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检索条件"任意字段=Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004"

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An overview of the Sandia national laboratories genomes to life project, "carbon sequestration in Synechococcus sp.: from molecular machines to hierarchical modeling"

An overview of the Sandia national laboratories genomes to l...

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ieee conference on bioinformatics

作者： G.S. Heffelfinger Sandia National Laboratories Albuquerque NM USA

The Sandia-led Genomes to Life (GTL) project: "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling," is focused on developing, prototyping, and applying new computational tools and methods to ellucidate the biochemical mechanisms of the carbon sequestration of Synechococcus Sp., an abundant marine cyanobacteria known to play an important role in the global carbon cycle. Our effort includes five subprojects: an experimental investigation, three computational biology efforts, and a fifth which deals with addressing computational infrastructure challenges of relevance to this project and the genomes to life program as a whole. Our experimental effort is designed to provide biology and data to drive the computational efforts and includes significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. Our computational efforts include coupling molecular simulation methods with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes and developing a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies.

关键词： Laboratories Genomics bioinformatics Biology computing Protein engineering Biological system modeling computational biology Prototypes Investments computational modeling

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Genomic sequence analysis using gap sequences and pattern filtering

Genomic sequence analysis using gap sequences and pattern fi...

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ieee conference on bioinformatics

作者： S.-C. Su C.H. Yeh C.-C. Jay Kuo Department of Electrical Engineering University of Southern California CA USA

A new pattern filtering technique is developed to analyze the genomic sequence in this research based on gap sequences, in which the distance of the same symbol is recorded consecutively as a sequence of integers. Sequence alignment and similarity testing can be performed on a family of gap sequences over selected patterns. The gap sequence offers a new way for sequence structural analysis. The match between the gap sequences is considered as a frame match while a true match requires both frame and stuffing match. Simulation results show that the extension of gap match indicates the corresponding segment extension in the original genomic sequence. Thus, we are able to generalize the conventional alignment and scoring methods in a more adaptive way.

关键词： Genomics bioinformatics Pattern analysis Sequences DNA Proteins Information filtering Information filters Testing Performance evaluation

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Automatic construction of 3D structural motifs for protein function prediction

Automatic construction of 3D structural motifs for protein f...

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ieee conference on bioinformatics

作者： M.P. Liang D.L. Brutlag R.B. Altman Department of Genetics Stanford Medical Informatics USA Department of Biochemistry Stanford Medical Informatics USA

Structural genomics initiatives are on the verge of generating a vast number of protein structures. The biological roles for many of these proteins are still unknown, and high-throughput methods for determining their function are necessary. Understanding the function of these proteins will have profound impact in drug development and protein engineering. Current methods for protein function prediction on structures require manual creation of structural motifs. Thus only few structural motifs are available. The lack of structural motifs limits the use of these methods for function prediction at a structural-genomics scale. To overcome this limitation, we describe a method for automatically creating a library of three dimensional structural motifs. Automatically generating a library of structural motifs can be used for structural-genomic scale function prediction on protein structures.

关键词： bioinformatics Protein engineering Genomics Biomedical informatics Libraries Atomic measurements Genetics Calcium Amino acids Databases

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Probability profiles-novel approach in tandem mass spectrometry De Novo sequencing

Probability profiles-novel approach in tandem mass spectrome...

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ieee conference on bioinformatics

作者： T. Fridman R. Day J. Razumovskaya D. Xu A. Gorin Oak Ridge National Laboratory Oak Ridge TN US Life Sciences Division ORNL Oak Ridge TN USA

A novel method is proposed for deciphering experimental tandem mass spectra. A large database of previously resolved peptide spectra was used to determine "neighborhood patterns" for each peak category: C- or N-terminus ions, their dehydrated fragments, etc. The established patterns are applied to assign probabilities for new spectra peaks to fit into these categories. A few peaks often could be identified with a fair confidence creating strong "anchor points" for De Novo algorithm assembling sequence subgraphs. Our approach is utilizing all informational content of a given MS experimental data set, including peak intensities, weak and noisy peaks, and unusual fragments. We also discuss ways to provide learning features in our method: adjustments for a specific MS device and user initiated changes in the list of considered peak identities.

关键词： Mass spectroscopy bioinformatics

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A new approach for gene annotation using unambiguous sequence joining

A new approach for gene annotation using unambiguous sequenc...

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ieee conference on bioinformatics

作者： A. Tchourbanov D. Quest H. Ali M. Pauley R. Norgren Department of Computer Science University of Nebraska at Omaha Omaha NE USA Department of Genetics Cell Biology and Anatomy University of Nebraska Medical Center Omaha NE

The problem addressed by this paper is accurate and automatic gene annotation following precise identification/annotation of exon and intron boundaries of biologically verified nucleotide sequences using the alignment of human genomic DNA to curated mRNA transcripts. We provide a detailed description of a new cDNA/DNA homology gene annotation algorithm that combines the results of BLASTN searches and spliced alignments. Compared to other programs currently in use, annotation quality is significantly increased through the unambiguous junction of genomic DNA sequences. We also address gene annotation with both noncanonic splice sites and short exons. The approach has been tested on the genie learning subset as well as full-scale human RefSeq, and has demonstrated performance as high as 97%.

关键词： DNA bioinformatics Genomics Sequences Humans Testing Proteins Databases Computer science Educational institutions

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A new approach to gene prediction using the self-organizing map

A new approach to gene prediction using the self-organizing ...

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ieee conference on bioinformatics

作者： S. Mahony T.J. Smith J.O. Mclnerney A. Golden National Centre for Biomedical Engineering Science NUI Galway Galway Ireland Department of Information Technology NUI Galway Galway Ireland

In this poster we present a gene prediction approach based on the self-organizing map that has the ability to automatically identify all the major patterns of content variation within a genome. The genome may then be scanned for regions displaying the same properties as one of these automatically identified models. Even using a relatively simple coding measure (codon usage), this method can predict the location of protein-coding sequences with a reasonably high accuracy. We also show other advantages of the approach, such as the ability to indicate genes that contain frame-shifts. We believe that this method has the potential to become a useful addition to the genome annotation process.

关键词： bioinformatics Genomics Proteins Lattices Predictive models Clustering algorithms Biomedical engineering Laboratories Information technology Biomedical measurements

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Substrate recognition by enzymes: a theoretical study

Substrate recognition by enzymes: a theoretical study

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ieee conference on bioinformatics

作者： K. Ueno-Noto K. Takano M. Hara-Yokoyama Graduate School of Humanities and Sciences Ochanomizu University Japan Graduate School of Dental Tokyo Medical and Dental University Japan

We previously reported that a series of gangliosides inhibited the activity of an enzyme NAD glycohydrolase (CD38), and that those with tandem sialic acid residues in the sugar chain had great inhibitory effect. We describe the results of computer simulations on three-dimensional and electronic structures of gangliosides to clarify the causative factors of difference in the inhibitory effect and the recognition mechanisms of the enzyme. We found that dipole moments and HOMO were correlated with inhibitory effect by conformational analyses and molecular orbital (MO) calculations. CD38 is likely to recognize the two carboxyl groups in tandem sialic acid residues of gangliosides, as well as the phosphate groups in NAD. A strong correlation was found between the orbital energies of HOMO by MO calculations and the extent of the inhibitory effect. Salvation effects were also considered to interpret the substrate recognition mechanisms in the biological system, which supported the above results.

关键词： Biochemistry Orbital calculations Dentistry Computer simulation Solid modeling Biological systems Extracellular Performance analysis Algorithm design and analysis bioinformatics

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Can we identify cellular pathways implicated in cancer using gene expression data?

Can we identify cellular pathways implicated in cancer using...

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ieee conference on bioinformatics

作者： N. Shah J. Lepre Y. Tu G. Stolovitzky Pennsylvania State University University Park PA USA IBM Computational Biology Center Yorktown Heights NY USA

The cancer state of a cell is characterized by alterations of important cellular processes such as cell proliferation, apoptosis, DNA-damage repair, etc. The expression of genes associated with cancer related pathways, therefore, may exhibit differences between the normal and the cancerous states. We explore various means to find these differences. We analyze 6 different pathways (p53, Ras, Brca, DNA damage repair, NF/spl kappa/b and /spl beta/-catenin) and 4 different types of cancer: colon, pancreas, prostate and kidney. Our results are found to be mostly consistent with existing knowledge of the involvement of these pathways in different cancers. Our analysis constitutes proof of principle that it may be possible to predict the involvement of a particular pathway in cancer or other diseases by using gene expression data. Such method would be particularly useful for the types of diseases where biology is poorly understood.

关键词： Cancer Gene expression DNA bioinformatics Noise measurement Colon Pancreas Diseases Biomedical measurements Genomics

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Identifying gene and protein names from biological texts

Identifying gene and protein names from biological texts

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ieee conference on bioinformatics

作者： W. Xuan S.J. Watson H. Akil F. Meng Mental Health Research Institute and Department of Psychatry University of Michigan Ann Arbor MI USA

Extracting and identifying gene and protein names from literature is a critical step for mining functional information of genes and proteins. While extensive efforts have been devoted to this important task, most of them were aiming at extracting gene/protein name per se without paying much attention to associate the extracted name with existing gene and protein database entries. We developed a simple and efficient method to identify gene and protein names in literature using a combination of heuristic and statistical strategies. Our approach will map the extracted names to individual LocusLink entries thus enable the seamless integration of literature information with existing gene/protein databases. Evaluation on a test corpus shows that our method can achieve both high recall and precision. Our method exhibits good performance and can be used as a building block for large biomedical literature mining systems.

关键词： Proteins Biology computing bioinformatics

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Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks

Combining microarrays and biological knowledge for estimatin...

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ieee conference on bioinformatics

作者： S. Imoto T. Higuchi T. Goto K. Tashiro S. Kuhara S. Miyano Human Genome Center Institute of Medical Science University of Tokyo Tokyo Japan Institute for Statistical Mathematics Tokyo Japan Graduate School of Genetic Resources Technology Kyushu University Fukuoka Japan

We propose a statistical method for estimating a gene network based on Bayesian networks from microarray gene expression data together with biological knowledge including protein-protein interactions, protein-DNA interactions, binding site information, existing literature and so on. Unfortunately, microarray data do not contain enough information for constructing gene networks accurately in many cases. Our method adds biological knowledge to the estimation method of gene networks under a Bayesian statistical framework, and also controls the trade-off between microarray information and biological knowledge automatically. We conduct Monte Carlo simulations to show the effectiveness of the proposed method. We analyze Saccharomyces cerevisiae gene expression data as an application.

关键词： Bayesian methods Biological system modeling Gene expression Proteins bioinformatics Biological control systems Humans Genomics Mathematics Genetics

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