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16th international conference on Artificial Reality and Telexistence - Workshops, ICAT 2006

作者： Zhu, Ping Tang, Xuqing Xu, Zhenyuan Guan, Weihong School of Science Southern Yangtze University Wuxi 214122 China Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University Hefei 230039 China

ISBN: (纸本)076952754X

In this paper, we offers a new algebraic point of view for dna molecules and introduce the algebraic system by using the natural operation based on the Σ = {A, C, G, T}. We characterize its structure by using the algebraic theory. We show that (L, ∠, ⊗) is the distribution lattice of rings with identical element. Furthermore, we generalize this result to the W ρ(V), a set which elements simulates the dna molecules with sticky ends, the element is called an incomplete double stranded molecules consist of mixed dna molecules with double and single strands. © 2006 IEEE.

关键词： dna

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Scalable, Time-Responsive, Digital, Energy-Efficient molecular Circuits Using dna Strand Displacement

Scalable, Time-Responsive, Digital, Energy-Efficient Molecul...

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16th international conference on dna computing and molecular programming

作者： Chiniforooshan, Ehsan Doty, David Kari, Lila Seki, Shinnosuke Univ Western Ontario Dept Comp Sci London ON Canada

ISBN: (纸本)9783642183041

We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of dna strand displacement. the design is scalable: all species of dna strands can in principle be mixed and prepared in a single test tube, rather than requiring separate purification of each species, which is a barrier to large-scale synthesis. the design is time-responsive: the concentration of output species changes in response to the concentration of input species, so that time-varying inputs may be continuously processed. the design is digital: Boolean values of wires in the circuit are represented as high or low concentrations of certain species, and we show how to construct a single-input, single-output signal restoration gate that amplifies the difference between high and low, which can be distributed to each wire in the circuit to overcome signal degradation. this means we can achieve a digital abstraction of the analog values of concentrations. Finally, the design is energy-efficient: if input species are specified ideally (meaning absolutely 0 concentration of unwanted species), then output species converge to their ideal concentrations at steady-state, and the system at steady-state is in (dynamic) equilibrium, meaning that no energy is consumed by irreversible reactions until the input again changes.

关键词： Timing circuits

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dna Chips for Species Identification and Biological Phylogenies

DNA Chips for Species Identification and Biological Phylogen...

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15th international conference on dna computing and molecular programming

作者： Garzon, Max H. Wong, Tit-Yee Phan, Vinhthuy Univ Memphis Memphis TN 38152 USA

ISBN: (纸本)9783642106033

the codeword design problem is an important problem in dna computing and its applications. Several theoretical analyses as well as practical solutions for short oligonucleotides (up to 20-mers) have been generated recently. these solutions have, in turn, suggested new applications to dna-based indexing and natural language processing, in addition to the obvious applications to the problems of reliability and scalability that generated them. Here we continue the exploration of this type of dna-based indexing for biological applications and show that dna noncrosshybridizing (nxh) sets can be successfully applied to infer ab initio phylogenetic trees by providing a way to measure distances among different genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. these phylogenies are solidly established and well accepted in biology. the new technique is much more effective in terms of signal-to-noise ratio, cost and time than current methods. Second, it can be scaled up to newly available universal dna chips readily available both in vitro and in silica. In particular, we show how a recently obtained such set of nxh 16-mers can be used as a universal coordinate system in dna spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform reference system, a veritable and comprehensive "Atlas of Life", as it is or as it could be on earth.

关键词： dna codeword design noncrosshybridizing oligonucleotide bases phylogenetic analysis genomic signatures dna chips 16S rRNA tree of life

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A GPU-Based Bit-Parallel Multiple Pattern Matching Algorithm 20

A GPU-Based Bit-Parallel Multiple Pattern Matching Algorithm

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20th IEEE international conference on High Performance computing and Communications (HPCC) / 16th IEEE international conference on Smart City (SmartCity) / 4th IEEE international conference on Data Science and Systems (DSS)

作者： Hung, Che-Lun Wang, Hsiao-Hsi Hsu, Tzu-Hung Lin, Chun-Yuan Providence Univ Dept Comp Sci & Commun Engn Taichung Taiwan Providence Univ Dept Comp Sci & Informat Management Taichung Taiwan Chang Gung Univ Dept Comp Sci & Informat Engn Taoyuan Taiwan

ISBN: (纸本)9781538666142

String matching algorithms have played critical role in many applications, such as dna sequence comparison, network intrusion detection systems, and so forth. In this paper, we present a parallel multiple pattern matching method based on general purpose graphic processing units to realize fast string searching. In proposed method, we adopt a bit-parallel pattern comparison concept to accelerates string search to achieve efficient parallel search of multiple patterns of different lengths. In addition, we use CUDA framework to enhance the performance of searching string by leveraging GPU computing power. From the experimental results, the proposed method can achieve higher search throughput than other string matching methods. the proposed method is useful for genome sequence comparison and packet payload filtering.

关键词： Multiple Pattern String Match Bit-Parallel Parallel computing GPU

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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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the Osmium Tetroxide Bipyridine-labeled dna Probe: Hairpin Conformations and Characterization of Redox-label Behavior

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ELECTROANALYSIS 2017年第1期29卷 51-59页

作者： Joda, Hamdi Sedova, Ada Awan, Waqas Flechsig, Gerd-Uwe SUNY Albany 1400 Washington Ave Albany NY 12222 USA Univ Miami Miller Sch Med Dept Biochem & Mol Biol 1011 NW 15th St Miami FL 33136 USA Oak Ridge Natl Lab Sci Comp Grp Natl Ctr Computat Sci 1 Bethel Valley Rd Oak Ridge TN 37831 USA

Osmium tetroxide bipyridine ([OsO4(bpy)]) is a versatile label for dna electrochemistry. Here we report our efforts to create an osmium tetroxide-labeled immobilized dna probe for use in biosensing experiments. Our label is applied in-house, as opposed to many other covalent redox labels used with dna. We developed an on-electrode labeling method that was able to avoid attack of our disulfide-based linker by the [OsO4(bpy)]. Our results include two different hairpin-based signal-off hybridization detection assays, each with robust, reproducible signal decrease on binding to complementary target. We also found that 6-mercapto-1-hexa-nol was able to interact with [OsO4(bpy)] in a stable manner when assembled at the surface, but was able to remove excess [OsO4(bpy)], which was found to adsorb strongly to the gold surface, and avoid MCH transformation, when applied after the labeling process. Furthermore, we found an increased adsorption affinity of [OsO4(bpy)]-labeled dna onto gold, characterized the redox behavior of adsorbed [OsO4(bpy)], and determined voltammetric signals on the HMDE of our intact disulfide linker while verifying that this linker is attacked by [OsO4(bpy)] when in solution.

关键词： Voltammetry Gold electrode Osmium tetroxide bipyridine dna Hybridization molecular beacon

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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...

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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...

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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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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Robert Brijder Lulu Qian

ISBN: (数字)9783319667997

ISBN: (纸本)9783319667980

this book constitutes the refereed proceedings of the 23th international conference on dna computing and molecular programming, dna 23, held Austin, TX, USA, in September 2017. the 16 full papers presented were carefully selected from 23 submissions. Research in dna computing aims to draw together mathematics, computerscience, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. the papers address all areas related to biomolecular computing such as: algorithms and models for computation with biomolecular systems; computational processes in vitro and in vivo; molecular motors and molecular robotics; studies of fault-tolerance and error correction; software tools for analysis, simulation, and design; synthetic biology and in vitro evolution; applications in engineering, physics, chemistry, biology, and medicine.

关键词： Computation by Abstract Devices Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics Artificial Intelligence Data Structures Discrete Mathematics in Computer Science

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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Yannick Rondelez Damien Woods

ISBN: (数字)9783319439945

ISBN: (纸本)9783319439938

this book constitutes the refereed proceedings of the 22nd international conference on dna computing and molecular programming, dna 22, held Munich, Germany, in September 16;the 11 full papers presented together with 10 invited and tutorial talks were carefully selected from 55 submissions;Research in dna computing and molecular programming draws together mathematics, computer science, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems

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