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  1. Article ; Online: Latent periodicity-2 in coronavirus SARS-CoV-2 genome: Evolutionary implications.

    Yin, Changchuan

    Journal of theoretical biology

    2021  Volume 515, Page(s) 110604

    Abstract: The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy. The genome of SARS-CoV-2 had been sequenced and structurally ... ...

    Abstract The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy. The genome of SARS-CoV-2 had been sequenced and structurally annotated, yet little is known of the intrinsic organization and evolution of the genome. To this end, we present a mathematical method for the genomic spectrum, a kind of barcode, of SARS-CoV-2 and common human coronaviruses. The genomic spectrum is constructed according to the periodic distributions of nucleotides and therefore reflects the unique characteristics of the genome. The results demonstrate that coronavirus SARS-CoV-2 exhibits predominant latent periodicity-2 regions of non-structural proteins 3, 4, 5, and 6. Further analysis of the latent periodicity-2 regions suggests that the dinucleotide imbalances are increased during evolution and may confer the evolutionary fitness of the virus. Especially, SARS-CoV-2 isolates have increased latent periodicity-2 and periodicity-3 during COVID-19 pandemic. The special strong periodicity-2 regions and the intensity of periodicity-2 in the SARS-CoV-2 whole genome may become diagnostic and pharmaceutical targets in monitoring and curing the COVID-19 disease.
    MeSH term(s) Base Sequence ; COVID-19/epidemiology ; COVID-19/virology ; DNA Barcoding, Taxonomic/methods ; Evolution, Molecular ; Genome, Viral/genetics ; Genomics ; History, 21st Century ; Humans ; Models, Theoretical ; Open Reading Frames/genetics ; Pandemics ; Period Circadian Proteins/genetics ; Phylogeny ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; Sequence Analysis, DNA ; Virulence/genetics
    Chemical Substances Period Circadian Proteins ; RNA, Viral
    Language English
    Publishing date 2021-01-26
    Publishing country England
    Document type Historical Article ; Journal Article
    ZDB-ID 2972-5
    ISSN 1095-8541 ; 0022-5193
    ISSN (online) 1095-8541
    ISSN 0022-5193
    DOI 10.1016/j.jtbi.2021.110604
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 923: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: Genotyping coronavirus SARS-CoV-2: methods and implications.

    Yin, Changchuan

    Genomics

    2020  Volume 112, Issue 5, Page(s) 3588–3596

    Abstract: The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has ... ...

    Abstract The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has gone through various pathways of evolution. To understand the evolution and transmission of SARS-CoV-2, genotyping of virus isolates is of great importance. This study presents an accurate method for effectively genotyping SARS-CoV-2 viruses using complete genomes. The method employs the multiple sequence alignments of the genome isolates with the SARS-CoV-2 reference genome. The single-nucleotide polymorphism (SNP) genotypes are then measured by Jaccard distances to track the relationship of virus isolates. The genotyping analysis of SARS-CoV-2 isolates from the globe reveals that specific multiple mutations are the predominated mutation type during the current epidemic. The proposed method serves an effective tool for monitoring and tracking the epidemic of pathogenic viruses in their global and local genetic variations. The genotyping analysis shows that the genes encoding the S proteins and RNA polymerase, RNA primase, and nucleoprotein, undergo frequent mutations. These mutations are critical for vaccine development in disease control.
    MeSH term(s) Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections ; Evolution, Molecular ; Genome, Viral ; Genomics ; Genotyping Techniques/methods ; Humans ; Mutation ; Pandemics ; Pneumonia, Viral ; Polymorphism, Single Nucleotide ; SARS-CoV-2 ; Sequence Alignment
    Keywords covid19
    Language English
    Publishing date 2020-04-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2020.04.016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2367: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Encoding and Decoding DNA Sequences by Integer Chaos Game Representation.

    Yin, Changchuan

    Journal of computational biology : a journal of computational molecular cell biology

    2018  Volume 26, Issue 2, Page(s) 143–151

    Abstract: DNA sequences are fundamental for encoding genetic information. The genetic information may be understood not only from symbolic sequences but also from the hidden signals inside the sequences. The symbolic sequences need to be transformed into numerical ...

    Abstract DNA sequences are fundamental for encoding genetic information. The genetic information may be understood not only from symbolic sequences but also from the hidden signals inside the sequences. The symbolic sequences need to be transformed into numerical sequences so the hidden signals can be revealed by signal processing techniques. All current transformation methods encode DNA sequences into numerical values of the same length. These representations have limitations in the applications of genomic signal compression, encryption, and steganography. We propose a novel integer chaos game representation (inter-CGR or iCGR) of DNA sequences and a lossless encoding method DNA sequences by the iCGR. In the iCGR method, a DNA sequence is represented by the iterated function of the nucleotides and their positions in the sequence. Then the DNA sequence can be uniquely encoded and recovered using three integers from iCGR. One integer is the sequence length and the other two integers represent the accumulated distributions of nucleotides in the sequence. The integer encoding scheme can compress a DNA sequence by 2 bits per nucleotide. The integer representation of DNA sequences provides a prospective tool for sequence analysis and operations.
    MeSH term(s) Algorithms ; DNA, Mitochondrial/chemistry ; DNA, Mitochondrial/genetics ; Game Theory ; Humans ; Nonlinear Dynamics ; Sequence Analysis, DNA/methods
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2018-12-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2030900-4
    ISSN 1557-8666 ; 1066-5277
    ISSN (online) 1557-8666
    ISSN 1066-5277
    DOI 10.1089/cmb.2018.0173
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genotyping coronavirus SARS-CoV-2

    Yin, Changchuan

    Genomics

    methods and implications

    2020  Volume 112, Issue 5, Page(s) 3588–3596

    Keywords Genetics ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2020.04.016
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2367: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article: Genotyping coronavirus SARS-CoV-2: methods and implications

    Yin, Changchuan

    Genomics

    Abstract: The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has ... ...

    Abstract The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has gone through various pathways of evolution. To understand the evolution and transmission of SARS-CoV-2, genotyping of virus isolates is of great importance. This study presents an accurate method for effectively genotyping SARS-CoV-2 viruses using complete genomes. The method employs the multiple sequence alignments of the genome isolates with the SARS-CoV-2 reference genome. The single-nucleotide polymorphism (SNP) genotypes are then measured by Jaccard distances to track the relationship of virus isolates. The genotyping analysis of SARS-CoV-2 isolates from the globe reveals that specific multiple mutations are the predominated mutation type during the current epidemic. The proposed method serves an effective tool for monitoring and tracking the epidemic of pathogenic viruses in their global and local genetic variations. The genotyping analysis shows that the genes encoding the S proteins and RNA polymerase, RNA primase, and nucleoprotein, undergo frequent mutations. These mutations are critical for vaccine development in disease control.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #125250
    Database COVID19

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  6. Article: Dinucleotide repeats in coronavirus SARS-CoV-2 genome: evolutionary implications

    Yin, Changchuan

    Abstract: The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy since it was identified in China, December 2019. The genome of SARS- ...

    Abstract The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy since it was identified in China, December 2019. The genome of SARS-CoV-2 had been sequenced and structurally annotated, yet little is known of the intrinsic organization and evolution of the genome. To this end, we present a mathematical method for the genomic spectrum, a kind of barcode, of SARS-CoV-2 and common human coronaviruses. The genomic spectrum is constructed according to the periodic distributions of nucleotides, and therefore reflects the unique characteristics of the genome. The results demonstrate that coronavirus SARS-CoV-2 exhibits dinucleotide TT islands in the non-structural proteins 3, 4, 5, and 6. Further analysis of the dinucleotide regions suggests that the dinucleotide repeats are increased during evolution and may confer the evolutionary fitness of the virus. The special dinucleotide regions in the SARS-CoV-2 genome identified in this study may become diagnostic and pharmaceutical targets in monitoring and curing the COVID-19 disease.
    Keywords covid19
    Publisher ArXiv
    Document type Article
    Database COVID19

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  7. Book ; Online: Genotyping coronavirus SARS-CoV-2

    Yin, Changchuan

    methods and implications

    2020  

    Abstract: The emerging global infectious COVID-19 coronavirus disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. ... ...

    Abstract The emerging global infectious COVID-19 coronavirus disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has gone through various pathways of evolution. For understanding the evolution and transmission of SARS-CoV-2, genotyping of virus isolates is of great importance. We present an accurate method for effectively genotyping SARS-CoV-2 viruses using complete genomes. The method employs the multiple sequence alignments of the genome isolates with the SARS-CoV-2 reference genome. The SNP genotypes are then measured by Jaccard distances to track the relationship of virus isolates. The genotyping analysis of SARS-CoV-2 isolates from the globe reveals that specific multiple mutations are the predominated mutation type during the current epidemic. Our method serves a promising tool for monitoring and tracking the epidemic of pathogenic viruses in their gradual and local genetic variations. The genotyping analysis shows that the genes encoding the S proteins and RNA polymerase, RNA primase, and nucleoprotein, undergo frequent mutations. These mutations are critical for vaccine development in disease control.
    Keywords Quantitative Biology - Genomics ; Statistics - Applications ; 92B05 ; covid19
    Subject code 616
    Publishing date 2020-03-24
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Book ; Online: Dinucleotide repeats in coronavirus SARS-CoV-2 genome

    Yin, Changchuan

    evolutionary implications

    2020  

    Abstract: The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy since it was identified in China, December 2019. The genome of SARS- ...

    Abstract The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy since it was identified in China, December 2019. The genome of SARS-CoV-2 had been sequenced and structurally annotated, yet little is known of the intrinsic organization and evolution of the genome. To this end, we present a mathematical method for the genomic spectrum, a kind of barcode, of SARS-CoV-2 and common human coronaviruses. The genomic spectrum is constructed according to the periodic distributions of nucleotides, and therefore reflects the unique characteristics of the genome. The results demonstrate that coronavirus SARS-CoV-2 exhibits dinucleotide TT islands in the non-structural proteins 3, 4, 5, and 6. Further analysis of the dinucleotide regions suggests that the dinucleotide repeats are increased during evolution and may confer the evolutionary fitness of the virus. The special dinucleotide regions in the SARS-CoV-2 genome identified in this study may become diagnostic and pharmaceutical targets in monitoring and curing the COVID-19 disease.
    Keywords Quantitative Biology - Genomics ; 92D20 ; 92B05 ; covid19
    Subject code 572
    Publishing date 2020-05-30
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Biological Intelligence Inspired Trajectory Design for Energy Harvesting UAV Networks.

    Liu, Xuanlin / Wang, Sihua / Yin, Changchuan

    Sensors (Basel, Switzerland)

    2023  Volume 23, Issue 2

    Abstract: In this paper, the problem of trajectory design for energy harvesting unmanned aerial vehicles (UAVs) is studied. In the considered model, the UAV acts as a moving base station to serve the ground users, while collecting energy from the charging stations ...

    Abstract In this paper, the problem of trajectory design for energy harvesting unmanned aerial vehicles (UAVs) is studied. In the considered model, the UAV acts as a moving base station to serve the ground users, while collecting energy from the charging stations located at the center of a user group. For this purpose, the UAV must be examined and repaired regularly. In consequence, it is necessary to optimize the trajectory design of the UAV while jointly considering the maintenance costs, the reward of serving users, the energy management, and the user service time. To capture the relationship among these factors, we first model the completion of service and the harvested energy as the reward, and the energy consumption during the deployment as the cost. Then, the
    MeSH term(s) Physical Phenomena ; Algorithms ; Computer Simulation ; Intelligence ; Reward
    Language English
    Publishing date 2023-01-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s23020863
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online: Attention-based UNet enabled Lightweight Image Semantic Communication System over Internet of Things

    Ma, Guoxin / Tong, Haonan / Yang, Nuocheng / Yin, Changchuan

    2024  

    Abstract: This paper studies the problem of the lightweight image semantic communication system that is deployed on Internet of Things (IoT) devices. In the considered system model, devices must use semantic communication techniques to support user behavior ... ...

    Abstract This paper studies the problem of the lightweight image semantic communication system that is deployed on Internet of Things (IoT) devices. In the considered system model, devices must use semantic communication techniques to support user behavior recognition in ultimate video service with high data transmission efficiency. However, it is computationally expensive for IoT devices to deploy semantic codecs due to the complex calculation processes of deep learning (DL) based codec training and inference. To make it affordable for IoT devices to deploy semantic communication systems, we propose an attention-based UNet enabled lightweight image semantic communication (LSSC) system, which achieves low computational complexity and small model size. In particular, we first let the LSSC system train the codec at the edge server to reduce the training computation load on IoT devices. Then, we introduce the convolutional block attention module (CBAM) to extract the image semantic features and decrease the number of downsampling layers thus reducing the floating-point operations (FLOPs). Finally, we experimentally adjust the structure of the codec and find out the optimal number of downsampling layers. Simulation results show that the proposed LSSC system can reduce the semantic codec FLOPs by 14%, and reduce the model size by 55%, with a sacrifice of 3% accuracy, compared to the baseline. Moreover, the proposed scheme can achieve a higher transmission accuracy than the traditional communication scheme in the low channel signal-to-noise (SNR) region.

    Comment: 6 pages, 6 figures, accepted by IEEE WCNC 2024
    Keywords Computer Science - Neural and Evolutionary Computing
    Subject code 600
    Publishing date 2024-01-14
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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