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  1. Book ; Online: Bioinformatics of Genome Regulation and Systems Biology

    Orlov, Yuriy L. / Baranova, Ancha

    2020  

    Keywords Science: general issues ; Medical genetics ; genomics ; bioinformactics ; systems biology ; plant science ; gene expression ; special issue
    Size 1 electronic resource (258 pages)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021230913
    ISBN 9782889660148 ; 2889660141
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article: Bioinformatics tools for the sequence complexity estimates.

    Orlov, Yuriy L / Orlova, Nina G

    Biophysical reviews

    2023  Volume 15, Issue 5, Page(s) 1367–1378

    Abstract: We review current methods and bioinformatics tools for the text complexity estimates (information and entropy measures). The search DNA regions with extreme statistical characteristics such as low complexity regions are important for biophysical models ... ...

    Abstract We review current methods and bioinformatics tools for the text complexity estimates (information and entropy measures). The search DNA regions with extreme statistical characteristics such as low complexity regions are important for biophysical models of chromosome function and gene transcription regulation in genome scale. We discuss the complexity profiling for segmentation and delineation of genome sequences, search for genome repeats and transposable elements, and applications to next-generation sequencing reads. We review the complexity methods and new applications fields: analysis of mutation hotspots loci, analysis of short sequencing reads with quality control, and alignment-free genome comparisons. The algorithms implementing various numerical measures of text complexity estimates including combinatorial and linguistic measures have been developed before genome sequencing era. The series of tools to estimate sequence complexity use compression approaches, mainly by modification of Lempel-Ziv compression. Most of the tools are available online providing large-scale service for whole genome analysis. Novel machine learning applications for classification of complete genome sequences also include sequence compression and complexity algorithms. We present comparison of the complexity methods on the different sequence sets, the applications for gene transcription regulatory regions analysis. Furthermore, we discuss approaches and application of sequence complexity for proteins. The complexity measures for amino acid sequences could be calculated by the same entropy and compression-based algorithms. But the functional and evolutionary roles of low complexity regions in protein have specific features differing from DNA. The tools for protein sequence complexity aimed for protein structural constraints. It was shown that low complexity regions in protein sequences are conservative in evolution and have important biological and structural functions. Finally, we summarize recent findings in large scale genome complexity comparison and applications for coronavirus genome analysis.
    Language English
    Publishing date 2023-09-15
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-023-01140-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Special Issue on "Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0".

    Orlov, Yuriy L / Chen, Ming

    International journal of molecular sciences

    2023  Volume 24, Issue 24

    Abstract: The analysis of molecular mechanisms underlying plant adaptation to environmental changes and stress response is crucial for plant biotechnology [ ... ]. ...

    Abstract The analysis of molecular mechanisms underlying plant adaptation to environmental changes and stress response is crucial for plant biotechnology [...].
    MeSH term(s) Genomics ; Computational Biology ; Plants/genetics ; Biotechnology
    Language English
    Publishing date 2023-12-18
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms242417588
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Deciphering the Molecular Mechanism of the Intermediate Secondary Growth and Internode Elongation of the Castor Bean (

    Chen, Yujie / Orlov, Yuriy L / Chen, Ming

    International journal of molecular sciences

    2024  Volume 25, Issue 2

    Abstract: The length of internodes plays a crucial role in determining the height of the castor plant ( ...

    Abstract The length of internodes plays a crucial role in determining the height of the castor plant (
    MeSH term(s) Ricinus communis/genetics ; Transcriptome ; Plant Breeding ; Ricinus ; Metabolome ; Castor Oil
    Chemical Substances Castor Oil (8001-79-4)
    Language English
    Publishing date 2024-01-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms25021053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Biophysics education section and computational training discussion at VII Congress of Russian Biophysicists.

    Turkina, Vasilisa A / Orlova, Nina G / Orlov, Yuriy L

    Biophysical reviews

    2023  Volume 15, Issue 5, Page(s) 807–809

    Abstract: We present commentaries on the section "Biophysical education" of the VII Congress of Russian Biophysicists. Presentations are briefly introduced along with the current problems of biophysical education and the educational approach development. We ... ...

    Abstract We present commentaries on the section "Biophysical education" of the VII Congress of Russian Biophysicists. Presentations are briefly introduced along with the current problems of biophysical education and the educational approach development. We discuss educational course on bioinformatics based on the integration of online databases and the usage of internet platforms for functional annotation of genes and proteins.
    Language English
    Publishing date 2023-09-19
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-023-01147-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Application of Artificial Intelligence or machine learning in risk sharing agreements for pharmacotherapy risk management.

    Oborotov, Grigory A / Koshechkin, Konstantin A / Orlov, Yuriy L

    Journal of integrative bioinformatics

    2023  Volume 20, Issue 3

    Abstract: Applications of Artificial Intelligence in medical informatics solutions risk sharing have social value. At a time of ever-increasing cost for the provision of medicines to citizens, there is a need to restrain the growth of health care costs. The search ...

    Abstract Applications of Artificial Intelligence in medical informatics solutions risk sharing have social value. At a time of ever-increasing cost for the provision of medicines to citizens, there is a need to restrain the growth of health care costs. The search for computer technologies to stop or slow down the growth of costs acquires a new very important and significant meaning. We discussed the two information technologies in pharmacotherapy and the possibility of combining and sharing them, namely the combination of risk-sharing agreements and Machine Learning, which was made possible by the development of Artificial Intelligence (AI). Neural networks could be used to predict the outcome to reduce the risk factors for treatment. AI-based data processing automation technologies could be also used for risk-sharing agreements automation.
    MeSH term(s) Artificial Intelligence ; Machine Learning ; Neural Networks, Computer ; Automation ; Risk Management
    Language English
    Publishing date 2023-12-12
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2147212-9
    ISSN 1613-4516 ; 1613-4516
    ISSN (online) 1613-4516
    ISSN 1613-4516
    DOI 10.1515/jib-2023-0014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: BioGraph: Data Model for Linking and Querying Diverse Biological Metadata.

    Veljković, Aleksandar N / Orlov, Yuriy L / Mitić, Nenad S

    International journal of molecular sciences

    2023  Volume 24, Issue 8

    Abstract: Studying the association of gene function, diseases, and regulatory gene network reconstruction demands data compatibility. Data from different databases follow distinct schemas and are accessible in heterogenic ways. Although the experiments differ, ... ...

    Abstract Studying the association of gene function, diseases, and regulatory gene network reconstruction demands data compatibility. Data from different databases follow distinct schemas and are accessible in heterogenic ways. Although the experiments differ, data may still be related to the same biological entities. Some entities may not be strictly biological, such as geolocations of habitats or paper references, but they provide a broader context for other entities. The same entities from different datasets can share similar properties, which may or may not be found within other datasets. Joint, simultaneous data fetching from multiple data sources is complicated for the end-user or, in many cases, unsupported and inefficient due to differences in data structures and ways of accessing the data. We propose BioGraph-a new model that enables connecting and retrieving information from the linked biological data that originated from diverse datasets. We have tested the model on metadata collected from five diverse public datasets and successfully constructed a knowledge graph containing more than 17 million model objects, of which 2.5 million are individual biological entity objects. The model enables the selection of complex patterns and retrieval of matched results that can be discovered only by joining the data from multiple sources.
    MeSH term(s) Metadata ; Databases, Factual
    Language English
    Publishing date 2023-04-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24086954
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Life: Computational Genomics Applications in Life Sciences.

    Orlov, Yuriy L / Anashkina, Anastasia A

    Life (Basel, Switzerland)

    2021  Volume 11, Issue 11

    Abstract: This Special Issue, "Life: Computational Genomics", presents research articles on systems biology applications, computational genomics, and bioinformatics methods in life sciences [ ... ]. ...

    Abstract This Special Issue, "Life: Computational Genomics", presents research articles on systems biology applications, computational genomics, and bioinformatics methods in life sciences [...].
    Language English
    Publishing date 2021-11-09
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2662250-6
    ISSN 2075-1729
    ISSN 2075-1729
    DOI 10.3390/life11111211
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Glutathione Non-Covalent Binding Sites on Hemoglobin and Major Glutathionylation Target betaCys93 Are Conservative among Both Hypoxia-Sensitive and Hypoxia-Tolerant Mammal Species.

    Anashkina, Anastasia A / Simonenko, Sergey Yu / Orlov, Yuriy L / Petrushanko, Irina Yu

    International journal of molecular sciences

    2023  Volume 25, Issue 1

    Abstract: Intracellular tripeptide glutathione is an important agent of cell survival under hypoxia. Glutathione covalently binds to SH groups of hemoglobin cysteine residues, protecting them from irreversible oxidation, and changes its affinity to oxygen. Reduced ...

    Abstract Intracellular tripeptide glutathione is an important agent of cell survival under hypoxia. Glutathione covalently binds to SH groups of hemoglobin cysteine residues, protecting them from irreversible oxidation, and changes its affinity to oxygen. Reduced glutathione (GSH) can also form a noncovalent complex with hemoglobin. Previously, we showed that hemoglobin tetramer has four noncovalent binding sites of glutathione GSH molecules inside, two of which are released during hemoglobin transition to deoxy form. In this study, we characterized the conserved cysteine residues and residues of noncovalent glutathione binding sites in the sequences of a number of hypoxia-tolerant and hypoxia-sensitive mammals. The solvent accessibility of all HbA and HbB residues in oxy and deoxy forms was analyzed. The alpha subunit of all species considered was shown to have no conserved cysteines, whereas the beta subunit contains Cys93 residue, which is conserved across species and whose glutathionylation changes the affinity of hemoglobin for oxygen 5-6-fold. It was found that the key residues of noncovalent glutathione binding sites in both alpha and beta subunits are absolutely conserved in all species considered, suggesting a common mechanism of hemoglobin redox regulation for both hypoxia-sensitive and hypoxia-tolerant mammals.
    MeSH term(s) Animals ; Cysteine ; Hypoxia ; Oxygen ; Binding Sites ; Glutathione ; Hemoglobins ; Mammals
    Chemical Substances Cysteine (K848JZ4886) ; Oxygen (S88TT14065) ; Glutathione (GAN16C9B8O) ; Hemoglobins
    Language English
    Publishing date 2023-12-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms25010053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Editorial: Population and ancestry specific variation in disease susceptibility.

    Das, Ranajit / Savina, Ekaterina A / Tatarinova, Tatiana V / Orlov, Yuriy L

    Frontiers in genetics

    2023  Volume 14, Page(s) 1267719

    Language English
    Publishing date 2023-09-20
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1267719
    Database MEDical Literature Analysis and Retrieval System OnLINE

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