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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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A circuit simplification mechanism based on dna combinatorial strands displacement 12th

A circuit simplification mechanism based on DNA combinatoria...

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12th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2017

作者： Zhang, Xuncai Han, Feng Wang, Yanfeng College of Electrical and Electronic Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (纸本)9789811071782

through extensive application of dna strand displacement technology in the field of molecular computing, we know that the dna strand of the toehold domain and the branch migration domain are covalently connected to form logical gates in traditional dna strand displacement circuits. In this paper, we will adopt a composite strand mechanism that the toehold domain and branch migration domain in different single strand form displacing complex, and construct logical gates with combinatorial strand displacement mechanism. After that, a logic gate model is constructed, and the mechanism is verified by the design and simulation of the logical molecular model of the encoder. When the dna signal strand is input, the signal strand molecule can be output by combination of molecular specific hybridization reaction and intermolecular strand displacement reaction. the results of Visual DSD simulation show the feasibility and accuracy of the encoder logic calculation model designed in this article. © Springer Nature Singapore Pte Ltd 2017.

关键词： Timing circuits

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the logic circuit design of fire alarm system device by dna strand displacement 12th

The logic circuit design of fire alarm system device by DNA ...

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12th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2017

作者： Wang, Yanfeng Li, Jixiang Huang, Chun Sun, Junwei Henan Key Lab of Information-Based Electrical Appliances Zhengzhou University of Light Industry Zhengzhou450002 China College of Electrical and Electronic Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (纸本)9789811071782

dna strand displacement acted as a useful tool is most widely used in the majority computing system. In this paper, a four-input fire alarm system device based on dna strand displacement is designed. the whole reaction course is programmed and simulated in the software visual DSD, which presenting the superb simulation results with inputs and outputs through compiling the procedure for computation device. According to the results of the Visual DSD software, the method of dna strand displacement by dual-rail circuits is feasible to achieve more complex logic computation. this investigation on the basis of dna strand displacement by dual-rail circuits may have a great prospect for the development and application in the biological information processing, molecular computing, and so on. © Springer Nature Singapore Pte Ltd 2017.

关键词： Timing circuits

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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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A fast exact sequential algorithm for the partial digest problem

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BMC BIOINFORMATICS 2016年第SUPPL 19期17卷 139-148页

作者： Abbas, Mostafa M. Bahig, Hazem M. Hamad Bin Khalifa Univ Qatar Comp Res Inst Doha Qatar Ain Shams Univ Fac Sci Dept Math Div Comp Sci Cairo 11566 Egypt

Background: Restriction site analysis involves determining the locations of restriction sites after the process of digestion by reconstructing their positions based on the lengths of the cut dna. Using different reaction times with a single enzyme to cut dna is a technique known as a partial digestion. Determining the exact locations of restriction sites following a partial digestion is challenging due to the computational time required even with the best known practical algorithm. Results: In this paper, we introduce an efficient algorithm to find the exact solution for the partial digest problem. the algorithm is able to find all possible solutions for the input and works by traversing the solution tree with a breadth-first search in two stages and deleting all repeated subproblems. Two types of simulated data, random and Zhang, are used to measure the efficiency of the algorithm. We also apply the algorithm to real data for the Luciferase gene and the E. coli K12 genome. Conclusion: Our algorithm is a fast tool to find the exact solution for the partial digest problem. the percentage of improvement is more than 75% over the best known practical algorithm for the worst case. For large numbers of inputs, our algorithm is able to solve the problem in a suitable time, while the best known practical algorithm is unable.

关键词： Restriction site analysis Digestion process Partial digest problem dna Bioinformatics algorithm Breadth first search

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Self-assembling adaptive structures with dna 15th

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15th international conference on Unconventional Computation and Natural Computation, UCNC 2016

作者： Schulman, Rebecca Chemical and Biomolecular Engineering and Computer Science Johns Hopkins University United States

ISBN: (纸本)9783319413112

How could we program the self-assembly of a something as complex as an animal or a human being? From a strictly organizational point of view, self-assembly of such a structure would require organization across scales ranging from the angstrom scale to the meter scale. At the smallest size scales, it is possible to directly encode structure using a molecular sequence or set of sequences such that each unit of the structure is encoded by a specific molecular unit. But at larger size scales new mechanisms for organization are required. One general emerging principle of organization at these scales is that molecules encode a self-assembly process in which the final structure is functional but its shape can vary from one incarnation to the next. I’ll describe how we might phrase such a problem of "adaptive" or "self-adjusting" self-assembly as a computational question and how we might implement such processes using molecules such as dna. As a case study of adaptive materials, we will consider networks formed from one-dimensional structures and junctions. Such networks exist across all size scales: networks of wires and devices form circuits, beams and joints form buildings. In biological systems, networks of axons, dendrites and neuronal cell bodies make up the brain and filaments such as actin and organizing proteins make up the cytoskeleton. I’ll describe how we can consider how local programmable rules could be used to form such complex structures and how we could program many of these rules using interactions between dna molecules. © Springer international Publishing Switzerland 2016.

关键词： dna

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Finding a disease-related gene from microarray data using random forest

Finding a disease-related gene from microarray data using ra...

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IEEE international conference on Cognitive Informatics

作者： Kazutaka Nishiwaki Katsutoshi Kanamori Hayato Ohwada Department of Industrial Administration Tokyo University of Science Chiba Japan

ISBN: (纸本)9781509038473

Numerous databases of dna-microarrays are now widely available on the internet. Recently, there has been increasing interest in the analysis of microarray data using machine-learning techniques due to the amount of data, which is too massive for researchers to analyze using conventional techniques. In this study, we propose a method of finding a disease-related gene from microarray data using random forest, a machine-learning technique. More specifically, we focused on Alzheimer's disease and used microarray data related to Alzheimer's disease in the experiments. In the result, we found some genes that are believed to be related to Alzheimer's disease. Some genes discovered in the result have been investigated for their relevance to Alzheimer's disease, and this proves that our proposed methodology was successful in finding disease-related genes using microarray data. In addition, the proposed methodology is useful in providing new knowledge for biologists, medical scientists, and cognitive computing researchers since there is no previous work on genes that focused on finding a disease-related gene for Alzheimer's disease.

关键词： Gene expression Alzheimer's disease dna Support vector machines Decision support systems Internet

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A Formal Language Model of dna Polymerase Enzymatic Activity

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FUNDAMENTA INFORMATICAE 2015年第1-2期138卷 179-192页

作者： Enaganti, Srujan Kumar Kari, Lila Kopecki, Steffen Univ Western Ontario Dept Comp Sci London ON N6A 5B7 Canada

We propose and investigate a formal language operation inspired by the naturally occurring phenomenon of dna primer extension by a dna-template-directed dna Polymerase enzyme. Given two dna strings u and v, where the shorter string v (called primer) is Watson-Crick complementary and can thus bind to a substring of the longer string u (called template) the result of the primer extension is a dna string that is complementary to a suffix of the template which starts at the binding position of the primer. the operation of dna primer extension can be abstracted as a binary operation on two formal languages: a template language L-1 and a primer language L-2. We call this language operation L-1 - directed extension of L-2 and study the closure properties of various language classes, including the classes in the Chomsky hierarchy, under directed extension. Furthermore, we answer the question under what conditions can a given language of target strings be generated from a given template language when the primer language is unknown. We use the canonic inverse of directed extension in order to obtain the optimal solution (the minimal primer language) to this question.

关键词： FORMAL languages dna primers dna polymerases ENZYME kinetics BINARY system (Mathematics)

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dna and (Mandarin): Bringing introductory programming to the Life Sciences and Digital Humanities

DNA and (Mandarin): Bringing introductory programming to the...

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15th Annual international conference on Computational Science (ICCS)

作者： LeBlanc, Mark D. Drout, Michael D. C. Wheaton Coll Comp Sci Norton MA 02766 USA Wheaton Coll English Norton MA 02766 USA

the ability to write software (to script, to program, to code) is a vital skill for students and their future data-centric, multidisciplinary careers. We present a ten-year effort to teach introductory programming skills in domain-focused courses to students across divisions in our liberal arts college. By creatively working with colleagues in Biology, Statistics, and now English, we have designed, modified, and offered six iterations of two courses: "dna" and "computing for Poets". Larger percentages of women have consistently enrolled in these two courses vs. the traditional first course in the major. We share our open source course materials and present here our use of a blended learning classroom that leverages the increasing quality of online video lectures and programming practice sites in an attempt to maximize faculty-student interactions in class.

关键词： programming interdisciplinary multidisciplinary genomics bioinformatics digital humanities blended learning

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An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target dna

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BMC GENOMICS 2016年第Sup13期17卷 1033-1033页

作者： Dutta, Shayoni Madan, Spandan Parikh, Harsh Sundar, Durai Indian Inst Technol Delhi Dept Biochem Engn & Biotechnol DBT AIST Int Lab Adv Biomed DAILAB New Delhi 110016 India Indian Inst Technol Delhi Dept Comp Sci & Engn New Delhi 110016 India

Background: the ability to engineer zinc finger proteins binding to a dna sequence of choice is essential for targeted genome editing to be possible. Experimental techniques and molecular docking have been successful in predicting protein-dna interactions, however, they are highly time and resource intensive. Here, we present a novel algorithm designed for high throughput prediction of optimal zinc finger protein for 9 bp dna sequences of choice. In accordance with the principles of information theory, a subset identified by using K-means clustering was used as a representative for the space of all possible 9 bp dna sequences. the modeling and simulation results assuming synergistic mode of binding obtained from this subset were used to train an ensemble micro neural network. Synergistic mode of binding is the closest to the dna-protein binding seen in nature, and gives much higher quality predictions, while the time and resources increase exponentially in the trade off. Our algorithm is inspired from an ensemble machine learning approach, and incorporates the predictions made by 100 parallel neural networks, each with a different hidden layer architecture designed to pick up different features from the training dataset to predict optimal zinc finger proteins for any 9 bp target dna. Results: the model gave an accuracy of an average 83% sequence identity for the testing dataset. the BLAST e-value are well within the statistical confidence interval of E-05 for 100% of the testing samples. the geometric mean and median value for the BLAST e-values were found to be 1.70E-12 and 7.00E-12 respectively. For final validation of approach, we compared our predictions against optimal ZFPs reported in literature for a set of experimentally studied dna sequences. the accuracy, as measured by the average string identity between our predictions and the optimal zinc finger protein reported in literature for a 9 bp dna target was found to be as high as 81% for dna targets with a co

关键词： Zinc finger proteins Neural network Statistical sampling Targeted genome editing Domain adaptation

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