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    • Several versions

    Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function

    Berkhout Ben, Lukashov Vladimir V, van Hemert Formijn J
    Virology journal, 01 March 2007, Vol.4(1), p.25 [Peer Reviewed Journal]

    • Several versions

    The Hepatitis B Virus X Protein Inhibits Thymine DNA Glycosylase Initiated Base Excision Repair (Inhibition of BER by the HBV Protein X)

    van de Klundert, Maarten A. A, van Hemert, Formijn J, Zaaijer, Hans L, Kootstra, Neeltje A
    2012, Vol.7(11), p.e48940 [Peer Reviewed Journal]

    • Several versions

    Differential Binding of Tenofovir and Adefovir to Reverse Transcriptase of Hepatitis B Virus

    Van Hemert, Formijn J, Berkhout, Ben, Zaaijer, Hans L
    PLoS ONE, 2014, Vol.9(9) [Peer Reviewed Journal]

    • Several versions

    Protein X of Hepatitis B Virus: Origin and Structure Similarity with the Central Domain of DNA Glycosylase (3D-Structure Similarity of HBx with DNA Glycosylase)

    van Hemert, Formijn J, van de Klundert, Maarten A. A, Lukashov, Vladimir V, Kootstra, Neeltje A, Berkhout, Ben, Zaaijer, Hans L
    PLoS ONE, 2011, Vol.6(8), p.e23392 [Peer Reviewed Journal]

    • Several versions

    Nucleotide composition of the Zika virus RNA genome and its codon usage

    Van Hemert, Formijn, Berkhout, Ben
    Virology journal, 08 June 2016, Vol.13, pp.95 [Peer Reviewed Journal]

    • Several versions

    The A-nucleotide preference of HIV-1 in the context of its structured RNA genome

    van Hemert, Formijn J, van Der Kuyl, Antoinette C, Berkhout, Ben
    RNA biology, 01 February 2013, Vol.10(2), pp.211-215 [Peer Reviewed Journal]

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    Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage

    Van Hemert, Formijn, Van Der Kuyl, Antoinette C, Berkhout, Ben
    The Journal of general virology, October 2016, Vol.97(10), pp.2608-2619 [Peer Reviewed Journal]
    MEDLINE/PubMed (U.S. National Library of Medicine)
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    Title: Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage
    Author: Van Hemert, Formijn; Van Der Kuyl, Antoinette C; Berkhout, Ben
    Subject: Genome, Viral ; Codon -- Genetics ; RNA Viruses -- Genetics ; RNA, Viral -- Genetics
    Description: We are interested in the influence of nucleotide composition on the fundamental characteristics of the virus RNA genome. Most RNA viruses have genomes with a distinct nucleotide composition, e.g. ranging from minimally 12.9 % to maximally 40.3 % (C- and U-count, respectively, in coronavirus HKU). We present a global analysis of diverse virus types, including plus-strand, minus-strand and double-strand RNA viruses, for the impact of this nucleotide preference on the predicted structure of the RNA genome that is packaged in virion particles and on the codon usage in the viral open reading frames. Several virus-specific features will be described, but also some general conclusions were drawn. Without exception, the virus-specific nucleotide bias was enriched in the unpaired, single-stranded regions of the RNA genome, thus creating an even more striking virus-specific signature. We present a simple mechanism that is based on elementary aspects of RNA structure folding to explain this general...
    Is part of: The Journal of general virology, October 2016, Vol.97(10), pp.2608-2619
    Identifier: 1465-2099 (E-ISSN); 27519195 Version (PMID); 10.1099/jgv.0.000579 (DOI)

    • Several versions

    Euclidean Distance Analysis Enables Nucleotide Skew Analysis in Viral Genomes

    Van Hemert, Formijn, Jebbink, Maarten, Van Der Ark, Andries, Scholer, Frits, Berkhout, Ben
    Computational and mathematical methods in medicine, 2018, Vol.2018, pp.6490647 [Peer Reviewed Journal]

    • Several versions

    HIV-1 tolerates changes in A-count in a small segment of the pol gene

    Klaver, Bep, Van Der Velden, Yme, Van Hemert, Formijn, Van Der Kuyl, Antoinette C, Berkhout, Ben
    Retrovirology, 05 September 2017, Vol.14(1), pp.43 [Peer Reviewed Journal]

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    Euclidean distance analysis enables nucleotide skew analysis in viral genomes

    van Hemert, Formijn, Jebbink, Maarten, van der Ark, Andries, Scholer, Frits, Berkhout, Ben
    Computational and Mathematical Methods in Medicine, 2018, Vol.2018, pp.urn:issn:1748-670x [Peer Reviewed Journal]
    NARCIS (National Academic Research and Collaborations Information System)
    Available
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    Title: Euclidean distance analysis enables nucleotide skew analysis in viral genomes
    Author: van Hemert, Formijn; Jebbink, Maarten; van der Ark, Andries; Scholer, Frits; Berkhout, Ben
    Contributor: Medical Microbiology; AII - Infectious diseases
    Description: Nucleotide skew analysis is a versatile method to study the nucleotide composition of RNA/DNA molecules, in particular to reveal characteristic sequence signatures. For instance, skew analysis of the nucleotide bias of several viral RNA genomes indicated that it is enriched in the unpaired, single-stranded genome regions, thus creating an even more striking virus-specific signature. The comparison of skew graphs for many virus isolates or families is difficult, time-consuming, and nonquantitative. Here, we present a procedure for a more simple identification of similarities and dissimilarities between nucleotide skew data of coronavirus, flavivirus, picornavirus, and HIV-1 RNA genomes. Window and step sizes were normalized to correct for differences in length of the viral genome. Cumulative skew data are converted into pairwise Euclidean distance matrices, which can be presented as neighbor-joining trees. We present skew value trees for the four virus families and show that closely related...
    Is part of: Computational and Mathematical Methods in Medicine, 2018, Vol.2018, pp.urn:issn:1748-670x
    Identifier: (ISSN); 1748-670X (ISSN)