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  1. Article ; Online: Multi-Omics and Artificial Intelligence-Guided Drug Repositioning: Prospects, Challenges, and Lessons Learned from COVID-19.

    Cong, Yi / Endo, Toshinori

    Omics : a journal of integrative biology

    2022  Volume 26, Issue 7, Page(s) 361–371

    Abstract: Drug repurposing is of interest for therapeutics innovation in many human diseases including coronavirus disease 2019 (COVID-19). Methodological innovations in drug repurposing are currently being empowered by convergence of omics systems science and ... ...

    Abstract Drug repurposing is of interest for therapeutics innovation in many human diseases including coronavirus disease 2019 (COVID-19). Methodological innovations in drug repurposing are currently being empowered by convergence of omics systems science and digital transformation of life sciences. This expert review article offers a systematic summary of the application of artificial intelligence (AI), particularly machine learning (ML), to drug repurposing and classifies and introduces the common clustering, dimensionality reduction, and other methods. We highlight, as a present-day high-profile example, the involvement of AI/ML-based drug discovery in the COVID-19 pandemic and discuss the collection and sharing of diverse data types, and the possible futures awaiting drug repurposing in an era of AI/ML and digital technologies. The article provides new insights on convergence of multi-omics and AI-based drug repurposing. We conclude with reflections on the various pathways to expedite innovation in drug development through drug repurposing for prompt responses to the current COVID-19 pandemic and future ecological crises in the 21st century.
    MeSH term(s) Artificial Intelligence ; Drug Repositioning ; Humans ; Machine Learning ; Pandemics ; COVID-19 Drug Treatment
    Language English
    Publishing date 2022-06-28
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2030312-9
    ISSN 1557-8100 ; 1536-2310
    ISSN (online) 1557-8100
    ISSN 1536-2310
    DOI 10.1089/omi.2022.0068
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Inference of selective forces on house mouse genomes during secondary contact in East Asia.

    Fujiwara, Kazumichi / Kubo, Shunpei / Endo, Toshinori / Takada, Toyoyuki / Shiroishi, Toshihiko / Suzuki, Hitoshi / Osada, Naoki

    Genome research

    2024  Volume 34, Issue 3, Page(s) 366–375

    Abstract: The house mouse ( ...

    Abstract The house mouse (
    MeSH term(s) Animals ; Mice ; Female ; Male ; Genome ; Asia, Eastern ; Y Chromosome/genetics ; Haplotypes ; Selection, Genetic ; Humans ; Phylogeny ; Evolution, Molecular
    Language English
    Publishing date 2024-04-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.278828.123
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  3. Article ; Online: Current trends in RNA virus detection through metatranscriptome sequencing data

    Nakagawa, So / Sakaguchi, Shoichi / Ogura, Atsushi / Mineta, Katsuhiko / Endo, Toshinori / Suzuki, Yoshiyuki / Gojōbori, Takashi

    FEBS Open Bio 2023 Jun., v. 13, no. 6, p. 992-1000

    2023  , Page(s) 992–1000

    Abstract: With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled ...

    Abstract With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.
    Keywords RNA ; Severe acute respiratory syndrome coronavirus 2 ; bioinformatics ; computer software ; genome ; invertebrates ; vertebrates
    Language English
    Dates of publication 2023-06
    Size p. 992-1000
    Publishing place Elsevier B.V.
    Document type Article ; Online
    Note REVIEW ; Resource is Open Access ; Wiley License Information
    ZDB-ID 2651702-4
    ISSN 2211-5463
    ISSN 2211-5463
    DOI 10.1002/2211-5463.13626
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: A New Approach to Drug Repurposing with Two-Stage Prediction, Machine Learning, and Unsupervised Clustering of Gene Expression.

    Cong, Yi / Shintani, Misaki / Imanari, Fuga / Osada, Naoki / Endo, Toshinori

    Omics : a journal of integrative biology

    2022  Volume 26, Issue 6, Page(s) 339–347

    Abstract: Drug repurposing has broad importance in planetary health for therapeutics innovation in infectious diseases as well as common or rare chronic human diseases. Drug repurposing has also proved important to develop interventions against the COVID-19 ... ...

    Abstract Drug repurposing has broad importance in planetary health for therapeutics innovation in infectious diseases as well as common or rare chronic human diseases. Drug repurposing has also proved important to develop interventions against the COVID-19 pandemic. We propose a new approach for drug repurposing involving two-stage prediction and machine learning. First, diseases are clustered by gene expression on the premise that similar patterns of altered gene expression imply critical pathways shared in different disease conditions. Next, drug efficacy is assessed by the reversibility of abnormal gene expression, and results are clustered to identify repurposing targets. To cluster similar diseases, gene expression data from 262 cases of 31 diseases and 268 controls were analyzed by Uniform Manifold Approximation and Projection for Dimension Reduction followed by
    MeSH term(s) COVID-19/genetics ; Cluster Analysis ; Drug Repositioning/methods ; Gene Expression ; Humans ; Machine Learning ; Pandemics ; COVID-19 Drug Treatment
    Language English
    Publishing date 2022-06-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2030312-9
    ISSN 1557-8100 ; 1536-2310
    ISSN (online) 1557-8100
    ISSN 1536-2310
    DOI 10.1089/omi.2022.0026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Current trends in RNA virus detection through metatranscriptome sequencing data.

    Nakagawa, So / Sakaguchi, Shoichi / Ogura, Atsushi / Mineta, Katsuhiko / Endo, Toshinori / Suzuki, Yoshiyuki / Gojobori, Takashi

    FEBS open bio

    2023  Volume 13, Issue 6, Page(s) 992–1000

    Abstract: With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled ...

    Abstract With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19/genetics ; RNA Viruses/genetics ; RNA, Viral/genetics
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2023-05-20
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2651702-4
    ISSN 2211-5463 ; 2211-5463
    ISSN (online) 2211-5463
    ISSN 2211-5463
    DOI 10.1002/2211-5463.13626
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Computational Drug-repositioning Approach Identifying Sirolimus as a Potential Therapeutic Option for Inflammatory Dilated Cardiomyopathy.

    Shibata, Kyoko / Endo, Toshinori / Kuribayashi, Yoshikazu

    Drug research

    2019  Volume 69, Issue 10, Page(s) 565–571

    Abstract: Objective: The aim of this study was to determine promising treatment options for human inflammatory dilated cardiomyopathy using a computational drug-repositioning approach (repurposing established drug compounds for new therapeutic indications).: ... ...

    Abstract Objective: The aim of this study was to determine promising treatment options for human inflammatory dilated cardiomyopathy using a computational drug-repositioning approach (repurposing established drug compounds for new therapeutic indications).
    Background: If the myocardial tissue is detected to be infiltrated with inflammatory cells, primarily of lymphocytes, and if the virus is confirmed using genetic examination (PCR) or immunostaining, the infection is suspected. However, there is no specific treatment (i. e., an antiviral drug) even if the virus is identified; therefore, we used Connectivity Map to identify compounds showing inverse drug-disease signatures, indicating activity against inflammatory dilated cardiomyopathy.
    Results: Potential drug-repositioning candidates for the treatment of inflammatory dilated cardiomyopathy were explored through a systematic comparison of the gene expression profiles induced by drugs using Gene Expression Omnibus and Connectivity Map databases.
    Conclusion: Using a computational drug-repositioning approach based on the integration of publicly available gene expression signatures of drugs and diseases, sirolimus was suggested as a novel therapeutic option for inflammatory dilated cardiomyopathy.
    MeSH term(s) Cardiomyopathy, Dilated/drug therapy ; Cardiomyopathy, Dilated/pathology ; Computational Biology/methods ; Datasets as Topic ; Drug Repositioning/methods ; Gene Expression Profiling ; Humans ; Myocardium/pathology ; Sirolimus/therapeutic use ; Tissue Array Analysis
    Chemical Substances Sirolimus (W36ZG6FT64)
    Language English
    Publishing date 2019-06-25
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2703847-6
    ISSN 2194-9387 ; 2194-9379
    ISSN (online) 2194-9387
    ISSN 2194-9379
    DOI 10.1055/a-0950-9608
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uf I Zs.151: Show issues Location:
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  7. Article: Achiasmy and sex chromosome evolution

    Satomura, Kazuhiro / Endo, Toshinori / Osada, Naoki

    Ecological Genetics and Genomics. 2019 Dec., v. 13

    2019  

    Abstract: Achiasmy is a phenomenon whereby chiasma (“chromosomal cross–over”) formation is absent during meiosis in one or both sexes. It is one of the strategies that have evolved to cease recombination between sex chromosomes in various taxa. Absence of ... ...

    Abstract Achiasmy is a phenomenon whereby chiasma (“chromosomal cross–over”) formation is absent during meiosis in one or both sexes. It is one of the strategies that have evolved to cease recombination between sex chromosomes in various taxa. Absence of recombination makes Y (W) chromosome diverge from X (Z) chromosome via natural selection on linked genes. In the present review, we first review the research history of achiasmy in Drosophila species and summarize the prevalence of achiasmy in a wide range of animal taxa and the rapid turnover of achiasmy. We then briefly describe the mechanism of achiasmatic meiosis in Drosophila melanogaster and the evolution of meiotic genes in Drosophila species. Second, we discuss sex chromosome evolution in achiasmatic species. If meiotic recombination had been suppressed between sex chromosomes, heterogametic sex chromosomes have no chance of meiotic recombination. Therefore, the neo–Y chromosome which originated from Y–autosome fusion in achiasmatic species has no chance of recombination and no pre-existing genetic diversity since its origination. On the contrary, if the neo-Y chromosome had chance of recombination, it can maintain ancestral polymorphisms. We compare three different evolutionary trajectories of neo–Y chromosome in Drosophila americana, Drosophila miranda, and Drosophila albomicans. Lastly, we discuss the origin of Y chromosome in achiasmatic species. In particular, we introduce hypotheses proposed in three insect species that achiasmatic meiosis may facilitate the recruitment of an accessory B chromosome to a Y (W) chromosome.
    Keywords animals ; Drosophila americana ; Drosophila melanogaster ; genes ; genetic variation ; insects ; meiosis ; natural selection ; Y chromosome
    Language English
    Dates of publication 2019-12
    Publishing place Elsevier Inc.
    Document type Article
    ISSN 2405-9854
    DOI 10.1016/j.egg.2019.100046
    Database NAL-Catalogue (AGRICOLA)

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  8. Article: Whole-Genome Sequencing of Vero E6 (VERO C1008) and Comparative Analysis of Four Vero Cell Sublines.

    Konishi, Kazuhiro / Yamaji, Toshiyuki / Sakuma, Chisato / Kasai, Fumio / Endo, Toshinori / Kohara, Arihiro / Hanada, Kentaro / Osada, Naoki

    Frontiers in genetics

    2022  Volume 13, Page(s) 801382

    Abstract: The Vero cell line is an immortalized cell line established from kidney epithelial cells of the African green monkey. A variety of Vero sublines have been developed and can be classified into four major cell lineages. In this study, we determined the ... ...

    Abstract The Vero cell line is an immortalized cell line established from kidney epithelial cells of the African green monkey. A variety of Vero sublines have been developed and can be classified into four major cell lineages. In this study, we determined the whole-genome sequence of Vero E6 (VERO C1008), which is one of the most widely used cell lines for the proliferation and isolation of severe acute respiratory syndrome coronaviruses (SARS-CoVs), and performed comparative analysis among Vero JCRB0111, Vero CCL-81, Vero 76, and Vero E6. Analysis of the copy number changes and loss of heterozygosity revealed that these four sublines share a large deletion and loss of heterozygosity on chromosome 12, which harbors type I interferon and
    Language English
    Publishing date 2022-03-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.801382
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Computational Drug-repositioning Approach Identifying Sirolimus as a Potential Therapeutic Option for Inflammatory Dilated Cardiomyopathy

    Shibata, Kyoko / Endo, Toshinori / Kuribayashi, Yoshikazu

    Drug Research

    2019  Volume 69, Issue 10, Page(s) 565–571

    Abstract: Objective: The aim of this study was to determine promising treatment options for human inflammatory dilated cardiomyopathy using a computational drug-repositioning approach (repurposing established drug compounds for new therapeutic indications).: ... ...

    Abstract Objective: The aim of this study was to determine promising treatment options for human inflammatory dilated cardiomyopathy using a computational drug-repositioning approach (repurposing established drug compounds for new therapeutic indications).
    Background: If the myocardial tissue is detected to be infiltrated with inflammatory cells, primarily of lymphocytes, and if the virus is confirmed using genetic examination (PCR) or immunostaining, the infection is suspected. However, there is no specific treatment (i. e., an antiviral drug) even if the virus is identified; therefore, we used Connectivity Map to identify compounds showing inverse drug–disease signatures, indicating activity against inflammatory dilated cardiomyopathy.
    Results: Potential drug-repositioning candidates for the treatment of inflammatory dilated cardiomyopathy were explored through a systematic comparison of the gene expression profiles induced by drugs using Gene Expression Omnibus and Connectivity Map databases.
    Conclusion: Using a computational drug-repositioning approach based on the integration of publicly available gene expression signatures of drugs and diseases, sirolimus was suggested as a novel therapeutic option for inflammatory dilated cardiomyopathy.
    Keywords inflammation dilated cardiomyopathy ; connectivity map ; gene expression omnibus ; rapamycin
    Language English
    Publishing date 2019-06-25
    Publisher © Georg Thieme Verlag KG
    Publishing place Stuttgart ; New York
    Document type Article
    ZDB-ID 2703847-6
    ISSN 2194-9387 ; 2194-9379
    ISSN (online) 2194-9387
    ISSN 2194-9379
    DOI 10.1055/a-0950-9608
    Database Thieme publisher's database

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    In stock of ZB MED Cologne/Königswinter

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  10. Article ; Online: A Generalized Linear Model for Decomposing

    Takada, Yasuaki / Miyagi, Ryutaro / Takahashi, Aya / Endo, Toshinori / Osada, Naoki

    G3 (Bethesda, Md.)

    2017  Volume 7, Issue 7, Page(s) 2227–2234

    Abstract: Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles ...

    Abstract Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with
    MeSH term(s) Alleles ; Animals ; Drosophila melanogaster ; Female ; Gene Expression Regulation ; Genomic Imprinting ; Genotype ; Male ; Mice ; Models, Genetic ; Mutation ; Plants
    Language English
    Publishing date 2017--05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.117.042895
    Database MEDical Literature Analysis and Retrieval System OnLINE

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