The Experts below are selected from a list of 222 Experts worldwide ranked by ideXlab platform

Pei Chen - One of the best experts on this subject based on the ideXlab platform.

  • Computer-aided method for identification of major flavone/flavonol glycosides by high-performance liquid chromatography–diode array detection–tandem mass spectrometry (HPLC–DAD–MS/MS)
    Analytical and Bioanalytical Chemistry, 2014
    Co-Authors: Zhengfang Wang, Longze Lin, James M. Harnly, Peter De B. Harrington, Pei Chen
    Abstract:

    A new computational tool is proposed here for tentatively identifying major (UV quantifiable) flavone/flavonol glycoside peaks of high performance liquid chromatogram (HPLC)–diode array detection (DAD)–tandem mass spectrometry (MS/MS) profiles based on a MATLAB-based Script implementing an in-house algorithm. The HPLC–DAD–MS/MS profiles of red onion, Chinese lettuce, carrot leaf, and celery seed extracts were analyzed by the proposed computer-aided screening method for identifying possible flavone/flavonol glycoside peaks from the HPLC–UV and MS total ion current (TIC) chromatograms. The number of identified flavone/flavonol glycoside peaks of the HPLC–UV chromatograms is four, four, six, and nine for red onion, Chinese lettuce, carrot leaf, and celery seed, respectively. These results have been validated by human(s) experts. For the batch processing of nine HPLC–DAD–MS/MS profiles of celery seed extract, the entire Script Execution time was within 15 s while manual calculation of only one HPLC–DAD–MS/MS profile by a flavonoid expert could take hours. Therefore, this MATLAB-based screening method is able to facilitate the HPLC–DAD–MS/MS analysis of flavone/flavonol glycosides in plants to a large extent.

  • Computer-aided method for identification of major flavone/flavonol glycosides by high-performance liquid chromatography-diode array detection-tandem mass spectrometry (HPLC-DAD-MS/MS).
    Analytical and bioanalytical chemistry, 2014
    Co-Authors: Zhengfang Wang, Longze Lin, James M. Harnly, Peter De B. Harrington, Pei Chen
    Abstract:

    A new computational tool is proposed here for tentatively identifying major (UV quantifiable) flavone/flavonol glycoside peaks of high performance liquid chromatogram (HPLC)–diode array detection (DAD)–tandem mass spectrometry (MS/MS) profiles based on a MATLAB-based Script implementing an in-house algorithm. The HPLC–DAD–MS/MS profiles of red onion, Chinese lettuce, carrot leaf, and celery seed extracts were analyzed by the proposed computer-aided screening method for identifying possible flavone/flavonol glycoside peaks from the HPLC–UV and MS total ion current (TIC) chromatograms. The number of identified flavone/flavonol glycoside peaks of the HPLC–UV chromatograms is four, four, six, and nine for red onion, Chinese lettuce, carrot leaf, and celery seed, respectively. These results have been validated by human(s) experts. For the batch processing of nine HPLC–DAD–MS/MS profiles of celery seed extract, the entire Script Execution time was within 15 s while manual calculation of only one HPLC–DAD–MS/MS profile by a flavonoid expert could take hours. Therefore, this MATLAB-based screening method is able to facilitate the HPLC–DAD–MS/MS analysis of flavone/flavonol glycosides in plants to a large extent.

Zhengfang Wang - One of the best experts on this subject based on the ideXlab platform.

  • Computer-aided method for identification of major flavone/flavonol glycosides by high-performance liquid chromatography–diode array detection–tandem mass spectrometry (HPLC–DAD–MS/MS)
    Analytical and Bioanalytical Chemistry, 2014
    Co-Authors: Zhengfang Wang, Longze Lin, James M. Harnly, Peter De B. Harrington, Pei Chen
    Abstract:

    A new computational tool is proposed here for tentatively identifying major (UV quantifiable) flavone/flavonol glycoside peaks of high performance liquid chromatogram (HPLC)–diode array detection (DAD)–tandem mass spectrometry (MS/MS) profiles based on a MATLAB-based Script implementing an in-house algorithm. The HPLC–DAD–MS/MS profiles of red onion, Chinese lettuce, carrot leaf, and celery seed extracts were analyzed by the proposed computer-aided screening method for identifying possible flavone/flavonol glycoside peaks from the HPLC–UV and MS total ion current (TIC) chromatograms. The number of identified flavone/flavonol glycoside peaks of the HPLC–UV chromatograms is four, four, six, and nine for red onion, Chinese lettuce, carrot leaf, and celery seed, respectively. These results have been validated by human(s) experts. For the batch processing of nine HPLC–DAD–MS/MS profiles of celery seed extract, the entire Script Execution time was within 15 s while manual calculation of only one HPLC–DAD–MS/MS profile by a flavonoid expert could take hours. Therefore, this MATLAB-based screening method is able to facilitate the HPLC–DAD–MS/MS analysis of flavone/flavonol glycosides in plants to a large extent.

  • Computer-aided method for identification of major flavone/flavonol glycosides by high-performance liquid chromatography-diode array detection-tandem mass spectrometry (HPLC-DAD-MS/MS).
    Analytical and bioanalytical chemistry, 2014
    Co-Authors: Zhengfang Wang, Longze Lin, James M. Harnly, Peter De B. Harrington, Pei Chen
    Abstract:

    A new computational tool is proposed here for tentatively identifying major (UV quantifiable) flavone/flavonol glycoside peaks of high performance liquid chromatogram (HPLC)–diode array detection (DAD)–tandem mass spectrometry (MS/MS) profiles based on a MATLAB-based Script implementing an in-house algorithm. The HPLC–DAD–MS/MS profiles of red onion, Chinese lettuce, carrot leaf, and celery seed extracts were analyzed by the proposed computer-aided screening method for identifying possible flavone/flavonol glycoside peaks from the HPLC–UV and MS total ion current (TIC) chromatograms. The number of identified flavone/flavonol glycoside peaks of the HPLC–UV chromatograms is four, four, six, and nine for red onion, Chinese lettuce, carrot leaf, and celery seed, respectively. These results have been validated by human(s) experts. For the batch processing of nine HPLC–DAD–MS/MS profiles of celery seed extract, the entire Script Execution time was within 15 s while manual calculation of only one HPLC–DAD–MS/MS profile by a flavonoid expert could take hours. Therefore, this MATLAB-based screening method is able to facilitate the HPLC–DAD–MS/MS analysis of flavone/flavonol glycosides in plants to a large extent.

Jiří Macas - One of the best experts on this subject based on the ideXlab platform.

  • Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2
    Nature Protocols, 2020
    Co-Authors: Petr Novák, Pavel Neumann, Jiří Macas
    Abstract:

    RepeatExplorer2 is a novel version of a computational pipeline that uses graph-based clustering of next-generation sequencing reads for characterization of repetitive DNA in eukaryotes. The clustering algorithm facilitates repeat identification in any genome by using relatively small quantities of short sequence reads, and additional tools within the pipeline perform automatic annotation and quantification of the identified repeats. The pipeline is integrated into the Galaxy platform, which provides a user-friendly web interface for Script Execution and documentation of the results. Compared to the original version of the pipeline, RepeatExplorer2 provides automated annotation of transposable elements, identification of tandem repeats and enhanced visualization of analysis results. Here, we present an overview of the RepeatExplorer2 workflow and provide procedures for its application to (i) de novo repeat identification in a single species, (ii) comparative repeat analysis in a set of species, (iii) development of satellite DNA probes for cytogenetic experiments and (iv) identification of centromeric repeats based on ChIP-seq data. Each procedure takes approximately 2 d to complete. RepeatExplorer2 is available at https://repeatexplorer-elixir.cerit-sc.cz . RepeatExplorer is a software tool for repeat identification and quantification using unassembled sequencing reads. The authors describe four pipelines implemented on the Galaxy platform, highlighting different applications.

  • Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2.
    Nature protocols, 2020
    Co-Authors: Petr Novák, Pavel Neumann, Jiří Macas
    Abstract:

    RepeatExplorer2 is a novel version of a computational pipeline that uses graph-based clustering of next-generation sequencing reads for characterization of repetitive DNA in eukaryotes. The clustering algorithm facilitates repeat identification in any genome by using relatively small quantities of short sequence reads, and additional tools within the pipeline perform automatic annotation and quantification of the identified repeats. The pipeline is integrated into the Galaxy platform, which provides a user-friendly web interface for Script Execution and documentation of the results. Compared to the original version of the pipeline, RepeatExplorer2 provides automated annotation of transposable elements, identification of tandem repeats and enhanced visualization of analysis results. Here, we present an overview of the RepeatExplorer2 workflow and provide procedures for its application to (i) de novo repeat identification in a single species, (ii) comparative repeat analysis in a set of species, (iii) development of satellite DNA probes for cytogenetic experiments and (iv) identification of centromeric repeats based on ChIP-seq data. Each procedure takes approximately 2 d to complete. RepeatExplorer2 is available at https://repeatexplorer-elixir.cerit-sc.cz .

Longze Lin - One of the best experts on this subject based on the ideXlab platform.

  • Computer-aided method for identification of major flavone/flavonol glycosides by high-performance liquid chromatography–diode array detection–tandem mass spectrometry (HPLC–DAD–MS/MS)
    Analytical and Bioanalytical Chemistry, 2014
    Co-Authors: Zhengfang Wang, Longze Lin, James M. Harnly, Peter De B. Harrington, Pei Chen
    Abstract:

    A new computational tool is proposed here for tentatively identifying major (UV quantifiable) flavone/flavonol glycoside peaks of high performance liquid chromatogram (HPLC)–diode array detection (DAD)–tandem mass spectrometry (MS/MS) profiles based on a MATLAB-based Script implementing an in-house algorithm. The HPLC–DAD–MS/MS profiles of red onion, Chinese lettuce, carrot leaf, and celery seed extracts were analyzed by the proposed computer-aided screening method for identifying possible flavone/flavonol glycoside peaks from the HPLC–UV and MS total ion current (TIC) chromatograms. The number of identified flavone/flavonol glycoside peaks of the HPLC–UV chromatograms is four, four, six, and nine for red onion, Chinese lettuce, carrot leaf, and celery seed, respectively. These results have been validated by human(s) experts. For the batch processing of nine HPLC–DAD–MS/MS profiles of celery seed extract, the entire Script Execution time was within 15 s while manual calculation of only one HPLC–DAD–MS/MS profile by a flavonoid expert could take hours. Therefore, this MATLAB-based screening method is able to facilitate the HPLC–DAD–MS/MS analysis of flavone/flavonol glycosides in plants to a large extent.

  • Computer-aided method for identification of major flavone/flavonol glycosides by high-performance liquid chromatography-diode array detection-tandem mass spectrometry (HPLC-DAD-MS/MS).
    Analytical and bioanalytical chemistry, 2014
    Co-Authors: Zhengfang Wang, Longze Lin, James M. Harnly, Peter De B. Harrington, Pei Chen
    Abstract:

    A new computational tool is proposed here for tentatively identifying major (UV quantifiable) flavone/flavonol glycoside peaks of high performance liquid chromatogram (HPLC)–diode array detection (DAD)–tandem mass spectrometry (MS/MS) profiles based on a MATLAB-based Script implementing an in-house algorithm. The HPLC–DAD–MS/MS profiles of red onion, Chinese lettuce, carrot leaf, and celery seed extracts were analyzed by the proposed computer-aided screening method for identifying possible flavone/flavonol glycoside peaks from the HPLC–UV and MS total ion current (TIC) chromatograms. The number of identified flavone/flavonol glycoside peaks of the HPLC–UV chromatograms is four, four, six, and nine for red onion, Chinese lettuce, carrot leaf, and celery seed, respectively. These results have been validated by human(s) experts. For the batch processing of nine HPLC–DAD–MS/MS profiles of celery seed extract, the entire Script Execution time was within 15 s while manual calculation of only one HPLC–DAD–MS/MS profile by a flavonoid expert could take hours. Therefore, this MATLAB-based screening method is able to facilitate the HPLC–DAD–MS/MS analysis of flavone/flavonol glycosides in plants to a large extent.

James M. Harnly - One of the best experts on this subject based on the ideXlab platform.

  • Computer-aided method for identification of major flavone/flavonol glycosides by high-performance liquid chromatography–diode array detection–tandem mass spectrometry (HPLC–DAD–MS/MS)
    Analytical and Bioanalytical Chemistry, 2014
    Co-Authors: Zhengfang Wang, Longze Lin, James M. Harnly, Peter De B. Harrington, Pei Chen
    Abstract:

    A new computational tool is proposed here for tentatively identifying major (UV quantifiable) flavone/flavonol glycoside peaks of high performance liquid chromatogram (HPLC)–diode array detection (DAD)–tandem mass spectrometry (MS/MS) profiles based on a MATLAB-based Script implementing an in-house algorithm. The HPLC–DAD–MS/MS profiles of red onion, Chinese lettuce, carrot leaf, and celery seed extracts were analyzed by the proposed computer-aided screening method for identifying possible flavone/flavonol glycoside peaks from the HPLC–UV and MS total ion current (TIC) chromatograms. The number of identified flavone/flavonol glycoside peaks of the HPLC–UV chromatograms is four, four, six, and nine for red onion, Chinese lettuce, carrot leaf, and celery seed, respectively. These results have been validated by human(s) experts. For the batch processing of nine HPLC–DAD–MS/MS profiles of celery seed extract, the entire Script Execution time was within 15 s while manual calculation of only one HPLC–DAD–MS/MS profile by a flavonoid expert could take hours. Therefore, this MATLAB-based screening method is able to facilitate the HPLC–DAD–MS/MS analysis of flavone/flavonol glycosides in plants to a large extent.

  • Computer-aided method for identification of major flavone/flavonol glycosides by high-performance liquid chromatography-diode array detection-tandem mass spectrometry (HPLC-DAD-MS/MS).
    Analytical and bioanalytical chemistry, 2014
    Co-Authors: Zhengfang Wang, Longze Lin, James M. Harnly, Peter De B. Harrington, Pei Chen
    Abstract:

    A new computational tool is proposed here for tentatively identifying major (UV quantifiable) flavone/flavonol glycoside peaks of high performance liquid chromatogram (HPLC)–diode array detection (DAD)–tandem mass spectrometry (MS/MS) profiles based on a MATLAB-based Script implementing an in-house algorithm. The HPLC–DAD–MS/MS profiles of red onion, Chinese lettuce, carrot leaf, and celery seed extracts were analyzed by the proposed computer-aided screening method for identifying possible flavone/flavonol glycoside peaks from the HPLC–UV and MS total ion current (TIC) chromatograms. The number of identified flavone/flavonol glycoside peaks of the HPLC–UV chromatograms is four, four, six, and nine for red onion, Chinese lettuce, carrot leaf, and celery seed, respectively. These results have been validated by human(s) experts. For the batch processing of nine HPLC–DAD–MS/MS profiles of celery seed extract, the entire Script Execution time was within 15 s while manual calculation of only one HPLC–DAD–MS/MS profile by a flavonoid expert could take hours. Therefore, this MATLAB-based screening method is able to facilitate the HPLC–DAD–MS/MS analysis of flavone/flavonol glycosides in plants to a large extent.