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  1. Article ; Online: Mitochondrial genome plasticity of mammalian species.

    Biró, Bálint / Gál, Zoltán / Fekete, Zsófia / Klecska, Eszter / Hoffmann, Orsolya Ivett

    BMC genomics

    2024  Volume 25, Issue 1, Page(s) 278

    Abstract: There is an ongoing process in which mitochondrial sequences are being integrated into the nuclear genome. The importance of these sequences has already been revealed in cancer biology, forensic, phylogenetic studies and in the evolution of the ... ...

    Abstract There is an ongoing process in which mitochondrial sequences are being integrated into the nuclear genome. The importance of these sequences has already been revealed in cancer biology, forensic, phylogenetic studies and in the evolution of the eukaryotic genetic information. Human and numerous model organisms' genomes were described from those sequences point of view. Furthermore, recent studies were published on the patterns of these nuclear localised mitochondrial sequences in different taxa.However, the results of the previously released studies are difficult to compare due to the lack of standardised methods and/or using few numbers of genomes. Therefore, in this paper our primary goal is to establish a uniform mining pipeline to explore these nuclear localised mitochondrial sequences.Our results show that the frequency of several repetitive elements is higher in the flanking regions of these sequences than expected. A machine learning model reveals that the flanking regions' repetitive elements and different structural characteristics are highly influential during the integration process.In this paper, we introduce a general mining pipeline for all mammalian genomes. The workflow is publicly available and is believed to serve as a validated baseline for future research in this field. We confirm the widespread opinion, on - as to our current knowledge - the largest dataset, that structural circumstances and events corresponding to repetitive elements are highly significant. An accurate model has also been trained to predict these sequences and their corresponding flanking regions.
    MeSH term(s) Animals ; Humans ; Genome, Mitochondrial ; Phylogeny ; DNA, Mitochondrial/genetics ; Mammals/genetics ; Repetitive Sequences, Nucleic Acid
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2024-03-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-024-10201-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Complementarity of the residue-level protein function and structure predictions in human proteins

    Biró, Bálint / Zhao, Bi / Kurgan, Lukasz

    Computational and Structural Biotechnology Journal. 2022, v. 20

    2022  

    Abstract: Sequence-based predictors of the residue-level protein function and structure cover a broad spectrum of characteristics including intrinsic disorder, secondary structure, solvent accessibility and binding to nucleic acids. They were catalogued and ... ...

    Abstract Sequence-based predictors of the residue-level protein function and structure cover a broad spectrum of characteristics including intrinsic disorder, secondary structure, solvent accessibility and binding to nucleic acids. They were catalogued and evaluated in numerous surveys and assessments. However, methods focusing on a given characteristic are studied separately from predictors of other characteristics, while they are typically used on the same proteins. We fill this void by studying complementarity of a representative collection of methods that target different predictions using a large, taxonomically consistent, and low similarity dataset of human proteins. First, we bridge the gap between the communities that develop structure-trained vs. disorder-trained predictors of binding residues. Motivated by a recent study of the protein-binding residue predictions, we empirically find that combining the structure-trained and disorder-trained predictors of the DNA-binding and RNA-binding residues leads to substantial improvements in predictive quality. Second, we investigate whether diverse predictors generate results that accurately reproduce relations between secondary structure, solvent accessibility, interaction sites, and intrinsic disorder that are present in the experimental data. Our empirical analysis concludes that predictions accurately reflect all combinations of these relations. Altogether, this study provides unique insights that support combining results produced by diverse residue-level predictors of protein function and structure.
    Keywords biotechnology ; data collection ; empirical research ; humans ; protein binding ; solvents
    Language English
    Size p. 2223-2234.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.05.003
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: Complementarity of the residue-level protein function and structure predictions in human proteins.

    Biró, Bálint / Zhao, Bi / Kurgan, Lukasz

    Computational and structural biotechnology journal

    2022  Volume 20, Page(s) 2223–2234

    Abstract: Sequence-based predictors of the residue-level protein function and structure cover a broad spectrum of characteristics including intrinsic disorder, secondary structure, solvent accessibility and binding to nucleic acids. They were catalogued and ... ...

    Abstract Sequence-based predictors of the residue-level protein function and structure cover a broad spectrum of characteristics including intrinsic disorder, secondary structure, solvent accessibility and binding to nucleic acids. They were catalogued and evaluated in numerous surveys and assessments. However, methods focusing on a given characteristic are studied separately from predictors of other characteristics, while they are typically used on the same proteins. We fill this void by studying complementarity of a representative collection of methods that target different predictions using a large, taxonomically consistent, and low similarity dataset of human proteins. First, we bridge the gap between the communities that develop structure-trained vs. disorder-trained predictors of binding residues. Motivated by a recent study of the protein-binding residue predictions, we empirically find that combining the structure-trained and disorder-trained predictors of the DNA-binding and RNA-binding residues leads to substantial improvements in predictive quality. Second, we investigate whether diverse predictors generate results that accurately reproduce relations between secondary structure, solvent accessibility, interaction sites, and intrinsic disorder that are present in the experimental data. Our empirical analysis concludes that predictions accurately reflect all combinations of these relations. Altogether, this study provides unique insights that support combining results produced by diverse residue-level predictors of protein function and structure.
    Language English
    Publishing date 2022-05-06
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.05.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Nuclear mitochondrial DNA sequences in the rabbit genome.

    Biró, Bálint / Gál, Zoltán / Schiavo, Giuseppina / Ribari, Anisa / Joe Utzeri, Valerio / Brookman, Michael / Fontanesi, Luca / Hoffmann, Orsolya Ivett

    Mitochondrion

    2022  Volume 66, Page(s) 1–6

    Abstract: Numtogenesis is observable in the mammalian genomes resulting in the integration of mitochondrial segments into the nuclear genomes (numts). To identify numts in rabbit, we aligned mitochondrial and nuclear genomes. Alignment significance threshold was ... ...

    Abstract Numtogenesis is observable in the mammalian genomes resulting in the integration of mitochondrial segments into the nuclear genomes (numts). To identify numts in rabbit, we aligned mitochondrial and nuclear genomes. Alignment significance threshold was calculated and individual characteristics of numts were analysed. We found 153 numts in the nuclear genome. The GC content of numts were significantly lower than the GC content of their genomic flanking regions or the genome itself. The frequency of three mammalian-wide interspersed repeats were increased in the proximity of numts. The decreased GC content around numts strengthen the theory which supposes a link between DNA structural instability and numt integration.
    MeSH term(s) Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/chemistry ; DNA, Mitochondrial/genetics ; Genome ; Genome, Mitochondrial ; Mammals/genetics ; Mitochondria/genetics ; Phylogeny ; Rabbits ; Sequence Analysis, DNA
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2022-07-13
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2056923-3
    ISSN 1872-8278 ; 1567-7249
    ISSN (online) 1872-8278
    ISSN 1567-7249
    DOI 10.1016/j.mito.2022.07.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options.

    Basu, Sushmita / Zhao, Bi / Biró, Bálint / Faraggi, Eshel / Gsponer, Jörg / Hu, Gang / Kloczkowski, Andrzej / Malhis, Nawar / Mirdita, Milot / Söding, Johannes / Steinegger, Martin / Wang, Duolin / Wang, Kui / Xu, Dong / Zhang, Jian / Kurgan, Lukasz

    Nucleic acids research

    2023  Volume 52, Issue D1, Page(s) D426–D433

    Abstract: The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its release in 2020. This expansion includes substantial increase in the size, scope, and quality of the underlying data, the ... ...

    Abstract The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its release in 2020. This expansion includes substantial increase in the size, scope, and quality of the underlying data, the addition of experimental structural information, the inclusion of new data download options, and an upgraded graphical interface. DescribePROT currently covers 19 structural and functional descriptors for proteins in 273 reference proteomes generated by 11 accurate and complementary predictive tools. Users can search our resource in multiple ways, interact with the data using the graphical interface, and download data at various scales including individual proteins, entire proteomes, and whole database. The annotations in DescribePROT are useful for a broad spectrum of studies that include investigations of protein structure and function, development and validation of predictive tools, and to support efforts in understanding molecular underpinnings of diseases and development of therapeutics. DescribePROT can be freely accessed at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/.
    MeSH term(s) Proteome/chemistry ; Databases, Factual ; Amino Acids
    Chemical Substances Proteome ; Amino Acids
    Language English
    Publishing date 2023-11-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad985
    Database MEDical Literature Analysis and Retrieval System OnLINE

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