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Annual international conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： M.V. Olson Department of Molecular Biotechnology University of Washington Seattle DC USA

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Spiking dna neural trees with applications to conceptual design

Spiking DNA neural trees with applications to conceptual des...

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international conference on Computer Supported Cooperative Work in Design

作者： Xiyu Liu Hongyan Zhang School of Management and Economics Shandong Normal University Jinan Shandong China

this paper presents a design evaluation technique by dna neural trees. We propose a new dna tree computing model to represent a neural tree. the optimization of the neural tree is performed by the dna operations. this is a new technique different with other evolutionary optimization methods and scale well for large optimizations. Finally, we present an application framework in conceptual architectural design.

关键词： Vegetation dna Optimization Educational institutions Connectors Electron tubes Biochemistry

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Solid state dna polymer based molecular electronic/photonic structures

Solid state DNA polymer based molecular electronic/photonic ...

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Annual international conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： M.J. Heller E. Tu Nano-Tera Materials Inc.orporated San Diego CA USA

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Understanding the core of RNA interference: the dynamic aspects of Argonaute-mediated processes

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PROGRESS IN BIOPHYSICS & molecular BIOLOGY 2017年 128卷 39-46页

作者： Zhu, Lizhe Jiang, Hanlun Sheong, Fu Kit Cui, Xuefeng Wang, Yanli Gao, Xin Huang, Xuhui Hong Kong Univ Sci & Technol Dept Chem Kowloon Hong Kong Peoples R China Hong Kong Univ Sci & Technol Ctr Syst Biol & Human Hlth Kowloon Hong Kong Peoples R China Hong Kong Univ Sci & Technol Bioengn Grad Program Kowloon Hong Kong Peoples R China KAUST CBRC Comp Elect & Math Sci & Engn CEMSE Div Thuwal 23955 Saudi Arabia Chinese Acad Sci Inst Biophys Lab Noncoding RNA Beijing 100101 Peoples R China

At the core of RNA interference, the Argonaute proteins (Ago) load and utilize small guide nucleic acids to silence mRNAs or cleave foreign nucleic acids in a sequence specific manner. In recent years, based on extensive structural studies of Ago and its interaction with the nucleic acids, considerable progress has been made to reveal the dynamic aspects of various Ago-mediated processes. Here we review these novel insights into the guide-strand loading, duplex unwinding, and effects of seed mismatch, with a focus on two representative Agos, the human Ago 2 (hAgo2) and the bacterial thermus thermophilus Ago (TtAgo). In particular, comprehensive molecular simulation studies revealed that although sharing similar overall structures, the two Agos have vastly different conformational landscapes and guide-strand loading mechanisms because of the distinct rigidity of their Ll-PAZ hinge. Given the central role of the PAZ motions in regulating the exposure of the nucleic acid binding channel, these findings exemplify the importance of protein motions in distinguishing the overlapping, yet distinct, mechanisms of Ago mediated processes in different organisms. (C) 2016 Elsevier Ltd. All rights reserved.

关键词： Argonaute RNA interference Mechanism Kinetics Protein motions molecular dynamics simulation Protein-dna/RNA docking Markov-state-models Enhanced sampling

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Hierarchical Attention Network for Predicting dna-Protein Binding Sites 15th

Hierarchical Attention Network for Predicting DNA-Protein Bi...

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15th international conference on Intelligent computing, ICIC 2019

作者： Yu, Wenbo Yuan, Chang-An Qin, Xiao Huang, Zhi-Kai Shang, Li Institute of Machine Learning and Systems Biology School of Electronics and Information Engineering Tongji University Shanghai China Science Computing and Intelligent Information Processing of GuangXi Higher Education Key Laboratory Nanning Normal University NanningGuangxi China College of Mechanical and Electrical Engineering Nanchang Institute of Technology NanchangJiangxi330099 China Department of Communication Technology College of Electronic Information Engineering Suzhou Vocational University SuzhouJiangsu215104 China

ISBN: (纸本)9783030269685

Discovering dna-protein binding sites, also known as motif discovery, is the foundation for further analyses of transcription factors (TFs). Deep learning algorithms such as convolutional neural networks (CNN) and recurrent neural networks (RNN) are introduced to motif discovery task and have achieved state-of–art performance. However, these methods still have limitations such as neglecting the context information in large-scale sequencing data. thus, inspired by the similarity between dna sequence and human language, in this paper we propose a hierarchical attention network for predicting dna-protein binding sites which is based on a natural language processing method for document classification. the proposed method is tested on real ChIP-seq datasets and the experimental results show a considerable improvement compared with two well-tested deep learning-based sequence model, DeepBind and Deepsea. © 2019, Springer Nature Switzerland AG.

关键词： Transcription factors

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Research on the Application of dna Cryptography in Electronic Bidding System 14th

Research on the Application of DNA Cryptography in Electroni...

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14th international conference on Bio-inspired computing: theories and Applications, BIC-TA 2019

作者： Liu, Jianxia Jiao, Yangyang Wang, Yibo Li, Hongxuan Zhang, Xuncai Cui, Guangzhao School of Information Management Nanjing University Nanjing210000 China School of Economics and Management Wuhan University Wuhan430072 China School of Electrical and Information Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (纸本)9789811534140

With the rapid development of bidding market, a new type of bidding method-electronic bidding method has been widely used in the bidding market. this new-type of method is a program that the bidding is completed by graphics and textures. Generally, the electronic bidding provides doubles bidders with the data information of the transaction through the Internet. In this study we propose an information encryption and digital signature method based on dna cryptography which is combined with HASH function, symmetric encryption and asymmetric encryption comprehensively for the purpose of the information resources’ integrality, usability, security and reliability in the electronic bidding system. the results of the study show that our new method provides double guarantee for the bidding system under the role of symmetric encryption and asymmetric encryption used dna cryptography, and dna molecular encryption has the characteristics of electronic immunity, concealment, independent of mathematical problems, massive parallelism, etc. It provides a double guarantee for the bidding system. the security analysis results show that the algorithm can effectively protect the security and integrity of the bidder and bidder’s data information. © 2020, Springer Nature Singapore Pte Ltd.

关键词： dna

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Analysis of dna-Dimer Frequency in Retroviral Genomes with a Fuzzy Itemsets Pattern Induction Strategy

Analysis of DNA-Dimer Frequency in Retroviral Genomes with a...

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international conference on computing (CIC)

作者： R. Garza-Dominguez E. Bautista-thompson A. Quiroz-Gutierrez Centro de Tecnologías de Información UNACAR Mexico Facultad de Química UNACAR Mexico

Since dna dimer analysis has demonstrated to provide a much conserved pattern that has been suggested as a genome signature, we apply a strategy based on fuzzy sets theory and frequent itemsets pattern induction, for searching hidden structural relations in the dna-dimer frequency patterns of a collection of retrovirus genomes. We found an interesting differentiation between subsets of retroviruses, as well as some unexpected similarities in the context of the dna-dimer frequency patterns. We believe that identifying basic genomic patterns and connecting this information with other sources of information can give us new and important knowledge about how these patterns are related with the viral structure and its dynamics. the computational methodology presented in this paper has demonstrated to be a robust tool for the study and the analysis of genomic sequences

关键词： Pattern analysis Frequency Genomics Bioinformatics Itemsets dna Fuzzy set theory Joining processes Information resources Robustness

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Optimal design of dna coding based on multi-strategy JAYA algorithm

Optimal design of DNA coding based on multi-strategy JAYA al...

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international Workshop on Advanced Computational Intelligence (IWACI)

作者： Siwei Wang Donglin Zhu Xiao Wang School of Mathematics and Computer Science Zhejiang Normal University Jinhua China Xingzhi College Zhejiang Normal University Jinhua China

dna computing as a future method of computing, has been widely concerned by many scholars because of its high density, high parallelism and other characteristics, which have led to a significant improvement in the storage capacity and computational speed of dna computing, and the optimization problem of dna computing has remained a popular research area until now. this paper proposes an optimisation design for dna coding based on the improved JAYA algorithm, which incorporates saltation learning, lensing learning and the equalisation of random and Halton sequences to initialise populations, improving the standard JAYA algorithm’s shortcomings of strong randomness, uneven population distribution and insufficient inter-population communication, and cleverly balancing the convergence and population diversity of the algorithm, allowing the JAYA algorithm to be able to find better quality in the process of finding the best. the improved JAYA algorithm is proved to be highly practical through ablation study.

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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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Multiple sequence alignment a quick tour

Multiple sequence alignment a quick tour

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international conference on Advanced computing Technologies (ICACT)

作者： Radha Chintapalli Amit Kumar Laxminarayana Parayitam Research and Training Unit for Navigational Electronics Osmania University Hyderabad Andhra Pradesh India BIOAXIS DNA Research Center Hyderabad Andhra Pradesh India

Sequence alignment has a lot of significance in the field of bioinformatics. Since multiple sequence alignment (MSA) carries more information than pairwise alignment of the sequences, it has more number of applications. In the past few decades many algorithms and tools have been developed for the computation of multiple sequence alignment. However, accuracy of MSA still remains an open problem for further research. As more and more experimental data is being generated through sequencing technologies of second generation, there is an urgent need to develop tools that make use of integrative methods to derive biologically meaningful information from these immense data and use it to improve the accuracy of MSA. MSA tools that can scale upto the full length genome will also find wide applications in the near future.

关键词： Accuracy Hidden Markov models Probabilistic logic Heuristic algorithms Proteins Dynamic programming Matrices

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