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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671-680 订阅

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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...

引用

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...

引用

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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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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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...

引用

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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Pathway mapping with operon information: an integer-programming method

Pathway mapping with operon information: an integer-programm...

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： Fenglou Mao V. Olman Ying Xu Zhengchang Su D. Chuang Computational Systems Biology Lab Biochemistry & Molecular Biology Department Computational Biology Institute Oak Ridge National Laboratory University of Georgia USA

Biological pathway mapping is an important problem in the post-genomic era. We now present a new algorithm for pathway mapping in microbes. The algorithm considers not only sequence similarity among the template and target genes, but also the operon structures in the target genome. We formulated the mapping problem as a graph finding problem, and solved it by an integer-programming (IP) method. The goal is to minimize a linear object function subject to six constraints, such that maximal sequence similarity among the template and target genes are achieved, and at the same time, a minimal number of operons are covered in the target genome. Compared to our previous minimal spanning tree (MST) algorithm, the IP method has the following advantages: i) It is much faster and thus can map larger pathway involving a much large set of genes. ii) The IP method looks into the details of genes in the operons, and consequently avoids the many-to-one mapping mistakes that sometimes occur in the MST algorithm. We have compiled a large pathway training set to optimize the parameters of the program, and tested it by mapping 16 complex pathways from BioCyc onto *** K12 genome and the results are very promising.

关键词： Genomics bioinformatics Sequences computational systems biology Biochemistry computational biology Laboratories Testing Phylogeny Robustness

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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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A finite model theory for biological hypotheses

A finite model theory for biological hypotheses

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： S. Racunas C. Griffin N. Shah Pennslyvania State University University Park PA USA

We have designed and implemented a set of software tools for the composition and evaluation of hypotheses about gene regulation in biological systems. Our software uses a unified formal grammar for the representation of both diagram-based and text-based hypotheses. The objective of this paper is to show how to use this grammar as the basis for an effective logic for specifying hypotheses about biological systems in precise model-theoretic terms. To accomplish this, we take inspiration from inflationary extensions to fixed point logics and define a new type of logic: a deflationary logic for describing the effects of experiments upon models of biological systems. We present results that characterize decidability, satisfiability, and inflationary/deflationary properties of this logic. We formally define what it means for a set of assertions to be discoverable under this new logic, and show that our software generates discoverable queries. Thus, we lay the groundwork for a formal treatment of machine-aided experimental design under the conceptual framework we have developed for our hypothesis evaluation software.

关键词： Biological system modeling Biological systems Biological processes Chromium Software tools Software systems Design for experiments Testing Logic design bioinformatics

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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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Positive sample only learning (PSOL) for predicting RNA genes in E. coli

Positive sample only learning (PSOL) for predicting RNA gene...

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： R.F. Meraz Xiaofeng He C.H.Q. Ding S.R. Holbrook Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley CA USA Computational Research Division Lawrence Berkeley National Laboratory Berkeley CA USA

RNA genes lack most of the signals used for protein gene identification. A major shortcoming of previous discriminative methods to distinguish functional RNA (fRNA) genes from other non-coding genomic sequences is that only positive examples of fRNAs are known; there are no confirmed negatives - only intergenic sequences that may be positive or negative. To address this problem we developed the "positive sample only learning" (PSOL) method. This method can identify the most likely negative examples from an unlabeled set and is therefore able to distinguish putative functional RNA genes from other non-coding sequence. We compare RNA gene predictions using the PSOL method with previous large-scale analyses of the E. coli K12 genome.

关键词： RNA bioinformatics Genomics Iterative algorithms Helium Physics computing Laboratories Signal processing Proteins Large-scale systems

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The SSAHA trace server

The SSAHA trace server

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： Zemin Ning W. Spooner A. Spargo S. Leonard M. Rae A. Cox Wellcome Trust Sanger Institute Cambridge UK

We present a client/server database system with the potential to make all DNA sequences searchable. The database estimated to be approximately 200 Gbps, contains various types of sequences, including WGS and clone reads, draft assemblies, finished sequences, refSeq etc. The search engine will be SSAHA2, a package combined SSAHA (sequence search and alignment by hashing algorithm) with cross/spl ***/match. Matching seeds of a few kmer words are detected by the SSAHA algorithm. Both query and subject sequences are cut off according to the locations of the matching seeds and then passed to cross/spl ***/match for full alignment. We aim to develop a platform-independent client/server system which can provide a near real-time (under 10 seconds) search service for a clustered database.

关键词： Sequences DNA bioinformatics Genomics Cloning Packaging Encoding Database systems Assembly Search engines

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