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dna computing and molecular programming 1

丛书名： Lecture Notes in Computer Science

1000年

作者： Darko Stefanovic Andrew Turberfield

ISBN: (数字)9783642322082

ISBN: (纸本)9783642322075

this book constitutes the refereed proceedings of the 18th international conference on dna computing and molecular programming, dna 18, held in Aarhus, Denmark, in August 2012. the 11 full papers presented were carefully selected from 37 submissions. the papers are organized in topical sections on advancing the engineering and science of biology and chemistry from the point of view of computer science, physics, and mathematics.

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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An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data

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BIOINFORMATICS 2011年第13期27卷 I310-I316页

作者： Jin, Guangxu Zhao, Hong Zhou, Xiaobo Wong, Stephen T. C. Cornell Univ Weill Med Coll Methodist Hosp Res Inst Syst Med & Bioengn Dept Houston TX 77030 USA

Motivation: Prediction of synergistic effects of drug combinations has traditionally been relied on phenotypic response data. However, such methods cannot be used to identify molecular signaling mechanisms of synergistic drug combinations. In this article, we propose an enhanced Petri-Net (EPN) model to recognize the synergistic effects of drug combinations from the molecular response profiles, i.e. drug-treated microarray data. Methods: We addressed the downstream signaling network of the targets for the two individual drugs used in the pairwise combinations and applied EPN to the identified targeted signaling network. In EPN, drugs and signaling molecules are assigned to different types of places, while drug doses and molecular expressions are denoted by color tokens. the changes of molecular expressions caused by treatments of drugs are simulated by two actions of EPN: firing and blasting. Firing is to transit the drug and molecule tokens from one node or place to another, and blasting is to reduce the number of molecule tokens by drug tokens in a molecule node. the goal of EPN is to mediate the state characterized by control condition without any treatment to that of treatment and to depict the drug effects on molecules by the drug tokens. Results: We applied EPN to our generated pairwise drug combination microarray data. the synergistic predictions using EPN are consistent with those predicted using phenotypic response data. the molecules responsible for the synergistic effects with their associated feedback loops display the mechanisms of synergism.

关键词： dna microarrays PHENOTYPE BIOINFORMATICS DOSAGE of drugs programming languages (Electronic computers) DATA analysis COMPUTER software

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computing properties of thermodynamic binding networks: An integer programming approach 27

Computing properties of thermodynamic binding networks: An i...

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27th international conference on dna computing and molecular programming, dna 2021

作者： Haley, David Doty, David University of California DavisCA United States

ISBN: (纸本)9783959772051

the thermodynamic binding networks (TBN) model [9] is a tool for studying engineered molecular systems. the TBN model allows one to reason about their behavior through a simplified abstraction that ignores details about molecular composition, focusing on two key determinants of a system's energetics common to any chemical substrate: How many molecular bonds are formed, and how many separate complexes exist in the system. We formulate as an integer program the NP-hard problem of computing stable (a.k.a., minimum energy) configurations of a TBN: those configurations that maximize the number of bonds and complexes. We provide open-source software [13] solving this integer program. We give empirical evidence that this approach enables dramatically faster computation of TBN stable configurations than previous approaches based on SAT solvers [3]. Furthermore, unlike SAT-based approaches, our integer programming formulation can reason about TBNs in which some molecules have unbounded counts. these improvements in turn allow us to efficiently automate verification of desired properties of practical TBNs. Finally, we show that the TBN has a natural representation with a unique Hilbert basis describing the "fundamental components" out of which locally minimal energy configurations are composed. this characterization helps verify correctness of not only stable configurations, but entire "kinetic pathways" in a TBN. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： thermodynamics

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Optimizing Tile Concentrations to Minimize Errors and Time for dna Tile Self-assembly Systems

Optimizing Tile Concentrations to Minimize Errors and Time f...

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16th international conference on dna computing and molecular programming

作者： Chen, Ho-Lin Kao, Ming-Yang CALTECH Ctr Math Informat Pasadena CA 91101 USA Northwestern Univ Dept Elect Engn & Comp Sci Evanston IL USA

ISBN: (纸本)9783642183041

dna tile self-assembly has emerged as a rich and promising primitive for nano-technology. this paper studies the problems of minimizing assembly time and error rate by changing the tile concentrations because changing the tile concentrations is easy to implement in actual lab experiments. We prove that setting the concentration of tile T-i proportional to the square root of N-i where N-i is the number of times T-i appears outside the seed structure in the final assembled shape minimizes the rate of growth errors for rectilinear tile systems. We also show that the same concentrations minimize the expected assembly time for a feasible class of tile systems. Moreover, for general tile systems, given tile concentrations, we can approximate the expected assembly time with high accuracy and probability by running only a polynomial number of simulations in the size of the target shape.

关键词： Self assembly

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Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis

Sequence Assembly Validation by Multiple Restriction Digest ...

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6th international conference on Intelligent Systems for molecular Biology, ISMB 1998

作者： Rouchka, Eric C. States, David J. Institute for Biomedical Computing Washington University 700 South Euclid Avenue St. LouisMO63110-1012 United States

ISBN: (纸本)1577350537

dna sequence analysis depends on the accurate assembly of fragment reads for the determination of a consensus sequence. this report examines the possibility of analyzing multiple, independent restriction digests as a method for testing the fidelity of sequence assembly. A dynamic programming algorithm to determine the maximum likelihood alignment of error prone electrophoretic mobility data to the expected fragment mobilities given the consensus sequence and restriction enzymes is derived and used to assess the likelihood of detecting rearrangements in genonúc sequencing projects. the method is shown to reliably detect errors in sequence fragment assembly without the necessity of making reference to an overlying physical map. An html form-based interface is available at http://***/services/***. © 1998, AAAI (***). All rights reserved.

关键词： Dynamic programming

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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： Satoshi Murata Satoshi Kobayashi

ISBN: (数字)9783319112954

ISBN: (纸本)9783319112947

this book constitutes the refereed proceedings of the 20th international conference on dna computing and molecular programming, dna 20, held in Kyoto, Japan, in September 2014. the 10 full papers presented were carefully selected from 55 submissions. the papers are organized in many disciplines (including mathematics, computer science, physics, chemistry, material science and biology) to address the analysis, design, and synthesis of information-based molecular systems.

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Parallel pairwise operations on data stored in dna: Sorting, shifting, and searching 27

Parallel pairwise operations on data stored in dna: Sorting,...

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27th international conference on dna computing and molecular programming, dna 2021

作者： Chen, Tonglin Solanki, Arnav Riedel, Marc Department of Electrical and Computer Engineering University of Minnesota MinneapolisMN United States

ISBN: (纸本)9783959772051

Prior research has introduced the Single-Instruction-Multiple-Data paradigm for dna computing (SIMD dna). It offers the potential for storing information and performing in-memory computations on dna, with massive parallelism. this paper introduces three new SIMD dna operations: Sorting, shifting, and searching. Each is a fundamental operation in computer science. Our implementations demonstrate the effectiveness of parallel pairwise operations with this new paradigm. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Sorting

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the circular dna model of 0-1 programming problem based on dna strand displacement 14

The circular DNA model of 0-1 programming problem based on D...

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14th international conference on Natural Computation, Fuzzy Systems and Knowledge Discovery, ICNC-FSKD 2018

作者： Tang, Zhen Yin, Zhixiang Yang, Jing Sun, Xia Cui, Jianzhong School of Mathematics and Big Data AnHui University of Science and Technology Huainan AnHui232001 China School of Electronic and Information Engineering AnHui University of Science and Technology Huainan AnHui232001 China

ISBN: (纸本)9781538680971

dna strand displacement is a new molecular biological technology with strong operability and simple experimental conditions. In this paper, dna strand displacement is applied to solve the 0-1 programming problem, and a model is constructed using the class closed-loop dna structure (known as 'circular dna' in this paper). the model fixes the dna strands which represent the variables on the circular dna single strand in counterclockwise order. the dna strand 5' end is attached with the primers which are applied to the displacement of the dna strand. the 3' end is attached with the colored fluorophore. Taking the possible solutions as the input, the results are detected by different fluorescent colors resulting from the dna strand displacement. the dna computing model has better flexibility, realizability and applicability. © 2018 IEEE.

关键词： dna

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Nanopore decoding for dna computation with parallel self-assembly 24

Nanopore decoding for DNA computation with parallel self-ass...

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24th international conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2020

作者： Takiguchi, Sotaro Kawano, Ryuji Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Japan

ISBN: (纸本)9781733419017

this paper describes nanopore decoding for dna computation with parallel self-assembly. dna computing has been receiving attention as one of the molecular computing which can perform massively parallel computation. Here, we report simple decoding for mathematical dna computation using nanopore technology. In this method, the output information was electrically decoded with label-free. We demonstrated nanopore decoding with a graph encoding a Hamiltonian path problem (HPP). the results showed the feasibility of nanopore decoding as a precise decoding method for self-assembly-based dna computation. © 2020 CBMS-0001

关键词： Lipid bilayers

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Search and Validation of Short Genome-Wide Biomarkers for Bacterial Biological Phylogenies

Search and Validation of Short Genome-Wide Biomarkers for Ba...

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16th international conference on dna computing and molecular programming

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

ISBN: (纸本)9783642183041

We continue the exploration of dna-based indexing as a universal coordinate system in dna spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform biomarker reference system, a comprehensive "Atlas of Life", as it is or as it could be on earth. We provide a second confirmation that dna noncrosshybridizing (nxh) sets can be successfully applied to infer ab-alitio phylogenetic trees by providing a method to measure distances among entire genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. these phylogenies are solidly established and well accepted in bacterial biology, albeit done by analyses of relatively small segments of highly conserved rybozomic dna. Second, it is further demonstrated that dna indexing does provide novel and principled genome-wide predictions into the phylogenesis of organisms hitherto inaccessible by current methods, such as a prediction of the origin of the Salmonella plasmid 50 as being acquired horizontally, likely from some bacteria somewhat related to Yesinia. We conclude with some discussion about the scalability and potential of this method to develop a comprehensive tree of life based on genome-wide methods.

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

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