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

共 174 条记录，以下是61-70 订阅

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Functional Interpretation of Gene Sets: Semantic-Based Clustering of Gene Ontology Terms on the BioTest Platform 5th

Functional Interpretation of Gene Sets: Semantic-Based Clust...

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5th international conference on Man-Machine Interactions (ICMMI)

作者： Gruca, Aleksandra Jaksik, Roman Psiuk-Maksymowicz, Krzysztof Silesian Tech Univ Inst Informat Ul Akad 16 PL-44100 Gliwice Poland Silesian Tech Univ Inst Automat Control Ul Akad 16 PL-44100 Gliwice Poland

ISBN: (纸本)9783319677927;9783319677910

Modern high-throughput technologies based on genome, transcriptome or proteome profiling provide abundance of data that needs to be processed, analyzed and, finally, interpreted. Effective and efficient analysis of data coming from molecular profiling is crucial for a detailed diagnosis, prognosis, and prediction of therapy outcome. Meaningful conclusions can be drawn only by the use of sophisticated methods for biomedical and molecular data analysis and interpretation. In this study we present the approach for functional interpretation of gene or protein sets with clusters of Gene Ontology terms. We analyze transcription profiles of human cell line K562 and we show that clustering allows grouping functionally related GO terms and therefore obtaining more concise and comprehensive description. By applying cluster-specific data aggregation tool we are able to calculate statistics for the individual clusters of GO terms and compare the number of differentially expressed genes between two sample pairs. the presented tool is implemented as a part of annotation module available on the BioTest remote platform for hypothesis testing and analysis of biomedical data.

关键词： Gene Ontology Clustering Semantic similarity BioTest platform dna microarrays molecular profiling Functional interpretation

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Research on the addition, subtraction, multiplication and division complex logical operations based on the dna strand displacement 1

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13th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2018

作者： Huang, Chun Wang, Yanfeng Zhou, Qinglei School of Information Engineering Zhengzhou University Zhengzhou450001 China College of Electrical and Electronic Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (数字)9789811328299

ISBN: (纸本)9789811328282

In recent years, the development of biological computers has become faster and faster. In order to adapt to the development of science and technology, some novel logic circuits designs are necessary. In this paper, a complex molecular combinational logic circuit is designed to perform large-scale biological information processing by compound logic operation of addition, subtraction, multiplication and division. the design of compound logic operations of addition, subtraction, multiplication and division based on dna strand has four inputs signals and two output signals, and the dual-track design theory is used to perform the logic circuit operation, and the corresponding output result can be obtained in timely and accurately. the whole reaction progress of logic circuit operations can be programmed and simulated by the Visual DSD software. According to the simulation results of the Visual DSD software, the method of dna strand displacement is feasible to achieve more complex logic computations. this investigation for the addition, subtraction, multiplication and division complex logical operations of a binary number may have a great prospect for the development and application in the biological information processing, medicine diagnosis, molecular computing, and so on. © Springer Nature Singapore Pte Ltd. 2018.

关键词： Logic circuits

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the Circular dna Model of 0–1 programming Problem Based on dna Strand Displacement

The Circular DNA Model of 0–1 Programming Problem Based on ...

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international conference on Fuzzy Systems and Knowledge Discovery (FSKD)

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

ISBN: (纸本)9781538680988;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.

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Analog and Digital Memory in Living Cells 17

Analog and Digital Memory in Living Cells

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4th ACM international conference on Nanoscale computing and Communication (ACM NANOCOM)

作者： Farzadfard, Fahim Lu, Timothy K. Synthet Biol Grp Massachusetts Inst Technol Cambridge MA 02139 USA

ISBN: (纸本)9781450349314

the ability to dynamically manipulate information stored in a genome, in a targeted, controlled and recurring manner, confers the great potential to study and engineer living cells. Here, we review some of the recent advances in the development of dna writers, i.e., molecular devices that enable targeted editing of dna of living cells, and discuss some of the potential uses of these devices in studying and programming cellular phenotypes.

关键词： Synthetic biology analog memory digital memory dna writing dna memory

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Classification of Splice-Junction dna Sequences Using Multi-objective Genetic-Fuzzy Optimization Techniques 16th

Classification of Splice-Junction DNA Sequences Using Multi-...

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16th international conference on Artificial Intelligence and Soft computing (ICAISC)

作者： Gorzalczany, Marian B. Rudzinski, Filip Kielce Univ Technol Dept Elect & Comp Engn Al 1000 Lecia PP 7 PL-25314 Kielce Poland

ISBN: (纸本)9783319590639;9783319590622

the main goal of this paper is the application of our fuzzy rule-based classification technique with genetically optimized accuracy-interpretability trade-off to the classification of the splice-junction dna sequences coming from the molecular Biology (Splice-junction Gene Sequences) benchmark data set (available from the UCI repository). Two multi-objective evolutionary optimization algorithms are employed and compared in the framework of our technique, i.e., the well-known Strength Pareto Evolutionary Algorithm 2 (SPEA2) and our SPEA2's generalization (referred to as SPEA3) characterized by a higher spread and a better-balanced distribution of solutions. A comparative analysis with 15 alternative approaches is also performed.

关键词： Splice-junction dna sequence classification Fuzzy rule-based classifier Multi-objective evolutionary optimization Accuracy-interpretability trade-off optimization

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Design and Implementation of a Microfluidic Logic Gate Chip Based on Double-stranded dna 9

Design and Implementation of a Microfluidic Logic Gate Chip ...

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9th international conference on Intelligent Human-Machine Systems and Cybernetics (IHMSC)

作者： Wang, Jing Huang, Yourui Wang, Shibing Fuyang Normal Univ Sch Comp & Informat Engn Fuyang Peoples R China Anhui Univ Sci & Technol Inst Elect & Informat Engn Huainan Peoples R China

ISBN: (纸本)9781538630228

Since the traditional computer based on semiconductor technology is hard to meet people's requirements in information storage and processing, and the development of integrated circuit has been close to its technical limit, explore new calculation model to replace traditional electronic computing is extremely urgent. dna computing has gained significant research interest, the design of a biochip with dna computing as a carrier has become a key area in the development of a dna molecular computer. Logic operation is the basic function in computer operation system, therefore, the research of logic operation in dna computing system is the key to the realization of dna computing functions. In this study, logic AND and OR gates on microfluidic chip is developed by means of bio-reaction. this technology is combined with biochip and adopts PMMA (polymethylmecrylate) and PET (polyethylene terephthalate) to fabricate a microscale hybrid chip. Using a dna strand as an operand, realization of logic AND and OR operation on microfluidic chip is achieved by controlling the annealing of double-stranded dna. the computing results are rapidly and accurately obtained by detecting the presence of double-stranded dna in a solution by agarose gel electrophoresis. the microfluidic logic chip accurately realizes logic computations, and it provides a new way for the computation of dna computer.

关键词： Agarose gel electrophoresis dna computing logic gate microfluidic chip PMMA

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Towards Temporal Logic Computation Using dna Strand Displacement Reactions 16th

Towards Temporal Logic Computation Using DNA Strand Displace...

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16th international conference on Unconventional Computation and Natural Computation (UCNC)

作者： Lakin, Matthew R. Stefanovic, Darko Univ New Mexico Dept Chem & Biol Engn Albuquerque NM 87131 USA Univ New Mexico Dept Comp Sci Albuquerque NM 87131 USA Univ New Mexico Ctr Biomed Engn Albuquerque NM 87131 USA

ISBN: (纸本)9783319581873;9783319581866

Time-varying signals are ubiquitous throughout science, and studying the high-level temporal structure of such processes is of significant practical importance. In this context, techniques from computer science such as temporal logic are a powerful tool. Temporal logic allows one to describe temporal properties of time-varying processes, e.g., the order in which particular events occur. In this paper, we show that dna strand displacement reaction networks can be used to implement computations that check certain temporal relationships within time-varying input signals. A key aspect of this work is the development of dna circuits that incorporate a primitive memory, so that their behavior is influenced not just by the current observed chemical environment, but also by environments observed in the past. We formalize our circuit designs in the DSD programming language and use simulation results to confirm that they function as intended. this work opens up the possibility of developing dna circuits capable of long-term monitoring of processes such as cellular function, and points to possible designs of future dna circuits that can decide more sophisticated temporal logics.

关键词： Temporal logic

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Proceedings of the 4th ACM international conference on Nanoscale computing and Communication, NanoCom 2017

Proceedings of the 4th ACM International Conference on Nanos...

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4th ACM international conference on Nanoscale computing and Communication, NanoCom 2017

ISBN: (纸本)9781450349314

the proceedings contain 32 papers. the topics discussed include: received signal strength for randomly distributed molecular nanonodes;event and node identification from a single-pulse transmission in self-powered nanosensor networks;chemical reaction networks for maximum likelihood estimation of the concentration of signalling molecules;ratiometric logic in living cells via competitive binding of synthetic transcription factors;design principles of data converters for building large-scale gene networks in living cells;achieving in-phase synchronization in a diffusion-based nanonetwork with unknown propagation delay;increase detection algorithm for concentration-encoded diffusion-based molecular communication;simulation analysis of inter-symbol interference in diffusion-based molecular communication with non-absorbing receiver;a programming framework for neuromorphic systems with emerging technologies;brain-inspired computing accelerated by memristor technology;towards spiking neuromorphic system-on-a-chip with bio-plausible synapses using emerging devices;molecular communication with dna cellular storage system;prospects for the application of 2-dimensional materials to terahertz-band communications;and a folded wireless network-on-chip using graphene based thz-band antennas.

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Novel Method of Identifying dna Methylation Fingerprint of Acute Myeloid Leukaemia 11th

Novel Method of Identifying DNA Methylation Fingerprint of A...

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11th international conference on Practical Applications of Computational Biology and Bioinformatics (PACBB)

作者： Cecotka, Agnieszka Polanska, Joanna Silesian Tech Univ Inst Automat Control Fac Automat Control Elect & Comp Sci Data Min Grp Ul Akademicka 16 PL-44100 Gliwice Poland

ISBN: (纸本)9783319608167;9783319608150

Finding new statistical approaches to high throughput data analysis is a very hot topic nowadays. Such a data needs dedicated methods and algorithms of analysis due to huge number of features, but often also due to a small number of samples. Methylation data are also very special, because of dependencies between features and their neighbourhood. there is a need to find a novel, data driven algorithm for these data owing to big variety of distributions data sets. Purpose of this method is detection of regions with different levels of demethylation. From the biological point of view, the most important genome regions are TSS (transcription start site) regions. Hypermethylation of these part of a gene leads to repression and thus stop the gene expression. this phenomenon often happens in cancer disease and impairs a number of molecular processes in the cell. the proposed algorithm is performed for AML patients data in comparison to healthy control. By combination of statistics methods and mathematical modelling together, it enables detection of demethylated regions or dna and their classification as low, medium or high demethylated.

关键词： dna methylation Epigenetics Acute Myeloid Leukaemia Gaussian mixture model Mathematical modelling Robust estimator

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On a Parallel Algorithm for the Determination of Multiple Optimal Solutions for the LCSS Problem 16th

On a Parallel Algorithm for the Determination of Multiple Op...

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16th international conference on Algorithms and Architectures for Parallel Processing (ICA3PP)

作者： Ben Mabrouk, Bchira Hasni, Hamadi Mahjoub, Zaher Univ Tunis El Manar Fac Sci Tunis Univ CampusManar 2 Tunis 2092 Tunisia Higher Sch Technol & Comp Sci Charguia 2 Tunis 2035 Tunisia

ISBN: (纸本)9783319495835;9783319495828

For particular real world combinatorial optimization problems e.g. the longest common subsequence problem (LCSSP) from Bioinformatics, determining multiple optimal solutions (DMOS) is quite useful for experts. However, for large size problems, this may be too time consuming, thus the resort to parallel computing. We address here the parallelization of an algorithm for DMOS for the LCSSP. Considering the dynamic programming algorithm solving it, we derive a generic algorithm for DMOS (A-DMOS). Since the latter is a non perfect DO-loop nest, we adopt a three-step approach. the first consists in transforming the A-DMOS into a perfect nest. the second consists in choosing the granularity and the third carries out a dependency analysis in order to determine the type of each loop i.e. either parallel or serial. the practical performances of our approach are evaluated through experimentations achieved on input benchmarks and random dna sequences and targeting a parallel multicore machine.

关键词： Bioinformatics Combinatorial optimization problem Dependency analysis Dynamic programming Longest common subsequence Loop nest Multiple optimal solutions Multicore machine Parallelization Polyhedral algorithm

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