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  1. Book ; Online ; E-Book: Omics approaches and technologies in COVID-19

    Barh, Debmalya / Azevedo, Vasco

    2022  

    Author's details edited by Debmalya Barh, Vasco Azevedo
    Keywords Electronic books
    Language English
    Size 1 Online-Ressource (xxv, 436 Seiten), Illustrationen
    Publisher Elsevier Academic Press
    Publishing place London
    Publishing country Great Britain
    Document type Book ; Online ; E-Book
    Note Description based on publisher supplied metadata and other sources
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    HBZ-ID HT021719322
    ISBN 978-0-323-98621-2 ; 9780323917940 ; 0-323-98621-8 ; 0323917941
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Book ; Online ; E-Book: Pan-genomics

    Barh, Debmalya / Soares, Siomar C. / Tiwari, Sandeep / Azevedo, Vasco

    applications, challenges, and future prospects

    2020  

    Author's details edited by Debmalya Barh, Siomar C. Soares, Sandeep Tiwari, Vasco Azevedo
    Keywords Electronic books
    Language English
    Size 1 Online-Ressource (xxiv, 450 Seiten), Illustrationen
    Publisher Elsevier Academic Press
    Publishing place London
    Publishing country Great Britain
    Document type Book ; Online ; E-Book
    Note Description based on publisher supplied metadata and other sources
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    HBZ-ID HT020440616
    ISBN 978-0-12-817077-9 ; 9780128170762 ; 0-12-817077-8 ; 012817076X
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  3. Book ; Online ; E-Book: Genomics and biotechnological advances in veterinary, poultry, and fisheries

    Malik, Yashpal Singh / Barh, Debmalya / Azevedo, Vasco / Khurana, S. M. Paul

    2020  

    Author's details edited by Yashpal Singh Malik, Debmalya Barh, Vasco Azevedo, S.M. Paul Khurana
    Keywords Genomics ; Animal biotechnology ; Fisheries ; Veterinary microbiology ; Poultry
    Language English
    Size 1 Online-Ressource (xxxii, 532 Seiten), Illustrationen
    Publisher Elsevier
    Publishing place London
    Publishing country Great Britain
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    HBZ-ID HT020233895
    ISBN 978-0-12-816353-5 ; 9780128163528 ; 0-12-816353-4 ; 0128163526
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  4. Article ; Online: Resequencing and characterization of the first

    Giovanelli Tacconi Gimenez, Enrico / Viana, Marcus Vinicius Canário / de Jesus Sousa, Thiago / Aburjaile, Flávia / Brenig, Bertram / Silva, Artur / Azevedo, Vasco

    PeerJ

    2024  Volume 12, Page(s) e16513

    Abstract: Background: Corynebacterium pseudotuberculosis: Methods: In this work, we compared the quality of three genome assemblies of strain Cp162 that used data from the DNA sequencing platforms SOLiD v3 Plus, IonTorrent PGM, and Illumina HiSeq 2500 with an ... ...

    Abstract Background: Corynebacterium pseudotuberculosis
    Methods: In this work, we compared the quality of three genome assemblies of strain Cp162 that used data from the DNA sequencing platforms SOLiD v3 Plus, IonTorrent PGM, and Illumina HiSeq 2500 with an optical map and investigate the unique features of this strain. For this purpose, we applied comparative genomic analysis on the different Cp162 genome assembly versions and included other 129 genomes from the same species.
    Results: Since the first version of the genome, there was an increase of 88 Kbp and 121 protein-coding sequences, a decrease of pseudogenes from 139 to 53, and two inversions and one rearrangement corrected. We identified 30 virulence genes, none associated to the camel host, and the genes
    MeSH term(s) Animals ; Sheep/genetics ; Corynebacterium pseudotuberculosis/genetics ; Camelus/genetics ; Genome, Bacterial/genetics ; Genome-Wide Association Study ; Rifampin ; Sequence Analysis, DNA
    Chemical Substances Rifampin (VJT6J7R4TR)
    Language English
    Publishing date 2024-01-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359 ; 2167-8359
    ISSN (online) 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.16513
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Editorial: Probiogenomics of classic and next-generation probiotics.

    Carvalho, Rodrigo D O / Guédon, Eric / Aburjaile, Flávia F / Azevedo, Vasco

    Frontiers in microbiology

    2022  Volume 13, Page(s) 982642

    Language English
    Publishing date 2022-08-17
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.982642
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Applications of Proteomics in Probiotics Having Anticancer and Chemopreventive Properties.

    Raslan, Mohamed A / Raslan, Sara A / Shehata, Eslam M / Mahmoud, Amr S / Viana, Marcus Vinicius Canário / Barh, Debmalya / Sabri, Nagwa A / Azevedo, Vasco

    Advances in experimental medicine and biology

    2024  Volume 1443, Page(s) 243–256

    Abstract: Proteomics has grown in importance in molecular sciences because it gives vital information on protein identification, expression levels, and alteration. Cancer is one of the world's major causes of death and is the major focus of much research. Cancer ... ...

    Abstract Proteomics has grown in importance in molecular sciences because it gives vital information on protein identification, expression levels, and alteration. Cancer is one of the world's major causes of death and is the major focus of much research. Cancer risk is determined by hereditary variables as well as the body's immunological condition. Probiotics have increasing medical importance due to their therapeutic influence on the human body in the prevention and treatment of numerous chronic illnesses, including cancer, with no adverse effects. Several anticancer, anti-inflammatory, and chemopreventive probiotics are studied using different proteomic approaches like two-dimensional gel electrophoresis, liquid chromatography-mass spectrometry, and matrix-assisted laser desorption/ionization mass spectrometry. To gain relevant information about probiotic characteristics, data from the proteomic analysis are evaluated and processed using bioinformatics pipelines. Proteomic studies showed the significance of different proteomic approaches in characterization, comparing strains, and determination of oxidative stress of different probiotics. Moreover, proteomic approaches identified different proteins that are involved in glucose metabolism and the formation of cell walls or cell membranes, and the differences in the expression of critical enzymes in the HIF-1 signaling pathway, starch, and sucrose metabolism, and other critical metabolic pathways.
    MeSH term(s) Humans ; Bacterial Proteins/metabolism ; Proteomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Probiotics/therapeutic use ; Neoplasms/prevention & control ; Electrophoresis, Gel, Two-Dimensional
    Chemical Substances Bacterial Proteins
    Language English
    Publishing date 2024-02-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 410187-X
    ISSN 0065-2598
    ISSN 0065-2598
    DOI 10.1007/978-3-031-50624-6_13
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3192: 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)
    Einzelsignatur: Show issues

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  7. Article ; Online: Pathogenomics insights for understanding Pasteurella multocida adaptation.

    Hurtado, Raquel / Maturrano, Lenin / Azevedo, Vasco / Aburjaile, Flávia

    International journal of medical microbiology : IJMM

    2020  Volume 310, Issue 4, Page(s) 151417

    Abstract: Pasteurella multocida is an important veterinary pathogen able to infect a wide range of animals in a broad spectrum of diseases. P. multocida is a complex microorganism in relation to its genomic flexibility, host adaptation and pathogenesis. ... ...

    Abstract Pasteurella multocida is an important veterinary pathogen able to infect a wide range of animals in a broad spectrum of diseases. P. multocida is a complex microorganism in relation to its genomic flexibility, host adaptation and pathogenesis. Epidemiological analysis based on multilocus sequence typing, serotyping, genotyping, association with virulence genes and single nucleotide polymorphisms (SNPs), enables assessment of intraspecies diversity, phylogenetic and strain-specific relationships associated with host predilection or disease. A high number of sequenced genomes provides us a more accurate genomic and epidemiological interpretation to determine whether certain lineages can infect a host or produce disease. Comparative genomic analysis and pan-genomic approaches have revealed a flexible genome for hosting mobile genetic elements (MGEs) and therefore significant variation in gene content. Moreover, it was possible to find lineage-specific MGEs from the same niche, showing acquisition probably due to an evolutionary convergence event or to a genetic group with infective capacity. Furthermore, diversification selection analysis exhibits proteins exposed on the surface subject to selection pressures with an interstrain heterogeneity related to their ability to adapt. This article is the first review describing the genomic relationship to elucidate the diversity and evolution of P. multocida.
    MeSH term(s) Adaptation, Physiological ; Animals ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; Genomics ; Humans ; Interspersed Repetitive Sequences ; Pasteurella Infections/pathology ; Pasteurella Infections/transmission ; Pasteurella Infections/veterinary ; Pasteurella multocida/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Poultry/microbiology ; Virulence/genetics
    Language English
    Publishing date 2020-03-25
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2006518-8
    ISSN 1618-0607 ; 1438-4221
    ISSN (online) 1618-0607
    ISSN 1438-4221
    DOI 10.1016/j.ijmm.2020.151417
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5333: 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: A journey through the

    Marques da Silva, Wanderson / Seyffert, Nubia / Silva, Artur / Azevedo, Vasco

    PeerJ

    2021  Volume 9, Page(s) e12456

    Abstract: Background: Corynebacterium pseudotuberculosis: Methodology: In this study we performed an extensive search in Web of Science of original and relevant articles related to methods, strategy, technology, approaches, and bioinformatics tools focused on ... ...

    Abstract Background: Corynebacterium pseudotuberculosis
    Methodology: In this study we performed an extensive search in Web of Science of original and relevant articles related to methods, strategy, technology, approaches, and bioinformatics tools focused on the functional study of the genome of
    Results: Here, we highlight the use of proteomics for understating several aspects of the physiology and pathogenesis of
    Conclusion: In this review, we showed that the combination of proteomics and bioinformatics studies is a suitable strategy to elucidate the functional aspects of the
    Language English
    Publishing date 2021-12-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.12456
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: GENPPI: standalone software for creating protein interaction networks from genomes.

    Anjos, William F / Lanes, Gabriel C / Azevedo, Vasco A / Santos, Anderson R

    BMC bioinformatics

    2021  Volume 22, Issue 1, Page(s) 596

    Abstract: Background: Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships capable of being annotated ... ...

    Abstract Background: Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary characteristics with efficient and effective results.
    Results: We developed GENPPI software for the ab initio prediction of interaction networks using predicted proteins from a genome. In our case study, we employed 50 genomes of the genus Corynebacterium. Based on the PP relationship, GENPPI differentiated genomes between the ovis and equi biovars of the species Corynebacterium pseudotuberculosis and created groups among the other species analysed. If we inspected only the CN relationship, we could not entirely separate biovars, only species. Our software GENPPI was determined to be efficient because, for example, it creates interaction networks from the central genomes of 50 species/lineages with an average size of 2200 genes in less than 40 min on a conventional computer. Moreover, the interaction networks that our software creates reflect correct evolutionary relationships between species, which we confirmed with average nucleotide identity analyses. Additionally, this software enables the user to define how he or she intends to explore the PP and CN characteristics through various parameters, enabling the creation of customized interaction networks. For instance, users can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user's choice regarding which set of genomes they are going to study.
    Conclusions: GENPPI can help fill the gap concerning the considerable number of novel genomes assembled monthly and our ability to process interaction networks considering the noncore genes for all completed genome versions. With GENPPI, a user dictates how many and how evolutionarily correlated the genomes answer a scientific query.
    MeSH term(s) Animals ; Phylogeny ; Protein Interaction Maps/genetics ; Sheep ; Software
    Language English
    Publishing date 2021-12-16
    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/s12859-021-04501-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: PanViTa: Pan Virulence and resisTance analysis.

    Rodrigues, Diego Lucas Neres / Ariute, Juan Carlos / Rodrigues da Costa, Francielly Morais / Benko-Iseppon, Ana Maria / Barh, Debmalya / Azevedo, Vasco / Aburjaile, Flávia

    Frontiers in bioinformatics

    2023  Volume 3, Page(s) 1070406

    Language English
    Publishing date 2023-02-07
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2673-7647
    ISSN (online) 2673-7647
    DOI 10.3389/fbinf.2023.1070406
    Database MEDical Literature Analysis and Retrieval System OnLINE

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