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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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Fabrication of a Carbon Chain Based Nanosensor for Maximizing Spatial Resolution in dna Sequencing 15

Fabrication of a Carbon Chain Based Nanosensor for Maximizin...

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IEEE 15th international conference on Nano/Micro Engineered and molecular System (NEMS)

作者： Ma, Bo Tung, Steve Univ Arkansas Dept Mech Engn Fayetteville AR 72701 USA

ISBN: (纸本)9781728172309

Using a carbon chain as the sensing element can significantly improve the spatial resolution in nanodevice based single molecule dna sequencing. In this report, we demonstrate a top-down approach to reduce a single monolayer graphene attached to a silicon microelectrode chip to a sub-nanometer wide carbon chain suitable for dna sequencing. this approach consists three major processing steps to first transfer the graphene to the chip, dice the attached graphene into graphene nanoribbons using Focused Ion Beam (FIB), and finally reduce the ribbon width by knocking off carbon atoms on the ribbon edge using Transmission Electron Microscopy (TEM). A final carbon chain of 0.8 nm wide and 5 nm long is accomplished. the measured electrical properties of the reduced graphene agree well with previous studies.

关键词： Graphene

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dna destruction under the influence of VUV radiation 15

DNA destruction under the influence of VUV radiation

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15th international conference on Pulsed Lasers and Laser Applications

作者： Zvereva, G.N. Kirtsidely, I. Yu. MacHs, E.M. State University of Civil Aviation Pilotov str.-38 St. Petersburg196210 Russia Botanical Institute Professor Popov str.-2 St. Petersburg197376 Russia

ISBN: (数字)9781510650497

ISBN: (纸本)9781510650480

In the work were investigated the effect of vacuum ultraviolet (VUV) radiation (λ=147 nm, 173 nm) on the dna of microscopic fungi spores of the species Rhodotorula colostri, Aurobasidium pullulans (colored and uncolored types), Cladosporium herbarum containing different types of protective pigments. the dna molecules inside the spores (in vivo) and isolated from them (in vitro) were irradiated. the results of electrophoresis showed, that VUV irradiation leads to the appearance of light dna fragments with sizes 100-750 base pairs, as well as high molecular weight fragments containing more than 20 000 base pairs. the greatest features were observed during the irradiation of Rhodotorula colostri dna: 1) were formed longer fragments (100-750 base pairs);2) at λ=172 nm threshold effect was observed: dna destruction appeared starting from radiation energies of 35 mJ/cm2 during in vivo irradiation and, starting from radiation energies of 20 mJ/cm2, during in vitro irradiation;2) when irradiated at the wavelength λ=147 nm, the relative destruction of dna increased, while for other types of the spores it fell. these features can be explained by the presence in Rhodotorula colostri spores of carotene capable of exercising both the properties of the antioxidant and to produce reactive radicals. When irradiated at a wavelength of λ=173 nm in vivo and in vitro, each type of spore had the same characteristic features, which may indicate a small effect on dna of free water molecules photolysis products. When irradiated at the wavelength λ=147 nm, the influence of melanin was observed: in melanin containing spores the results in vivo and in vitro exposure had the same characteristic features, in the spores without melanin- differed. In the first case, this can be explained by a smaller concentration of reactive radicals due to VUV radiation absorption by melanin, in the second - participation in the dna destruction of free water molecules photolysis products. A common feature of th

关键词： Melanin

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

15th International Conference on Bio-Inspired Computing: The...

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

ISBN: (纸本)9789811613531

the proceedings contain 43 papers. the special focus in this conference is on Bio-Inspired computing: theories and Applications. the topics include: three-Variable Chaotic Oscillatory System Based on dna Chemical Reaction Networks;reversible Spiking Neural P Systems with Anti-spikes;multi-Objective Algorithm Based on Tissue P System for Solving Tri-objective Grain Dispatching and Transportation;A Multi-objective Algorithm Based on M-MOEA/D Algorithm and Tissue-Like P System for Solving Bi-objective Grain Dispatching and Transportation;short Text Similarity Calculation Based on Jaccard and Semantic Mixture;cell-Like P Systems with Request Rules and Rules Production/Removal;an Editable k-Nearest Neighbor Classifier Based on Tissue-Like P Systems;solving Urban Light Rail Route Planning Based on Probe Machine;cortical Neural P Systems;density-Based Population Initialization Strategy for Continuous Optimization;intelligent Prediction and Optimization of Extraction Process Parameters for Paper-Making Reconstituted Tobacco;point Cloud Registration Using Evolutionary Algorithm;heterogeneous Distributed Flow Shop Scheduling and Reentrant Hybrid Flow Shop Scheduling in Seamless Steel Tube Manufacturing;hyperchaotic Encryption Algorithm Based on Joseph Traversal and Bit Plane Reconstruction;preface;wingsuit Flying Search Enhanced by Spherical Evolution;trimmed Data-Driven Evolutionary Optimization Using Selective Surrogate Ensembles;research and Application of the Standard Formulation Technology for three Kinds of Specialized Raw Materials;a Hybrid Harmony Search Algorithm Based on Data Analysis to Solve Multi-objective Grain Transportation Problem;chicken Swarm Optimization Algorithm Based on Hybrid Improvement Strategy;a Data-Driven Model Analysis Method in Optimizing Raw Materials Standard for Glutinous Rice Products;incorporating the Confusion Effect into the Simulated Evolution of Crowded Selfish Herds.

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Predicting Locus-Specific dna Methylation Based on Deep Neural Network 15th

Predicting Locus-Specific DNA Methylation Based on Deep Neur...

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

作者： Ma, Baoshan Dong, Jiaxin Zhang, Shuzheng Yan, Haowen Pan, Jianqiao Li, Chongyang Liu, Guanghui Gao, Zongjiang Zhang, Xinyu College of Information Science and Technology Dalian Maritime University Dalian116026 China Dahua Technology Co. Ltd. Hangzhou310051 China Maritime Intelligent Transportation Research Group Dalian Maritime University Dalian116026 China

ISBN: (纸本)9789811613531

the next generation sequencing technologies have enabled dna methylation levels to be assayed at single-base resolution in the whole genome, but this method is relatively expensive. At present, many traditional machine-learning methods have been actively proposed for predicting dna methylation status, but the prediction accuracy of various models needs to be enhanced because they cannot fully extract important feature information. therefore, the prediction method of dna methylation based on state-of-the-art model is still a challenging topic. In the paper, we developed a deep-learning-based framework to address the issue by integrating a deep neural network (DNN) with random forest (RF). Initially, the DNN extracted potential and highly representative features from neighboring formation, genomic position, dna sequence properties and cis-regulatory element information with its unsupervised learning process and multi-layer structure. Furthermore, we systematically evaluated and compared prediction performance using each kind of feature of dna methylation and their combinations. Ultimately, the extracted dna methylation features were combined with the standardized features to train the RF model and further enhance the prediction accuracy. the results showed the proposed method achieved an accuracy of 92.2% and Area Under Curve of 0.97, and outperformed the existing deep-learning-based methods. In summary, our study could contribute to providing a potential framework for the application of deep learning in dna methylation prediction. © 2021, Springer Nature Singapore Pte Ltd.

关键词： Forecasting

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A Low-drift Extended-Gate Field Effect Transistor (EGFET) with Differential Amplifier for Cordyceps Sinensis dna Detection Optimized by gm/ID theory 15

A Low-drift Extended-Gate Field Effect Transistor (EGFET) wi...

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15th IEEE international conference on Nano/Micro Engineered and molecular System, NEMS 2020

作者： Xu, Yifan Tavakkoli, Hadi Xu, Jingting Lee, Yi-Kuen Hong Kong University of Science and Technology Department of Chemical and Biological Engineering China

ISBN: (纸本)9781728172309

An extended-gate field effect transistor (EGFET) integrated with a differential MOSFET amplifier and an open-source Arduino Yun MCU system was realized for detection of Cordyceps Sinensis dna molecules. A gold microelectrode chip coated with a single-stranded dna probe, as the extended gate was fabricated by MEMS fabrication processes. the differential MOSFET amplifier and additional coating of alkyl-thiol reduced the drifting by one order of magnitude. Moreover, generalized gm/ID theory was used to study the optimized working regime of the EGFET sensor. the highest electric-electrochemical sensitivity could be achieved in the Moderate Inversion (MI) regime. the sensitivity and limit of detection (LOD) of the EGFET sensor were obtained to be 13.85mV/dec and 10nM, respectively. this low-cost low-drift EGFET sensor system is promising for Internet of Living things in the near future. © 2020 IEEE.

关键词： dna

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dna Sequence Alignment Using Dynamic programming 3rd

DNA Sequence Alignment Using Dynamic Programming

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3rd international conference on Intelligent computing and Communication (ICICC)

作者： Singh, Niharika Rajput, Gaurav Dixit, Yash Sehgal, Aastha Univ Petr & Energy Studies Sch CS Dehra Dun Uttarakhand India GL Bajaj Inst Technol & Management Dept CS&E Greater Noida Utter Pradesh India UPES Sch Comp Sci Dept Informat Dehra Dun Uttarakhand India

ISBN: (纸本)9789811510847;9789811510830

In today's time, molecular Science is increasingly dependent on Software Engineering Calculations in the department of Research and Development. Aligning sequences of dna, RNA is becoming a major part of present-day natural sciences. A hereditary database holds a large amount of unprocessed data that resides very crucial information. A single pair of chromosomes contains approximately 3 billion dna base pairs. To look through this information, retrieve the connections, and subconnections in it is a very slow procedure. therefore, scientists are looking forward toward computer science algorithms for faster retrieval of information. this paper is focused upon using a parallel programming algorithm than the previous alignment algorithms.

关键词： dna Genetics Parallel algorithms thread

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Research on dna Cryptosystem Based on dna computing 14th

Research on DNA Cryptosystem Based on DNA Computing

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

作者： Cui, Shuang Peng, Weiping Song, Cheng School of Computer Science and Technology Henan Polytechnic University Jiaozuo454002 China

ISBN: (纸本)9789811534140

As a new type of cryptography, dna cryptography generally uses dna molecule as the information carrier and biological technology as the implementation tool. Due to its prominent advantages such as large storage capacity, high parallel computing, low energy consumption and abundant resources in nature, dna cryptography has attracted wide attention. dna cryptography involves biology, computer, mathematics and other disciplines. On the basis of the traditional cryptosystems, dna molecular computing methods are combined to form a more reliable and stable new cryptosystems, which brings opportunities and challenges to the modern cryptosystems. this paper depicts several dna cryptosystems, further analyzes the security and performance of these schemes, summarizes the shortcomings of current dna cryptography research, and looks forward to its development prospect in the field of information security. © 2020, Springer Nature Singapore Pte Ltd.

关键词： dna

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15th international conference on Body Area Networks, BodyNets 2020

15th International Conference on Body Area Networks, BodyNet...

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15th international conference on Body Area Networks, BodyNets 2020

ISBN: (纸本)9783030649906

the proceedings contain 15 papers. the special focus in this conference is on Body Area Networks. the topics include: Activity monitoring using smart glasses: Exploring the feasibility of pedometry on head mounted displays;real-time human activity recognition using textile-based sensors;extraction of respiratory signals and respiratory rates from the photoplethysmogram;an ultra-low-power integrated heartbeat detector for wearable sensors;anxiety detection leveraging mobile passive sensing;On the UWB in-body propagation measurements using pork meat;detection of brain hemorrhage in white matter using analysis of radio channel characteristics;UWB microwave imaging for inclusions detection: Methodology for comparing artefact removal algorithms;BSNCloud: Cloud-centered wireless body sensor data collection, streaming, and analytics system;model-based analysis of secure and patient-dependent pacemaker monitoring system;amplitude modulation in a molecular communication testbed with superparamagnetic iron oxide nanoparticles and a micropump;An enhanced dna sequence table for improved security and reduced computational complexity of dna cryptography;Solving generic decision problems by in-message computation in dna-based molecular nanonetworks.

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