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

共 371 条记录，以下是61-70 订阅

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BPAP: a computational tool for whole genome analysis and annotation

BPAP: a computational tool for whole genome analysis and ann...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： B. Abel M. Gollery Department of Biochemistry College of Agriculture Biotechnology and Natural Resources University of Nevada슠Reno Reno NV USA

Since the genesis of the Human Genome Project, more than 100 genomes have been, sequenced, and over 1000 genomes are expected to be sequenced in the next decade. With the advent of this extensive repertoire of raw sequence information, the next major challenge for a modern researcher is to interpret this wealth of information. At the remarkable rate of progress that is being made in sequencing organisms, experimental research techniques alone cannot keep up with the influx of genomic information. As a powerful complementary approach to experimental techniques, computational sequence analysis can assist in the categorization, characterization and creation of a functional definition of protein sequences. Our efforts have produced a biological protein analysis pipeline that can characterize proteins and attempts to produce working hypothesis of the functional and characteristic nature of a protein in a high throughput, automated manner with a minimum of amount of operational complexity for the user.

关键词： Genomics bioinformatics Search engines Sequences Software tools Computer interfaces Software packages Graphical user interfaces Protein engineering Chemical analysis

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Algorithms for association study design using a generalized model of haplotype conservation

Algorithms for association study design using a generalized ...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： R. Schwartz Department of Biological Sciences and School of Computer Science Carnegie Mellon University Pittsburgh PA USA

There is considerable interest in computational methods to assist in the use of genetic polymorphism data for locating disease-related genes. Haplotypes, contiguous sets of correlated variants, may provide a means of reducing the difficulty of the data analysis problems involved. The field to date has been dominated by methods based on the "haplotype block" hypothesis, which assumes discrete population-wide boundaries between conserved genetic segments, but there is strong reason to believe that haplotype blocks do not fully capture true haplotype conservation patterns. In this paper, we address the computational challenges of using a more flexible, block-free representation of haplotype structure called the "haplotype motif" model for downstream analysis problems. We develope algorithms for htSNP selection and missing data inference using this more generalized model of sequence conservation. Application to a dataset from the literature demonstrates the practical value of these block-free methods.

关键词： Algorithm design and analysis Genetics Inference algorithms Diseases bioinformatics Biological system modeling Computer science Biology computing Data analysis Humans

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CUBIC: search for binding sites

CUBIC: search for binding sites

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： V. Olman Jizhu Lu PhuongAn Dam Zhengchang Su Ying Xu Department of Biochemistry and Molecular Biology University of Georgia USA Institute of Computational Biology Oak Ridge National Laboratory USA

The regulation of gene transcription is achieved through specific interactions between transcription factors and their binding sites in the upstream region of the gene being regulated. Correct identification of these binding sites represents a key challenging problem in computational biology. Our approach to the problem is to find a "clear" cluster in the space of all k-mers from the upstream regulatory regions of a set of genes that potentially share similar binding sites. The cluster identification is performed by using minimal spanning tree (MST) technique with a special distance between k-mers based on the chosen profile. It's shown that widely used "conservation" characteristic in position is a result of a "common sense" requirement for "conservation". The local convergence of algorithm for "conservation" maximization of profile has been proved and the method for statistical significance evaluation of results is presented. All ideas have been implemented in a form of software CUBIC.

关键词： computational biology Clustering algorithms Biochemistry Laboratories DNA Sequences Mathematical model Frequency bioinformatics

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Qvalue methods may not always control false discovery rate in genomic applications

Qvalue methods may not always control false discovery rate i...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Xiao Yang Genomics Technology Monsanto Company Saint Louis MO USA

ISBN: (纸本)0769521940

The qvalue method by Storey (2002, 2003) has been proved to be theoretically sound for controlling false discovery rate in many high throughput genomic applications. However, empirical evidences suggest that this method can be more stringent than other methods, such as Bonferroni adjustment and the FDR method by Benjamini and Hochberg (1995). We compare these methods for detection of gene differential expression in microarray data analysis. For microarray experiment with the purpose of gene discovery, where many genes are expected to be differentially expressed across different experimental conditions, the qvalue method generally performs well. However, for experiments with only a few genes expected to be differentially expressed, the qvalue method performs much worse than other methods. Some insights are provided to examine this discrepancy. Adjustments to q-value method are recommended to accommodate many applications.

关键词： Genomics bioinformatics Testing Throughput Proportional control Histograms Data analysis Error analysis

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proceedings of the Third ieee International conference on Cognitive Informatics = ICCI 2004

Proceedings of the Third IEEE International Conference on Co...

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proceedings of the Third ieee International conference on Cognitive Informatics, ICCI 2004

ISBN: (纸本)0769521908

The proceedings contain 31 papers from the proceedings of the Third ieee International conference on Cognitive Informatics ICCI 2004. The topics discussed include: language, logic, and the brain;on autonomous computing and cognitive processes;is entropy suitable to characterize data and signals for cognitive informatics?;on the cognitive informatics foundations of software engineering;a parallel language for cognitive informatics;concept formation and learning: a cognitive informatics perspective;specification of the RTPA grammar and its recognition;formal description of the cognitive process of problem solving;and cognitive bioinformatics: computational cognitive model for dynamic problem solving.

关键词： Cognitive systems

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EGOMiner: a genomics and proteomics data computation and interpretation system for biomedical applications

EGOMiner: a genomics and proteomics data computation and int...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Weimin Feng G. Tuteja M.D. Wang Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University USA School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA USA

EGOMiner, stands for enhanced gene ontology mining system, is a CORBA based tool developed for genomic and proteomic data analysis. One key function of EGOMiner is to provide biological data interpretation based on gene ontology with quantitative and statistical analysis and visualization by direct acyclic graph. Cross comparison of multiple experimental studies is supported. The other function is quality analysis of microarray chip images. The input is raw chip data and output is visualization of the data quality of the chip image. This is system significantly improves the GoMiner system that was designed and developed by the authors.

关键词： Genomics bioinformatics Proteomics Biomedical computing Ontologies Data visualization Biology computing Data analysis Statistical analysis Image analysis

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A graph analysis method to detect metabolic sub-networks based on phylogenetic profile

A graph analysis method to detect metabolic sub-networks bas...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： S. Miyake Y. Takenaka H. Matsuda Department of Bioinformatic Engineering Graduate School of Information Science and Technology Osaka University Toyonaka Osaka Japan

To elucidate fundamental constituting principle of functional modules or building blocks of metabolic networks, computational methods to analyze the network structure of metabolism are getting much attention. We propose a graph search method to extract highly conserved sub-networks of metabolic networks based on phylogenetic profile. We formulated reaction-conservation score for the measure of the phylogenetic conservation of reactions. We also formulated compound-conservation score to eliminate biologically-meaningless compounds and reduce the size of the networks. By applying our approach to the metabolic networks of 19 representative organisms selected from bacteria, archaea, and eukaryotes in the KEGG database, we detected some highly conserved sub-networks among the organisms. Comparing them to the metabolic maps in KEGG, we found they were mainly included in energy metabolism, sugar metabolism, and amino acid metabolism.

关键词： Phylogeny Biochemistry Organisms bioinformatics Genomics Search methods Microorganisms Archaea Databases Proteins

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An exhaustive genome assembly algorithm using k-mers to indirectly perform N-squared comparisons in O(N)

An exhaustive genome assembly algorithm using k-mers to indi...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： M.K. Shah HoJoon Lee S.A. Rogers J.W. Touchman Translational Genomics Research Institute Phoenix Phoenix AZ USA Computational Biosciences Program Arizona State University Tempe AZ USA School of Life Sciences Arizona State University Tempe AZ USA

We present an algorithm that indirectly makes N/sup 2/ sequence comparisons in O(N) with respect to the size of the genome. This algorithm is very applicable in assembling whole genomes from the thousands of DNA sequence fragments that are generated in shotgun sequencing. First, we assume that fragments that share k-mers should overlap in the final assembly. We then catalog all k-mers that exist in the shotgun library and infer links between fragments that share k-mers. These links are then used to represent edges in a graph. This graph is generated in O(N) yet represents the result of comparing every fragment to every other fragment.

关键词： Genomics bioinformatics Assembly Libraries Sequences Capacitive sensors DNA Windows Data structures

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VirusFinder: a Web-based virus identification system using viral nucleotide signatures

VirusFinder: a Web-based virus identification system using v...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Yan Ding Hong Cao Shu Wen Department of Bioinformatics Manassas VA USA Department of Microecology Dalian Medical University Dalian China

ISBN: (纸本)0769521940

VirusFinder was developed as a Web-based virus identification system using viral signatures. Nucleotide signature-based detection has been proven to be a rapid and accurate pathogen identification approach in natural outbreaks or acts of bioterrorism. Species-specific signatures of selected families of HFVs including arenaviruses, bunyaviruses, filoviruses, and flaviviruses have been identified by comparative genomics. The unique signatures for each individual species of HFVs were derived from the multiple sequence alignments and were then saved into the signature database after validation. VirusFinder was implemented using J2EE technology with an intelligent signature recognition algorithm. As such, species-level differentiation and identification of HFVs was automatically achieved given an input of unknown nucleotide sequences. Results show that VirusFinder is able to identify HFVs at species level with 100% accuracy.

关键词： Pathogens Sequences bioinformatics Databases Genomics Web services Bioterrorism Hemorrhaging Computer viruses Web server

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Multi-knockout genetic network analysis: the Rad6 example

Multi-knockout genetic network analysis: the Rad6 example

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： A. Kaufman M. Kupiec E. Ruppin Center of Neural Computation Hebrew University Jerusalem Israel School of Computer Science and School of Medicine Tel-Aviv University Tel-Aviv Israel

A novel and rigorous multi-perturbation shapley value analysis (MSA) method has been recently presented. The method addresses the challenge of defining and calculating the functional causal contributions of elements of a biological system. This work presents the first study applying MSA to the analysis of gene knockout data. The MSA identifies the importance of genes in the Rad6 DNA repair pathway of the yeast S. cerevisiae, quantifying their contributions and characterizing their functional interactions. Incorporating additional biological knowledge, a new functional description of the Rad6 pathway is provided, predicting the existence of additional DNA polymerase and RFC-like complexes. The MSA is the first method for rigorously analyzing multi-knockout experiments, which are likely to soon become a standard and necessary tool for analyzing complex biological systems.

关键词： Genetics DNA Biological systems System identification Fungi bioinformatics Organisms Biology computing Biotechnology Computer science

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