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15th Annual international conference on Research in Computational molecular Biology

作者： Noble, William Duan, Zhi-jun Andronescu, Mirela Schutz, Kevin McIlwain, Sean Kim, Yoo Jung Lee, Choli Shendure, Jay Fields, Stanley Blau, C. Anthony Univ Washington Seattle WA 98195 USA

ISBN: (纸本)9783642200359

Layered on top of information conveyed by dna sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes. Interphase chromosomes are not positioned randomly within the nucleus, but instead adopt preferred conformations. Disparate dna elements co-localize into functionally defined aggregates or factories for transcription and dna replication. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. the map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between dna sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among transfer RNA genes, among origins of early dna replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome.

关键词： dna sequences

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A Hardware-Software Codesign Approach to Identity, Trust, and Resilience for IoT/CPS at Scale 12

A Hardware-Software Codesign Approach to Identity, Trust, an...

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IEEE Int Congr on Cybermat / 12th IEEE Int Conf on Cyber, Phys and Social Comp (CPSCom) / 15th IEEE Int Conf on Green computing and Communications (GreenCom) / 12th IEEE Int Conf on Internet of things (ithings) / 5th IEEE Int Conf on Smart Data

作者： Kandah, Farah Cancelleri, Joseph Reising, Donald Altarawneh, Amani Skjellum, Anthony Univ Tennessee Comp Sci & Engn Chattanooga TN 37403 USA Univ Tennessee Elect Engn Chattanooga TN USA Univ Tennessee SimCtr Chattanooga TN USA

ISBN: (纸本)9781728129808

Advancement in communication technologies and the Internet of things (IoT) is driving adoption in smart cities that aims to increase operational efficiency and improve the quality of services and citizen welfare, among other potential benefits. the privacy, reliability, and integrity of communications must be ensured so that actions can be appropriate, safe, accurate, and implemented promptly after receiving actionable information. In this work, we present a multi-tier methodology consisting of an authentication and trust-building/distribution framework designed to ensure the safety and validity of the information exchanged in the system. Blockchain protocols and Radio Frequency-Distinct Native Attributes (RF-dna) combine to provide a hardware-software codesigned system for enhanced device identity and overall system trustworthiness. Our threat model accounts for counterfeiting, breakout fraud, and bad mouthing of one entity by others. Entity trust (e.g., IoT devices) depends on quality and level of participation, quality of messages, lifetime of a given entity in the system, and the number of known "bad" (non-consensus) messages sent by that entity. Based on this approach to trust, we are able to adjust trust upward and downward as a function of real-time and past behavior, providing other participants with a trust value upon which to judge information from and interactions with the given entity. this approach thereby reduces the potential for manipulation of an IoT system by a bad or byzantine actor.

关键词： IoT RF-dna fingerprinting Trust management Blockchain

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Predicting TF-dna Binding Motifs from ChIP-seq Datasets Using the Bag-Based Classifier Combined With a Multi-Fold Learning Scheme

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021年第5期18卷 1743-1751页

作者： Zhang, Qinhu Wang, Dailun Han, Kyungsook Huang, De-Shuang Tongji Univ Sch Life Sci & Technol Siping Rd 1239 Shanghai 200092 Peoples R China Tongji Univ Sch Elect & Informat Engn Inst Machine Learning & Syst Biol 4800 Caoan Rd Shanghai 201804 Peoples R China Inha Univ Sch Comp Sci & Engn Incheon 21000 South Korea

the rapid development of high-throughput sequencing technology provides unique opportunities for studying of transcription factor binding sites, but also brings new computational challenges. Recently, a series of discriminative motif discovery (DMD) methods have been proposed and offer promising solutions for addressing these challenges. However, because of the huge computation cost, most of them have to choose approximate schemes that either sacrifice the accuracy of motif representation or tune motif parameter indirectly. In this paper, we propose a bag-based classifier combined with a multi-fold learning scheme (BCMF) to discover motifs from ChIP-seq datasets. First, BCMF formulates input sequences as a labeled bag naturally. then, a bag-based classifier, combining with a bag feature extracting strategy, is applied to construct the objective function, and a multi-fold learning scheme is used to solve it. Compared with the existing DMD tools, BCMF features three improvements: 1) Learning position weight matrix (PWM) directly in a continuous space;2) Proposing to represent a positive bag with a feature fused by its k "most positive" patterns. 3) Applying a more advanced learning scheme. the experimental results on 134 ChIP-seq datasets show that BCMF substantially outperforms existing DMD methods (including DREME, HOMER, XXmotif, motifRG, EDCOD and our previous work).

关键词： Tools Feature extraction dna Training Sequential analysis In vivo Color Discriminative motif discovery ChIP-seq bag-based classifier multi-fold learning

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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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Configuration-level optimization of RPC-based distributed programs

Configuration-level optimization of RPC-based distributed pr...

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international conference on Distributed computing Systems

作者： Tae-Hyung Kim J.M. Purtilo Computer Science Department University of Maryland College Park MD USA

Many strategies for improving performance of distributed programs can be described abstractly in terms of an application's overall configuration. But previously those techniques would need to be implemented manually, and the resulting programs, though yielding good performance, are more expensive to build and much less easy to reuse. this paper describes research towards an automatic system for introducing performance improvement techniques based upon an application's configuration description.

关键词： programming profession Sequences Writing Computer languages Computer science Educational institutions Functional programming Costs Employment dna

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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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Solving generic decision problems by in-message computation in dna-based molecular nanonetworks 15th

Solving generic decision problems by in-message computation ...

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15th international conference on Body Area Networks, BodyNets 2020

作者： Lau, Florian-Lennert Adrian Wendt, Regine Fischer, Stefan Institute of Telematics Ratzeburger Allee 160 Lübeck23562 Germany

ISBN: (纸本)9783030649906

One of the biggest unsolved problems in nanonetwork research is the actual construction of the components required for building such networks. Most existing ideas are limited to partial solutions of construction of nanodevices, computation within them, and communication between them. While many ideas are promising, the problem remains how to combine those various building blocks into operational and efficient nanonetworks. In this paper we use dna as the basic building block for all components of nanonetworks. the inherent properties of this molecule are used to assemble complex nanostructures. dna can be utilized to create both nanodevices and a communication mechanism. Properly designed dna-molecules can even be utilized for computational purposes. In summary, dna forms the base for an exhaustive nanonetwork concept. this work specifically presents an approach how to solve arbitrary mathematical problems that can be modeled as boolean formulas using dna-based nanonetworks by in-message computation. the computation itself is encoded in the assembly process of a message. this avoids often-stated space constraints for computations at the nanoscale, as the medium of transportation is commonly less constrained than the size of nanodevices dictates. this method thereby presents a constructive approach on how to actually create message molecules, rather than only proving the general possibility. © ICST Institute for Computer Sciences, Social Informatics and Telecommunications Engineering 2020.

关键词： Nanostructures

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Electrical molecular focusing for laser induced fluorescence based single dna detection

Electrical molecular focusing for laser induced fluorescence...

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15th IEEE international conference on Micro Electro Mechanical Systems MEMS 2002

作者： Wang, Tza-Huei Wong, Pak Kin Ho, Chih-Ming Mechanical and Aerospace Engineering Univ. of California Los Angeles Los Angeles CA United States

this paper details an electrokinetic focusing technique that significantly enhances the detection efficiency for laser induced fluorescence (LIF) based molecular sensing by concentrating fluorescence labeled molecules in a tiny probe region. 3-D electrodes were fabricated to generate wider and denser electric fields toward the probe region in the microchannel. the generated electric field is able to focus flowing dna molecules to widths as narrow as 3 μm in a 120 μm wide channel. A single molecule detection technique is developed and the enhancement of detection efficiency by using the focusing method is demonstrated.

关键词： Microelectrodes

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three-Variable Chaotic Oscillatory System Based on dna Chemical Reaction Networks 15th

Three-Variable Chaotic Oscillatory System Based on DNA Chemi...

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15th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2020

作者： Ji, Haoping Yang, Yuli Chen, Xiangwei Wang, Yanfeng Henan Key Lab of Information-Based Electrical Appliances Zhengzhou University of Light Industry Zhenzhou450002 China School of Electrical and Information Engineering Zhengzhou University of Light Industry Zhenzhou450002 China

ISBN: (纸本)9789811613531

dna strand displacement reactions as a new type of nanotechnology have great potential in the constructions of circuits. the classical step signal is realized by dna chemical reaction networks (CRNs) in the previous work. Up to now, few works have been done to realize chaotic system through dna CRNs. In this paper, a three-variable chaotic oscillatory system is proposed by dna CRNs. the chaotic system CRNs is made up of multiplication modules, combination modules and degradation modules, then chemical reaction equations are compiled into a three-variable chaotic oscillatory system by the law of mass action. the simulations are given to show our dna CRNs can generate chaotic oscillatory signals. © 2021, Springer Nature Singapore Pte Ltd.

关键词： dna

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Design of Blood Group Pairing Logic Circuit Based on dna Strand Displacement 15th

Design of Blood Group Pairing Logic Circuit Based on DNA Str...

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15th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2020

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

ISBN: (纸本)9789811613531

dna strand displacement provides an effective approach to construct complex nano logic circuits. In this work, a blood group pairing logic circuit with dna materials is designed to complete the function of blood group pairing. First, threshold gate, amplifier gate, fan-out gate and report gate are constructed on the basis of the reaction mechanism of dna strand displacement, and then the basic computing modules of logic AND and OR are formed. In order to make any digital logic circuit translate into a dual-rail digital circuit with dual-rail strategy conveniently, the universal math model of a dual-rail digital circuit is proposed. Next, with fluorescence labeling technology, the dual-rail digital circuit of blood group pairing is converted into the dna biochemical logic circuit consisting of fan-out gates, report gates, logic AND and OR gates. the simulation results are obtained by Visual DSD, which shows that the proposed dna-circuit is stable, effective, and highly sensitive for blood type signals. the method of constructing blood group pairing nano logic circuit proposed in this paper also greatly reduces the difficulty of experimental operation compared with the dna assembly technology for the same logic function, which can be applied to nano medicine diagnosis and large scale nano logical circuits in the future. © 2021, Springer Nature Singapore Pte Ltd.

关键词： Logic circuits

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