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检索条件"任意字段=16th International Conference on DNA Computing and Molecular Programming, DNA 16"

共 108 条记录，以下是51-60 订阅

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Central Dogma of molecular Biology - New Paradigm in Evolutionary Computation

Central Dogma of Molecular Biology - New Paradigm in Evoluti...

引用

international Symposium on Symbolic and Numeric Algorithms for Scientific computing (SYNASC)

作者： Corina Rotar Computer Science Department “1 Decembrie 1918” University Alba Iulia Romania

the aim of this study is to develop a new evolutionary computation paradigm in terms of molecular biology. Standard genetic algorithms are heuristics inspired by the simplified model of natural evolution and genetics. the latest discoveries and innovations from molecular biology, related to the conventional central dogma of molecular biology, generate the necessity of updating the genetic algorithms, although successfully applied in various complex tasks. In this direction, the research in Evolutionary Computation requires a reconsideration of the concepts and theories underlying the development of these popular optimization techniques. Since the emergence of the new features is important in the evolution, the dna code requires progress. Evolutionary Computation which is based on the mutation and the natural selection can be reconsidered in terms of protein synthesis and reverse transcription. From the computational perspective, a biological phenomenon might be interpreted in various forms in order to obtain reliable computational techniques.

关键词： dna Proteins RNA Optimization Evolution (biology)

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Intelligent and Efficient Web-based Middleware for Data Management in Motif Finding in Gene Regulation

Intelligent and Efficient Web-based Middleware for Data Mana...

引用

IEEE 16th international conference on Computational Science and Engineering (CSE)

作者： Hussain, Sajid Adeogun, Samuel Dotu, Bright Yang, Laurence T. Fisk Univ Comp Sci Nashville TN 37208 USA St Francis Univ Comp Sci Antinonish NS Canada

ISBN: (纸本)9781479948970

Due to the latest developments in next generation sequencing and bioinformatics tools, efficient data management is a major challenge in bioinformatics related research. While the availability of biological data facilitates research in genetics and genomics and there are databases where researchers can access these data, downloading and managing data has been a daring task for individuals with little or no programming expertise. the discovery of the right motif in a dna sequence has remained a challenge and important problem in the field of bioinformatics and regulatory genomics. While, a number of motif finding algorithms and applications have been developed over the years, the Gibbs sampling algorithm has shown great promise when it comes to discovering motifs in the promoter regions of genes. However Gibbs sampling algorithm does not extend to the processing of biological data obtained directly from laboratory experiments and stored in spread sheet applications, instead it focuses exclusively on processing of data already expressed as dna sequences. In this work, we develop a middleware that assists researchers to download and manage data from public databases like the National Center for Biotechnology Information (NCBI) databases. this is made possible using Biopython an open-source Python programming language module. A customized web-based interface is developed in order to assist non-programming scientists to easier access these biological databases. In the proposed middleware, HTML, CSS and PHP technologies are used for the front-end web-based interface and Python is used for the backend data processing. the proposed middleware was used in investigating motifs for gene regulation;where large number of dna sequences were downloaded from NCBI and analyzed using customized and open-source motif finding tools such as Gibbs Sampler, Meme Chip, Align Ace and an in-house modified Gibbs Sampler implementation. Our web-based middleware was very effective in automating

关键词： bioinformatics gene regulation middleware motif Middleware Gene regulation Bioinformatics Data management dna Sequence data download Biological data Database Pythonidae promoter regions Time Management

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Search for cellular stress biomarkers in lymphocytes from individuals exposed to arsenic: a pilot study 16

Search for cellular stress biomarkers in lymphocytes from in...

引用

16th international conference on Heavy Metals in the Environment (ICHMET)

作者： Scovassi, A. I. Grecchi, S. Cori, L. Bianchi, F. CNR Inst Mol Genet Pavia Italy CNR Inst Clin Physiol Environm Epidemiol Unit Pisa Italy

the molecular mechanisms of arsenic toxicity are not fully elucidated. the Italian project SEpiAs aims at developing and validating the assay to detect stress biomarkers in individuals living in areas characterized by... 详细信息

关键词： Apoptosis arsenic biomonitoring cellular stress dna damage

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the dna query language dnaQL

The DNA query language DNAQL

引用

16th international conference on Database theory, ICDT 2013

作者： Brijder, Robert Gillis, Joris J.M. Van Den Bussche, Jan Hasselt University Belgium

ISBN: (纸本)9781450315982

this paper presents an exposition of the authors' past and present work on the query language dnaQL for querying databases in dna. In dna computing, data is represented and stored in dna molecules. Accordingly, a logical data model is defined that models complexes of dna molecules in a graph-oriented fashion. Next, a set of formal operations on dna complexes is defined, much in the spirit of the operations of the relational algebra in the relational data model. these operations model laboratory operations on dna in solution. their combination leads to the query language dnaQL;but in order for programs to be well-defined on prescribed types of inputs, a type system is superimposed on the language. Finally a correspondence is shown between well-typed dnaQL programs and programs in a relationalalgebra query language. Copyright 2013 ACM.

关键词： Query languages

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Integrated Planar Waveguide Devices for Evanescent Field Sensing and Spectroscopy

Integrated Planar Waveguide Devices for Evanescent Field Sen...

引用

international conference on Transparent Optical Networks

作者： P. Cheben S. Janz N. Sabourin D.-X. Xu H. Ding S. Wang J. H. Schmid A. Delage J. Lapointe W. Sinclair R. Ma S. Logan R. MacKenzie Q.Y. Liu M. Gilmour R. Halir C. Alonso Ramos G. Wanguemert-Perez A. Ortega-Monux I. Molina Fernandez X. Le Roux L. Laurent A. Villafranca Velasco M. L. Calvo National Research Council Ottawa Canada

ISBN: (纸本)9781479956029

the silicon photonic wire evanescent field (PWEF) sensor platform offers the advantages of small sensor size, high levels of function integration, and low cost manufacturing that comes with the use of established semiconductor fabrication processes. the technology should be fully compatible with existing infrastructure in molecular analysis and research and the manufactured sensor array chip cost should be low enough that the chips can be considered disposable. Furthermore, since many applications require simultaneous monitoring of many different simultaneous binding reactions, the possibility of integrating tens or even hundreds of independent molecular sensors on a single disposable sensor chip is very compelling. We present an overview of our multiplexed photonic wire sensor chip and a reader instrument that allows up to 128 independent binding reactions to be monitored simultaneously [1]. A complete photonic wire molecular biosensor microarray chip architecture and supporting instrumentation is discussed. this microarray system is used to demonstrate a multiplexed assay for serotyping E. coli bacteria based on polyclonal antibody probe molecules. A coherent detection scheme that enables direct read-out of the optical phase and an order of magnitude enhancement of sensitivity compared to conventional detection is also discussed [2]. Finally, we present advances in Fourier-transform interferometer arrays for spectroscopic sensing. A planar waveguide Fourier-transform spectrometer with densely arrayed Mach-Zehnder interferometers is presented. Subwavelength gratings are used to produce an optical path difference without waveguide bends. the fabricated device comprises of an array of 32 Mach-Zehnder interferometers, which produce a spatial interferogram without any moving parts, yielding a spectral resolution of 50 pm and a free-spectral range of 0.78 nm. As a result of similar propagation losses in subwavelength grating waveguides and conventional strip waveguides,

关键词： Propagation losses MACH-ZEHNDER INTERFEROMETER Computer chips Planar waveguides Spectrography Escherichia coli dna Microarrays Sensors Waveguide Device Component Fabrication process moving parts photonic extinction coefficients Spectral resolution ELECTRIC WIRE

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Intelligent and Efficient Web-Based Middleware for Data Management in Motif Finding in Gene Regulation

Intelligent and Efficient Web-Based Middleware for Data Mana...

引用

IEEE international conference on Computational Science and Engineering, CSE

作者： Sajid Hussain Samuel Adeogun Bright Dotu Laurence T. Yang Computer Science Fisk University Nashville TN Computer Science St. Francis University Antinonish NS

Due to the latest developments in next generation sequencing and bioinformatics tools, efficient data management is a major challenge in bioinformatics related research. While the availability of biological data facilitates research in genetics and genomics and there are databases where researchers can access these data, downloading and managing data has been a daring task for individuals with little or no programming expertise. the discovery of the right motif in a dna sequence has remained a challenge and important problem in the field of bioinformatics and regulatory genomics. While, a number of motif finding algorithms and applications have been developed over the years, the Gibbs sampling algorithm has shown great promise when it comes to discovering motifs in the promoter regions of genes. However Gibbs sampling algorithm does not extend to the processing of biological data obtained directly from laboratory experiments and stored in spread sheet applications, instead it focuses exclusively on processing of data already expressed as dna sequences. In this work, we develop a middleware that assists researchers to download and manage data from public databases like the National Center for Biotechnology Information (NCBI) databases. this is made possible using Biopython - an open-source Python programming language module. A customized web-based interface is developed in order to assist non-programming scientists to easier access these biological databases. In the proposed middleware, HTML, CSS and PHP technologies are used for the front-end web-based interface and Python is used for the backend data processing. the proposed middleware was used in investigating motifs for gene regulation, where large number of dna sequences were downloaded from NCBI and analyzed using customized and open-source motif finding tools such as Gibbs Sampler, Meme Chip, Align Ace and an in-house modified Gibbs Sampler implementation. Our web-based middleware was very effective in automat

关键词： Bioinformatics dna Middleware Databases Genomics Mathematical model

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Using molecular computing for a data analysis prototype

Using molecular computing for a data analysis prototype

引用

16th international conference on Mechatronics Technology, ICMT 2012

作者： Wu, Kee-Rong Yeh, Chung-Wei Chu, Chih-Ping Department of Marine Engineering National Kaohsiung Marine University Kaohsiung Taiwan Department of Management Information System Kao Yuan University Kaohsiung Taiwan Department of Computer Science and Information Engineering National Cheng Kung University Tainan Taiwan

ISBN: (纸本)9787900769428

We present a promising development of a data analysis model, DAdna, with operational procedures by using deoxyribonucleic acid (dna) computing solution to exploit vast parallelism. the proposed solution is based mainly on the innovative bio-operations by Adleman and Amos to implement table design, simulate relational algebra, cluster and solve query problems. DAdna consists of three layers: (1) a Data definition layer, in which the records are represented by dna strands, (2) an Operational procedure layer, in which fundamental relational and extended operations are executed by dna-based procedures, and (3) a Query-analysis layer, in which the query is executed, involving the construction of relational tables and executing the operations in the Operational procedure layer. Hence, the dna based data cluster design proceeded with our well-organized scheme. Our proposed model can be used as an algorithmic basis for database operational procedures embedded in biomolecular computations for the further development and performing generalized data analysis with inherent molecular parallelism.

关键词： dna

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Identification of single molecular dna methylation points by microfluidic dna molecule stretching and quantum dot detection

Identification of single molecular DNA methylation points by...

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16th international conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012

作者： Okamoto, Yukihiro Sano, Tatsuki Kaji, Noritada Tokeshi, Manabu Baba, Yoshinobu FIRST Research Center for Innovative Nanobiodevices Nagoya University Japan Nagoya University Japan Hokkaido University Japan Japan

ISBN: (纸本)9780979806452

We report a rapid and simple epigenetic analysis based on microfluidic single dna molecular methylation detection. We developed a microfluidic device to stretch a single dna molecule and subsequent detection of a methylated dna base by quantum dot (QD)-immobilized methyl binding domain (MBD) protein. A QD-MBD complex specifically bound to a methylated base of stretched dna and was detected by a total internal reflection fluorescence microscope (TIRFM). Our method enables us to detect a number of methylation site and identify the methylated positions simultaneously in the simple and rapid manner compared with the conventional methods.

关键词： Microfluidics

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Silicon nano tweezers for real time biomechanical assay on dna damage by therapeutic radiation beams

Silicon nano tweezers for real time biomechanical assay on D...

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16th international conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012

作者： Collard, Dominique Lacornerie, thomas Kumemura, Momoko Lafitte, Nicolas Guillou, Herve Jalabert, Laurent Lartigau, Eric Fujii, Teruo Cleri, Fabrizio Fujita, Hiroyuki LIMMS/CNRS-IIS UMI2820 Japan Centre Oscar Lambret University of Lille 2 France IEMN CNRS University of Lille 1 France Institute of Industrial Science University of Tokyo Japan

ISBN: (纸本)9780979806452

We report the biomechanical characterization of a λ-dna bundle exposed to a therapeutic radiation beam by Silicon Nanotweezers. the device endures the harsh environment of radiation beams and still retains molecular-level accuracy. this result paves the way for both fundamental and clinical studies of dna degradation mechanisms under ionizing radiation for improved tumor treatment.

关键词： Silicon

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Semantic Information Integration with Transformations for Stream Reasoning

Semantic Information Integration with Transformations for St...

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international conference on Information Fusion

作者： Fredrik Heintz Daniel de Leng Department of Computer and Information Science Linkoping University Department of Information and Computing Sciences Utrecht University

ISBN: (纸本)9781479902842

the automatic, on-demand, integration of information from multiple diverse sources outside the control of the application itself is central to many fusion applications. An important problem is to handle situations when the requested information is not directly available but has to be generated or adapted through transformations. this paper extends the semantic information integration approach used in the stream-based knowledge processing middleware DyKnow with support for finding and automatically applying transformations. Two types of transformations are considered. Automatic transformation between different units of measurements and between streams of different types. DyKnow achieves semantic integration by creating a common ontology, specifying the semantic content of streams relative to the ontology and using semantic matching to find relevant streams. By using semantic mappings between ontologies it is also possible to do semantic matching over multiple ontologies. the complete stream reasoning approach is integrated in the Robot Operating System (ROS) and used in collaborative unmanned aircraft systems missions.

关键词： Ontology Semantics streams AUTOMATIC rivers dna Integration integration Reasoning

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