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  1. Article ; Online: Nanopore Sequencing Data Analysis of 16S rRNA Genes Using the GenomeSync-GSTK System.

    Kryukov, Kirill / Imanishi, Tadashi / Nakagawa, So

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2632, Page(s) 215–226

    Abstract: With the development of nanopore sequencing technology, long reads of DNA sequences can now be determined rapidly from various samples. This protocol introduces the GenomeSync-GSTK system for bacterial species identification in a given sample using ... ...

    Abstract With the development of nanopore sequencing technology, long reads of DNA sequences can now be determined rapidly from various samples. This protocol introduces the GenomeSync-GSTK system for bacterial species identification in a given sample using nanopore sequencing data of 16S rRNA genes as an example. GenomeSync is a collection of genome sequences designed to provide easy access to genomic data of the species as demanded. GSTK (genome search toolkit) is a set of scripts for managing local homology searches using genomes obtained from the GenomeSync database. Based on this protocol, nanopore sequencing data analyses of metagenomes and amplicons could be efficiently performed. We also noted reanalysis in conjunction with future developments in nanopore sequencing technology and the accumulation of genome sequencing data.
    MeSH term(s) Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Nanopore Sequencing ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; Nanopores
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-02-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2996-3_15
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.

    Kryukov, Kirill / Jin, Lihua / Nakagawa, So

    Patterns (New York, N.Y.)

    2022  Volume 3, Issue 9, Page(s) 100562

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome data are essential for epidemiology, vaccine development, and tracking emerging variants. Millions of SARS-CoV-2 genomes have been sequenced during the pandemic. However, downloading ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome data are essential for epidemiology, vaccine development, and tracking emerging variants. Millions of SARS-CoV-2 genomes have been sequenced during the pandemic. However, downloading SARS-CoV-2 genomes from databases is slow and unreliable, largely due to suboptimal choice of compression method. We evaluated the available compressors and found that Nucleotide Archival Format (NAF) would provide a drastic improvement compared with current methods. For Global Initiative on Sharing Avian Flu Data's (GISAID) pre-compressed datasets, NAF would increase efficiency 52.2 times for gzip-compressed data and 3.7 times for xz-compressed data. For DNA DataBank of Japan (DDBJ), NAF would improve throughput 40 times for gzip-compressed data. For GenBank and European Nucleotide Archive (ENA), NAF would accelerate data distribution by a factor of 29.3 times compared with uncompressed FASTA. This article provides a tutorial for installing and using NAF. Offering a NAF download option in sequence databases would provide a significant saving of time, bandwidth, and disk space and accelerate biological and medical research worldwide.
    Language English
    Publishing date 2022-07-07
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2666-3899
    ISSN (online) 2666-3899
    DOI 10.1016/j.patter.2022.100562
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  3. Article ; Online: Complete mitochondrial genomes of five subspecies of the Eurasian magpie

    Kryukov, Alexey P / Spiridonova, Liudmila N / Tyunin, Alexey P / Kryukov, Kirill A / Dorda, Beatriz A

    Mitochondrial DNA. Part B, Resources

    2020  Volume 5, Issue 3, Page(s) 3810–3811

    Abstract: The complete mitochondrial (mt) genomes of five subspecies of the Eurasian (Common) ... ...

    Abstract The complete mitochondrial (mt) genomes of five subspecies of the Eurasian (Common) magpie
    Language English
    Publishing date 2020-11-20
    Publishing country England
    Document type Journal Article
    ISSN 2380-2359
    ISSN (online) 2380-2359
    DOI 10.1080/23802359.2020.1838354
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  4. Article ; Online: MinION, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting.

    Komiya, Shinnosuke / Matsuo, Yoshiyuki / Nakagawa, So / Morimoto, Yoshiharu / Kryukov, Kirill / Okada, Hidetaka / Hirota, Kiichi

    BMC medical genomics

    2022  Volume 15, Issue 1, Page(s) 68

    Abstract: Background: It has been suggested that the local microbiota in the reproductive organs is relevant to women's health and may also affect pregnancy outcomes. Analysis of partial 16S ribosomal RNA (rRNA) gene sequences generated by short-read sequencers ... ...

    Abstract Background: It has been suggested that the local microbiota in the reproductive organs is relevant to women's health and may also affect pregnancy outcomes. Analysis of partial 16S ribosomal RNA (rRNA) gene sequences generated by short-read sequencers has been used to identify vaginal and endometrial microbiota, but it requires a long time to obtain the results, making it unsuitable for rapid bacterial identification from a small specimen amount in a clinical context.
    Methods: We developed a simple workflow using the nanopore sequencer MinION that allows high-resolution and rapid differentiation of vaginal microbiota. Vaginal samples collected from 18 participants were subjected to DNA extraction and full-length 16S rRNA gene sequencing with MinION.
    Results: The principal coordinate analysis showed no differences in the bacterial compositions regardless of the sample collection method. The analysis of vaginal microbiota could be completed with a total analysis time of approximately four hours, allowing same-day results. Taxonomic profiling by MinION sequencing revealed relatively low diversity of the vaginal bacterial community, identifying the prevailing Lactobacillus species and several causative agents of bacterial vaginosis.
    Conclusions: Full-length 16S rRNA gene sequencing analysis with MinION provides a rapid means for identifying vaginal bacteria with higher resolution. Species-level profiling of human vaginal microbiota by MinION sequencing can allow the analysis of associations with conditions such as genital infections, endometritis, and threatened miscarriage.
    MeSH term(s) Bacteria/genetics ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Microbiota/genetics ; Nanopore Sequencing ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2022-03-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2411865-5
    ISSN 1755-8794 ; 1755-8794
    ISSN (online) 1755-8794
    ISSN 1755-8794
    DOI 10.1186/s12920-022-01218-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: MinION, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting

    Shinnosuke Komiya / Yoshiyuki Matsuo / So Nakagawa / Yoshiharu Morimoto / Kirill Kryukov / Hidetaka Okada / Kiichi Hirota

    BMC Medical Genomics, Vol 15, Iss 1, Pp 1-

    2022  Volume 10

    Abstract: Abstract Background It has been suggested that the local microbiota in the reproductive organs is relevant to women's health and may also affect pregnancy outcomes. Analysis of partial 16S ribosomal RNA (rRNA) gene sequences generated by short-read ... ...

    Abstract Abstract Background It has been suggested that the local microbiota in the reproductive organs is relevant to women's health and may also affect pregnancy outcomes. Analysis of partial 16S ribosomal RNA (rRNA) gene sequences generated by short-read sequencers has been used to identify vaginal and endometrial microbiota, but it requires a long time to obtain the results, making it unsuitable for rapid bacterial identification from a small specimen amount in a clinical context. Methods We developed a simple workflow using the nanopore sequencer MinION that allows high-resolution and rapid differentiation of vaginal microbiota. Vaginal samples collected from 18 participants were subjected to DNA extraction and full-length 16S rRNA gene sequencing with MinION. Results The principal coordinate analysis showed no differences in the bacterial compositions regardless of the sample collection method. The analysis of vaginal microbiota could be completed with a total analysis time of approximately four hours, allowing same-day results. Taxonomic profiling by MinION sequencing revealed relatively low diversity of the vaginal bacterial community, identifying the prevailing Lactobacillus species and several causative agents of bacterial vaginosis. Conclusions Full-length 16S rRNA gene sequencing analysis with MinION provides a rapid means for identifying vaginal bacteria with higher resolution. Species-level profiling of human vaginal microbiota by MinION sequencing can allow the analysis of associations with conditions such as genital infections, endometritis, and threatened miscarriage.
    Keywords 16S rRNA ; Bacterial vaginosis ; Long-read sequencer ; MinION ; Nanopore ; Internal medicine ; RC31-1245 ; Genetics ; QH426-470
    Subject code 630
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Global Antimicrobial Resistance Gene Study of

    Alfaray, Ricky Indra / Saruuljavkhlan, Batsaikhan / Fauzia, Kartika Afrida / Torres, Roberto C / Thorell, Kaisa / Dewi, Selva Rosyta / Kryukov, Kirill A / Matsumoto, Takashi / Akada, Junko / Vilaichone, Ratha-Korn / Miftahussurur, Muhammad / Yamaoka, Yoshio

    Antibiotics (Basel, Switzerland)

    2023  Volume 12, Issue 7

    Abstract: We conducted a global-scale study to ... ...

    Abstract We conducted a global-scale study to identify
    Language English
    Publishing date 2023-06-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2681345-2
    ISSN 2079-6382
    ISSN 2079-6382
    DOI 10.3390/antibiotics12071118
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  7. Article ; Online: Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences.

    Kryukov, Kirill / Ueda, Mahoko Takahashi / Nakagawa, So / Imanishi, Tadashi

    GigaScience

    2020  Volume 9, Issue 7

    Abstract: Background: Nearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for a more efficient compression tool. Although numerous compressors exist, both specialized and general-purpose, ...

    Abstract Background: Nearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for a more efficient compression tool. Although numerous compressors exist, both specialized and general-purpose, choosing one of them was difficult because no comprehensive analysis of their comparative advantages for sequence compression was available.
    Findings: We systematically benchmarked 430 settings of 48 compressors (including 29 specialized sequence compressors and 19 general-purpose compressors) on representative FASTA-formatted datasets of DNA, RNA, and protein sequences. Each compressor was evaluated on 17 performance measures, including compression strength, as well as time and memory required for compression and decompression. We used 27 test datasets including individual genomes of various sizes, DNA and RNA datasets, and standard protein datasets. We summarized the results as the Sequence Compression Benchmark database (SCB database, http://kirr.dyndns.org/sequence-compression-benchmark/), which allows custom visualizations to be built for selected subsets of benchmark results.
    Conclusion: We found that modern compressors offer a large improvement in compactness and speed compared to gzip. Our benchmark allows compressors and their settings to be compared using a variety of performance measures, offering the opportunity to select the optimal compressor on the basis of the data type and usage scenario specific to a particular application.
    MeSH term(s) Algorithms ; Computational Biology/methods ; Data Compression/methods ; Databases, Nucleic Acid ; Genomics/methods ; Humans ; Models, Theoretical ; Mutation ; Neoplasms/genetics ; Sequence Analysis, DNA/methods ; Software
    Language English
    Publishing date 2020-07-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/giaa072
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  8. Article ; Online: Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer.

    Ohno, Ayumu / Umezawa, Kazuo / Asai, Satomi / Kryukov, Kirill / Nakagawa, So / Miyachi, Hayato / Imanishi, Tadashi

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 3436

    Abstract: Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized ... ...

    Abstract Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized propidium monoazide (PMA) that prohibits DNA amplifications from dead bacteria, and subjected the original and antibiotics-treated samples to 16S rRNA metagenome sequencing. We tested our protocol on bacterial mixtures, and observed that sequencing reads derived from drug-resistant bacteria were significantly increased compared with those from drug-sensitive bacteria when samples were treated by antibiotics. Our protocol is scalable and will be useful for quickly profiling drug-resistant bacteria.
    MeSH term(s) Bacteria/genetics ; Coloring Agents/chemistry ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Metagenome ; Nanopores ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA
    Chemical Substances Coloring Agents ; DNA, Bacterial ; RNA, Bacterial ; RNA, Ribosomal, 16S
    Language English
    Publishing date 2021-02-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-82903-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Human Contamination in Public Genome Assemblies.

    Kryukov, Kirill / Imanishi, Tadashi

    PloS one

    2016  Volume 11, Issue 9, Page(s) e0162424

    Abstract: Contamination in genome assembly can lead to wrong or confusing results when using such genome as reference in sequence comparison. Although bacterial contamination is well known, the problem of human-originated contamination received little attention. ... ...

    Abstract Contamination in genome assembly can lead to wrong or confusing results when using such genome as reference in sequence comparison. Although bacterial contamination is well known, the problem of human-originated contamination received little attention. In this study we surveyed 45,735 available genome assemblies for evidence of human contamination. We used lineage specificity to distinguish between contamination and conservation. We found that 154 genome assemblies contain fragments that with high confidence originate as contamination from human DNA. Majority of contaminating human sequences were present in the reference human genome assembly for over a decade. We recommend that existing contaminated genomes should be revised to remove contaminated sequence, and that new assemblies should be thoroughly checked for presence of human DNA before submitting them to public databases.
    MeSH term(s) Animals ; Computational Biology/methods ; Computational Biology/standards ; DNA Contamination ; Genome ; Genome, Human ; Genomics/methods ; Genomics/standards ; High-Throughput Nucleotide Sequencing ; Humans ; Mammals ; Phylogeny ; Sequence Analysis, DNA/standards
    Language English
    Publishing date 2016-09-09
    Publishing country United States
    Document type Journal Article
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0162424
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  10. Article ; Online: Robotic data acquisition with deep learning enables cell image-based prediction of transcriptomic phenotypes.

    Jin, Jianshi / Ogawa, Taisaku / Hojo, Nozomi / Kryukov, Kirill / Shimizu, Kenji / Ikawa, Tomokatsu / Imanishi, Tadashi / Okazaki, Taku / Shiroguchi, Katsuyuki

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 120, Issue 1, Page(s) e2210283120

    Abstract: Single-cell whole-transcriptome analysis is the gold standard approach to identifying molecularly defined cell phenotypes. However, this approach cannot be used for dynamics measurements such as live-cell imaging. Here, we developed a multifunctional ... ...

    Abstract Single-cell whole-transcriptome analysis is the gold standard approach to identifying molecularly defined cell phenotypes. However, this approach cannot be used for dynamics measurements such as live-cell imaging. Here, we developed a multifunctional robot, the automated live imaging and cell picking system (ALPS) and used it to perform single-cell RNA sequencing for microscopically observed cells with multiple imaging modes. Using robotically obtained data that linked cell images and the whole transcriptome, we successfully predicted transcriptome-defined cell phenotypes in a noninvasive manner using cell image-based deep learning. This noninvasive approach opens a window to determine the live-cell whole transcriptome in real time. Moreover, this work, which is based on a data-driven approach, is a proof of concept for determining the transcriptome-defined phenotypes (i.e., not relying on specific genes) of any cell from cell images using a model trained on linked datasets.
    MeSH term(s) Transcriptome ; Deep Learning ; Robotics ; Image Processing, Computer-Assisted/methods ; Robotic Surgical Procedures ; Gene Expression Profiling ; Phenotype
    Language English
    Publishing date 2022-12-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2210283120
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