to remove entire domain and avoid exposing hydrophobic cores when part of a domain was removed. Those observations support the notion that majority of splicing isoforms adopt same fold as full-length protein despite sequence substitutions and deletions. This principle was then utilized to generate high quality structures of splicing variants that could be a valuable resource for studying their structures and functions and may provide new insights into pathogenesis of related diseases. © 2005 ieee.

关键词： Genetic engineering

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