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international Workshop on Advanced Computational Intelligence (IWACI)

作者： Huaiyu Guo Zhiyu Feng Xiao Wang School of Computer Science and Math Zhejiang Normal University Jinhua China Xingzhi College Zhejiang Normal University Jinhua China

High stable and high reliable dna sequences are requisite in dna computing search field. dna sequences can be quantified in an array of thermodynamical and logical constraints which play an important role in process of hybridization. Since designing of dna sequences set regraded as a multi-objective optimization problem due to these constraints, epsilon constraint introduced in this paper which is a thought of reduce object dimensions. these constraints can be classified in single squence constraints and multiple sequences constraints, two meta heuristic algorithms tunicate swarm algorithm and grasshopper optimisation algorithm used in different steps according to their features and applicable scenarios. Result of this progress shows that epsilon constraints collaborate with other algorithms may produce advanced dna sequences set compare to previous work.

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FLR: A Revolutionary Alignment-Free Similarity Analysis Methodology for dna-Sequences

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021年第5期18卷 1924-1936页

作者： Medhat, Belal Shawish, Ahmed British Univ Egypt Dept Comp Sci Fac Informat & Comp Sci Cairo 11837 Egypt German Univ Cairo Dept Comp Sci Fac Media Engn & Technol Cairo 11837 Egypt Arab Open Univ Fac Comp Studies Headquarters Kuwait Kuwait Ain Shams Univ Fac Comp & Informat Sci Cairo 11566 Egypt

this paper introduces a novel alignment-free sequence analysis methodology. Its main idea is based on introducing a new representation of the dna-Sequence. this representation breaks the dependency between the dna bases that exist in the traditional string presentation. We called it the Four-Lists-Representation (FLR). Based on the FLR, a series of revolutionary algorithms for searching, map-discovery, similarity-score analysis, and similarity-visualization have been developed. they are combined in what we call the FLR Methodology. the paper also studies most of the available similarity analysis techniques in a comprehensive state-of-art review. the conducted extensive simulation and theoretical studies confirm the outperformance of the whole set of FLR-based algorithms in terms of speed and memory consumption in comparison to a long list of available similarity analysis algorithms. the ability to provide a similarity-map, similarity-score, and similarity-graph as a set of evidence-based rationales makes the quality of results provided by the proposed methodology presents a new edge in this field and promises a new area of genome-based research.

关键词： dna Sequences Genomics Bioinformatics Acceleration Organisms Diseases Sequence analysis similarity-score similarity analysis similarity measurements FLR alignment-free sequence analysis

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Lossy Compression of Quality Values in Sequencing Data

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021年第5期18卷 1958-1969页

作者： Morales, Veronica Suaste Houghten, Sheridan CONABIO Mexico City 14010 DF Mexico Brock Univ Dept Comp Sci St Catharines ON L2S 3A1 Canada

the dropping cost of sequencing human dna has allowed for fast development of several projects around the world generating huge amounts of dna sequencing data. this deluge of data has run up against limited storage space, a problem that researchers are trying to solve through compression techniques. In this study we address the compression of SAM files, the standard output files for dna alignment. We specifically study lossy compression techniques used for quality values reported in the SAM file and analyze the impact of such lossy techniques on the CRAM format. We present a series of experiments using a data set corresponding to individual NA12878 with three different fold coverages. We introduce a new lossy model, dynamic binning, and compare its performance to other lossy techniques, namely Illumina binning, LEON and QVZ. We analyze the compression ratio when using CRAM and also study the impact of the lossy techniques on SNP calling. Our results show that lossy techniques allow a better CRAM compression ratio. Furthermore, we show that SNP calling performance is not negatively affected and may even be boosted.

关键词： Sequential analysis dna Standards Genomics Bioinformatics Data models Compression algorithms Compression next-generation sequencing quality values SNP calling performance

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Multi-Scale Capsule Network for Predicting dna-Protein Binding Sites

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021年第5期18卷 1793-1800页

作者： Zhang, Qinhu Yu, Wenbo Han, Kyungsook Nandi, Asoke K. Huang, De-Shuang Tongji Univ Inst Machine Learning & Syst Biol Sch Elect & Informat Engn 4800 Caoan Rd Shanghai 201804 Peoples R China Tongji Univ Sch Life Sci & Technol Siping Rd 1239 Shanghai 200092 Peoples R China Inha Univ Sch Comp Sci & Engn Incheon 21000 South Korea Brunel Univ London Dept Elect & Comp Engn Uxbridge UB8 3PH Middx England

Discovering dna-protein binding sites, also known as motif discovery, is the foundation for further analysis of transcription factors (TFs). Deep learning algorithms such as convolutional neural networks (CNN) have been introduced to motif discovery task and have achieved state-of-art performance. However, due to the limitations of CNN, motif discovery methods based on CNN do not take full advantage of large-scale sequencing data generated by high-throughput sequencing technology. Hence, in this paper we propose multi-scale capsule network architecture (MSC) integrating multi-scale CNN, a variant of CNN able to extract motif features of different lengths, and capsule network, a novel type of artificial neural network architecture aimed at improving CNN. 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.

关键词： dna Machine learning Computational modeling Feature extraction Kernel Convolution Bioinformatics Multi-scale capsule network transcription factors binding specificity

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A Novel Autonomous molecular Mechanism Based on Spatially Localized dna Computation 15th

A Novel Autonomous Molecular Mechanism Based on Spatially Lo...

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

作者： Wang, Yue Qian, Mengyao Hu, Wenxiao Wang, Luhui Dong, Yafei School of Computer Science Shaanxi Normal University Xi’an Shaanxi710119 China College of Life Science Shaanxi Normal University Xi’an Shaanxi710119 China

ISBN: (纸本)9789811613531

Contemporary dna synthesis technology matures, and the development provides intriguing possibilities for dynamic manipulation of dna self-assembly, which plays a pivotal role in the behavior of designing versatile nanodevices and generating controllable networks. Similarly, in synthetic molecular circuits, the spatially localized architecture furnishes a different strategy, allowing for immobilized dna molecules in close vicinity to each other. Herein, the formal modeling language was utilized to mark the address with a specific sequence of location tags, thus a set of routes were precisely arranged at the nanoscale. Beyond building a collection of separate modules, computer simulations were used to explore further complex assemblies of the building blocks. By orchestrating a series of dna strand displacement operations locally, autonomous movement and addressing operations were realized, completing the group transport and partition storage of dissimilar molecules. the nanodevice gives the dna molecule its mechanical properties and follows an embedded "molecular program". the simulation results of the Visual DSD tool provided qualitative and quantitative proof for the operation of the system. © 2021, Springer Nature Singapore Pte Ltd.

关键词： dna

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In Silico De Novo Synthesis, Screening, and ADME/T Profiling of dna-pA104R Inhibitors as Potential African Swine Fever therapeutics

In Silico De Novo Synthesis, Screening, and ADME/T Profiling...

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15th international Joint conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2022

作者： Reyes, Kim Rafaelle E. Roxas, Timothy Jen R. Gomez, Marineil Tayo, Lemmuel L. School of Chemical Biological and Materials Engineering and Sciences Mapúa University 658 Muralla Street Intramuros Manila Philippines

African Swine Fever Virus (ASFV) is a dsdna virus causative of the African Swine Fever (ASF) in wild and domestic hogs. ASF is characterized by hemorrhagic fever, high mortality, and transmissibility. the binding of the dna to the pA104R protein mediates viral replication and genome packaging. In the present study, we generated nine (9) reference compounds that exhibited high docking affinities through de novo computer aided drug design (CADD). these compounds were then used as query molecules to find commercially available drug-like compounds using ligand-based virtual screening (VS). We were able to retrieve 900 hit compounds that exhibited the same pharmacophoric activities. then, these hit compounds were subjected to drug-likeness filtration to identify the most likely to be developed as commercial drugs based on established parameters. We identified sixty-two (62) drug-like molecules. molecular docking was then performed to determine the top five compounds with the highest binding affinities against the target protein. ADME/T profiling was done on these compounds to assess their pharmacokinetic properties. Compound 8.45 performed best based on our devised scoring system. this paper shall serve as a good reference in the discovery and development of anti-ASFV therapeutics. © 2022 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved.

关键词： molecular docking

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Label-Free Fluorescence Detection of Carbohydrate Antigen 15-3 via dna AND Logic Gate Based on Graphene Oxide 15th

Label-Free Fluorescence Detection of Carbohydrate Antigen 15...

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

作者： Hu, Wenxiao Wang, Luhui Wang, Yue Qian, Mengyao Dong, Yafei College of Life Science Shaanxi Normal University Xi’an710119 China School of Computer Sciences Shaanxi Normal University Xi’an710119 China

ISBN: (纸本)9789811613531

In this work, we have developed a dna AND logic gate based on graphene oxide (GO) absorbing single dna and G-quadruplex interacting with N-methyl mesoporphyrin IX(NMM) for detecting breast cancer biomarker carbohydrate antigen 15-3 (CA15-3). With CA15-3 and NMM as the two inputs, the fluorescence intensity of the NMM is the output signal. A hairpin dna probe is designed, consisting of CA15-3 aptamer and partly anti-CA15-3 aptamer sequences as a long stem and G-rich sequences as a quadruplex-forming oligomer. In the presence of CA15-3 or NMM alone, there is no significant fluorescence enhancing, and the output of the signal is "0". While in the presence of CA15-3 protein and NMM, the fluorescence signal was dramatically increasing and the output of the signal is "1". this biosensor platform also exhibited good reproducibility, selectivity and showed high sensitivity for CA15-3 protein in a range of 10U/mL-500U/mL with the detection limit of 10U/mL. In addition, the fluorescence dna AND logic gate can successfully be applied to the determination of CA15-3 in spiked human serum. In summary, the proposed fluorescent dna AND logic gate could construct a simple, fast, label-free and highly specific sensing methods for CA15-3. © 2021, Springer Nature Singapore Pte Ltd.

关键词： Antigens

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Laser spectroscopy of interactions of carbon nanoparticles with biomacromolecules 15

Laser spectroscopy of interactions of carbon nanoparticles w...

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15th international conference on Pulsed Lasers and Laser Applications

作者： Laptinskiy, Kirill A. Burikov, Sergey A. Khmeleva, Maria Yu. Dolenko, Tatiana A. D.V. Skobeltsyn Institute of Nuclear Physics M. V. Lomonosov Moscow State University Moscow Russia Physical Department M. V. Lomonosov Moscow State University Moscow Russia

ISBN: (数字)9781510650497

ISBN: (纸本)9781510650480

CARS method was used to study the interactions of biomacromolecules with carbon dots synthesized by the hydrothermal method. A significant effect of CDs on molecular bonds in dna chains during their interaction in water was found. As a result of the analysis of the obtained CARS dna spectra before and after their interactions with nanoparticles in water, markers were identified that indicate the presence of oxidative stress on dna strands in the presence of CDs. © COPYRIGHT SPIE. Downloading of the abstract is permitted for personal use only.

关键词： dna

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Magnetic tweezers manipulate dna slowdown based on nanopores 15

Magnetic tweezers manipulate DNA slowdown based on nanopores

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

作者： Wang, Gang Sun, Haisong Luo, Fan Chen, Chang Sha, Jingjie Southeast Univ Sch Mech Engn Nanjing 211189 Peoples R China Southeast Univ Jiangsu Key Lab Design & Manufacture Micronano Bi Nanjing 211189 Peoples R China

ISBN: (数字)9781728172309

ISBN: (纸本)9781728172309

As a nano-sensor, solid-state nanopores have demonstrated their high sensitivity in the field of rapid detection of single molecules, but they still face many challenges in distinguishing the internal bases of dna. Driven by voltage, the speed of dna passing through the nanopore is very fast. When the voltage is 200mv, the via speed of dna reaches 30base/us. At such a speed, the current change caused by a single base is difficult to be used by existing instruments. catch. Effectively reducing the speed of dna through nanopores has become a major challenge. In this paper, the magnetic tweezers system platform was designed and constructed;the biobeads-streptavidin was connected between the magnetic beads and dna, and the influence of the bias voltage on the structure of the magnetic beads-dna was studied;the magnetic heads were manipulated using the magnetic tweezers system , Actively control dna to reverse through nanopores, significantly reducing the speed of dna passing through solid nanopores, and achieving active control of the speed of dna passing through solid nanopores;solving key technical problems in detecting single bases in solid nanopores Provides ideas.

关键词： Solid nanopore Micro-nano system Magnetic tweezers sensor

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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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