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  1. Article: COVID-19 Associated Bacteremia with

    Yeh, Ting-Kuang / Li, Zong-Hao / Huang, Yao-Ting / Liu, Po-Yu

    Infection and drug resistance

    2022  Volume 15, Page(s) 167–170

    Abstract: We report a COVID-19 case with carbapenem ... ...

    Abstract We report a COVID-19 case with carbapenem resistant
    Language English
    Publishing date 2022-01-20
    Publishing country New Zealand
    Document type Case Reports
    ZDB-ID 2494856-1
    ISSN 1178-6973
    ISSN 1178-6973
    DOI 10.2147/IDR.S347066
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant

    Yang, Wan-Ting / Chiu, I-Ju / Huang, Yao-Ting / Liu, Po-Yu

    Frontiers in microbiology

    2022  Volume 13, Page(s) 886428

    Abstract: Escherichia ... ...

    Abstract Escherichia coli
    Language English
    Publishing date 2022-04-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.886428
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Corrigendum: Comparative genomics revealed fluoroquinolone resistance determinants and OmpF deletion in carbapenem-resistant

    Yang, Wan-Ting / Chiu, I-Ju / Huang, Yao-Ting / Liu, Po-Yu

    Frontiers in microbiology

    2022  Volume 13, Page(s) 1094324

    Abstract: This corrects the article DOI: 10.3389/fmicb.2022.886428.]. ...

    Abstract [This corrects the article DOI: 10.3389/fmicb.2022.886428.].
    Language English
    Publishing date 2022-11-24
    Publishing country Switzerland
    Document type Published Erratum
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.1094324
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants.

    Lin, Jyun-Hong / Chen, Liang-Chi / Yu, Shu-Chi / Huang, Yao-Ting

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue 7, Page(s) 1816–1822

    Abstract: Motivation: Long-read phasing has been used for reconstructing diploid genomes, improving variant calling and resolving microbial strains in metagenomics. However, the phasing blocks of existing methods are broken by large Structural Variations (SVs), ... ...

    Abstract Motivation: Long-read phasing has been used for reconstructing diploid genomes, improving variant calling and resolving microbial strains in metagenomics. However, the phasing blocks of existing methods are broken by large Structural Variations (SVs), and the efficiency is unsatisfactory for population-scale phasing.
    Results: This article presents a novel algorithm, LongPhase, which can simultaneously phase single nucleotide polymorphisms (SNPs) and SVs of a human genome in 10-20 min, 10× faster than the state-of-the-art WhatsHap, HapCUT2 and Margin. In particular, co-phasing SNPs and SVs produces much larger haplotype blocks (N50 = 25 Mbp) than those of existing methods (N50 = 10-15 Mbp). We show that LongPhase combined with Nanopore ultra-long reads is a cost-effective and highly contiguous solution, which can produce between one and 26 blocks per chromosome arm without the need for additional trios, chromosome-conformation and strand-seq data.
    Availabilityand implementation: LongPhase is freely available at https://github.com/twolinin/LongPhase/.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Humans ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Algorithms ; Genome, Human ; Haplotypes ; Chromosomes/genetics
    Language English
    Publishing date 2022-04-22
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac058
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: 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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  5. Article ; Online: Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing.

    Huang, Yao-Ting / Liu, Po-Yu / Shih, Pei-Wen

    Genome biology

    2021  Volume 22, Issue 1, Page(s) 95

    Abstract: Nanopore sequencing has been widely used for the reconstruction of microbial genomes. Owing to higher error rates, errors on the genome are corrected via neural networks trained by Nanopore reads. However, the systematic errors usually remain uncorrected. ...

    Abstract Nanopore sequencing has been widely used for the reconstruction of microbial genomes. Owing to higher error rates, errors on the genome are corrected via neural networks trained by Nanopore reads. However, the systematic errors usually remain uncorrected. This paper designs a model that is trained by homologous sequences for the correction of Nanopore systematic errors. The developed program, Homopolish, outperforms Medaka and HELEN in bacteria, viruses, fungi, and metagenomic datasets. When combined with Medaka/HELEN, the genome quality can exceed Q50 on R9.4 flow cells. We show that Nanopore-only sequencing can produce high-quality microbial genomes sufficient for downstream analysis.
    MeSH term(s) Bacteria/genetics ; Computational Biology/methods ; Computational Biology/standards ; Fungi/genetics ; Genomics/methods ; Genomics/standards ; Metagenome ; Metagenomics ; Nanopore Sequencing/methods ; Nanopore Sequencing/standards ; Sequence Analysis, DNA/methods ; Sequence Analysis, DNA/standards ; Viruses/genetics
    Language English
    Publishing date 2021-03-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-021-02282-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Comparative Genomics Identified PenR E151V Substitution Associated with Carbapenem-Resistance

    Liao, Ya-Chun / Huang, Yao-Ting / Tseng, Chien-Hao / Liu, Chia-Wei / Liu, Po-Yu

    Infection and drug resistance

    2023  Volume 16, Page(s) 5627–5635

    Abstract: Purpose: Burkholderia cepacia: Patients and methods: Ten strains of Bcc were identified by the MALDI-TOF MS, and the drug susceptibility test was using VITEK 2 system. The : Results: The genetic organization between carbapenem-sensitive and ... ...

    Abstract Purpose: Burkholderia cepacia
    Patients and methods: Ten strains of Bcc were identified by the MALDI-TOF MS, and the drug susceptibility test was using VITEK 2 system. The
    Results: The genetic organization between carbapenem-sensitive and carbapenem-resistant strains of Bcc showed no difference. However, in the carbapenem-sensitive strain, E151V substitution in PenR was detected. In addition, a novel specific OXA family subgroup,
    Conclusion: The E151V substitution in PenR may be associated with carbapenem-sensitive in Bcc. Moreover, the V151E mutation in PenR may be related to the activation of PenB, leading to Bcc resistance to carbapenems. Besides, a novel OXA family subgroup,
    Language English
    Publishing date 2023-08-28
    Publishing country New Zealand
    Document type Journal Article
    ZDB-ID 2494856-1
    ISSN 1178-6973
    ISSN 1178-6973
    DOI 10.2147/IDR.S418969
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Identification of combinatorial mutations associated with colistin resistance in Shewanella algae.

    Huang, Yao-Ting / Mao, Yan-Chiao / Tseng, Chien-Hao / Liu, Chia-Wei / Liu, Po-Yu

    Microbes and infection

    2023  Volume 25, Issue 7, Page(s) 105143

    Abstract: Colistin is a last-resort antibiotic used to treat infections caused by drug-resistant gram-negative bacteria. However, the genetic mechanisms underlying colistin resistance in Shewanella algae are not well understood. In this study, we sequenced and ... ...

    Abstract Colistin is a last-resort antibiotic used to treat infections caused by drug-resistant gram-negative bacteria. However, the genetic mechanisms underlying colistin resistance in Shewanella algae are not well understood. In this study, we sequenced and compared the genomes of 23 mcr-negative colistin-resistant and sensitive S. algae samples from various sources. We applied a computational approach to identify combinatorial mutations associated with colistin resistance. Our analysis revealed a combination of three mutations (PmrB 451, PmrE168, PmrH292) that were strongly associated with colistin resistance in S. algae. This study provides insights into the genetic mechanisms of colistin resistance in S. algae and demonstrates the utility of a computational approach for identifying epistatic interactions among mutations. Identifying the genetic mutations responsible for colistin resistance in S. algae can inform the development of new treatments or strategies to combat infections caused by this emerging pathogen.
    MeSH term(s) Colistin/pharmacology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Mutation ; Microbial Sensitivity Tests
    Chemical Substances Colistin (Z67X93HJG1) ; Anti-Bacterial Agents
    Language English
    Publishing date 2023-04-19
    Publishing country France
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1465093-9
    ISSN 1769-714X ; 1286-4579
    ISSN (online) 1769-714X
    ISSN 1286-4579
    DOI 10.1016/j.micinf.2023.105143
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5014: 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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  8. Article: Diagnosis of Legionnaires' Disease Assisted by Next-Generation Sequencing in a Patient with COVID-19.

    Huang, Po-Hsiu / Huang, Yao-Ting / Lee, Po-Hsin / Tseng, Chien-Hao / Liu, Po-Yu / Liu, Chia-Wei

    Infection and drug resistance

    2023  Volume 16, Page(s) 355–362

    Abstract: Coinfection in COVID-19 patients is associated with worsening outcome. Among patients with COVID-19, ...

    Abstract Coinfection in COVID-19 patients is associated with worsening outcome. Among patients with COVID-19,
    Language English
    Publishing date 2023-01-20
    Publishing country New Zealand
    Document type Journal Article
    ZDB-ID 2494856-1
    ISSN 1178-6973
    ISSN 1178-6973
    DOI 10.2147/IDR.S396254
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  9. Article: Insight into the Mechanisms of Carbapenem Resistance in

    Tseng, Chien-Hao / Huang, Yao-Ting / Mao, Yan-Chiao / Lai, Chung-Hsu / Yeh, Ting-Kuang / Ho, Chung-Mei / Liu, Po-Yu

    Antibiotics (Basel, Switzerland)

    2023  Volume 12, Issue 4

    Abstract: The emergence of carbapenem- ... ...

    Abstract The emergence of carbapenem-resistant
    Language English
    Publishing date 2023-04-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2681345-2
    ISSN 2079-6382
    ISSN 2079-6382
    DOI 10.3390/antibiotics12040749
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: An efficient error correction algorithm using FM-index.

    Huang, Yao-Ting / Huang, Yu-Wen

    BMC bioinformatics

    2017  Volume 18, Issue 1, Page(s) 524

    Abstract: Background: High-throughput sequencing offers higher throughput and lower cost for sequencing a genome. However, sequencing errors, including mismatches and indels, may be produced during sequencing. Because, errors may reduce the accuracy of subsequent ...

    Abstract Background: High-throughput sequencing offers higher throughput and lower cost for sequencing a genome. However, sequencing errors, including mismatches and indels, may be produced during sequencing. Because, errors may reduce the accuracy of subsequent de novo assembly, error correction is necessary prior to assembly. However, existing correction methods still face trade-offs among correction power, accuracy, and speed.
    Results: We develop a novel overlap-based error correction algorithm using FM-index (called FMOE). FMOE first identifies overlapping reads by aligning a query read simultaneously against multiple reads compressed by FM-index. Subsequently, sequencing errors are corrected by k-mer voting from overlapping reads only. The experimental results indicate that FMOE has highest correction power with comparable accuracy and speed. Our algorithm performs better in long-read than short-read datasets when compared with others. The assembly results indicated different algorithms has its own strength and weakness, whereas FMOE is good for long or good-quality reads.
    Conclusions: FMOE is freely available at https://github.com/ythuang0522/FMOC .
    MeSH term(s) Algorithms ; Animals ; Bacteria/genetics ; Base Sequence ; Caenorhabditis elegans/genetics ; Genome ; High-Throughput Nucleotide Sequencing/methods ; Sequence Alignment ; Time Factors
    Language English
    Publishing date 2017-11-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-017-1940-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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