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  1. Book ; Online: Artificial Intelligence Bioinformatics: Development and Application of Tools for Omics and Inter-Omics Studies

    Facchiano, Angelo / Heider, Dominik / Chicco, Davide

    2020  

    Keywords Science: general issues ; Medical genetics ; artificial intelligence ; bioinformatics ; genomics ; omics ; inter-omics ; machine learning ; data mining ; proteomics
    Size 1 electronic resource (175 pages)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021230286
    ISBN 9782889637522 ; 2889637522
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Book: Computational Intelligence Methods for Bioinformatics and Biostatistics

    Chicco, Davide / Facchiano, Angelo / Tavazzi, Erica / Cazzaniga, Paolo / Vettoretti, Martina / Bernasconi, Anna / Avesani, Simone / Longato, Enrico

    17th International Meeting, CIBB 2021, Virtual Event, November 15¿17, 2021, Revised Selected Papers

    (Lecture Notes in Bioinformatics)

    2022  

    Series title Lecture Notes in Bioinformatics
    Keywords artificial intelligence ; computational and systems biology ; computer networks ; Computer Systems ; Computer vision ; Correlation Analysis ; Data Mining ; education ; Image Analysis ; image processing ; Image segmentation ; Learning ; Machine Learning ; Neural Networks ; pattern recognition ; Signal Processing ; biostatistics ; computer systems ; computer vision ; correlation analysis ; data mining ; image analysis ; image segmentation ; learning ; machine learning ; neural networks ; signal processing
    Language English
    Size 272 p.
    Edition 1
    Publisher Springer International Publishing
    Document type Book
    Note PDA Manuell_17
    Format 155 x 235 x 15
    ISBN 9783031208362 ; 3031208366
    Database PDA

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  3. Article: Editorial: Artificial intelligence and bioinformatics applications for omics and multi-omics studies.

    Facchiano, Angelo / Heider, Dominik / Mutarelli, Margherita

    Frontiers in genetics

    2024  Volume 15, Page(s) 1371473

    Language English
    Publishing date 2024-01-30
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2024.1371473
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Food Plant Secondary Metabolites Antiviral Activity and Their Possible Roles in SARS-CoV-2 Treatment: An Overview.

    Giordano, Deborah / Facchiano, Angelo / Carbone, Virginia

    Molecules (Basel, Switzerland)

    2023  Volume 28, Issue 6

    Abstract: Natural products and plant extracts exhibit many biological activities, including that related to the defense mechanisms against parasites. Many studies have investigated the biological functions of secondary metabolites and reported evidence of ... ...

    Abstract Natural products and plant extracts exhibit many biological activities, including that related to the defense mechanisms against parasites. Many studies have investigated the biological functions of secondary metabolites and reported evidence of antiviral activities. The pandemic emergencies have further increased the interest in finding antiviral agents, and efforts are oriented to investigate possible activities of secondary plant metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection. In this review, we performed a comprehensive analysis of studies through in silico and in vitro investigations, also including in vivo applications and clinical trials, to evaluate the state of knowledge on the antiviral activities of secondary metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection, with a particular focus on natural compounds present in food plants. Although some of the food plant secondary metabolites seem to be useful in the prevention and as a possible therapeutic management against SARS-CoV-2, up to now, no molecules can be used as a potential treatment for COVID-19; however, more research is needed.
    MeSH term(s) Humans ; SARS-CoV-2 ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19 ; Biological Products/pharmacology ; Biological Products/therapeutic use ; Plants, Edible
    Chemical Substances Antiviral Agents ; Biological Products
    Language English
    Publishing date 2023-03-08
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules28062470
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Structural and Functional Characterization of Lipoxygenases from Diatoms by Bioinformatics and Modelling Studies.

    Giordano, Deborah / Bonora, Simone / D'Orsi, Ilenia / D'Alelio, Domenico / Facchiano, Angelo

    Biomolecules

    2024  Volume 14, Issue 3

    Abstract: Lipoxygenases make several biological functions in cells, based on the products of the catalyzed reactions. In diatoms, microalgae ubiquitous in aquatic ecosystems, lipoxygenases have been noted for the oxygenation of fatty acids with the production of ... ...

    Abstract Lipoxygenases make several biological functions in cells, based on the products of the catalyzed reactions. In diatoms, microalgae ubiquitous in aquatic ecosystems, lipoxygenases have been noted for the oxygenation of fatty acids with the production of oxylipins, which are involved in many physiological and pathological processes in marine organisms. The interest in diatoms' lipoxygenases and oxylipins has increased due to their possible biotechnological applications, ranging from ecology to medicine. We investigated using bioinformatics and molecular docking tools the lipoxygenases of diatoms and the possible interaction with substrates. A large-scale analysis of sequence resources allowed us to retrieve 45 sequences of lipoxygenases from diatoms. We compared and analyzed the sequences by multiple alignments and phylogenetic trees, suggesting the possible clustering in phylogenetic groups. Then, we modelled the 3D structure of representative enzymes from the different groups and investigated in detail the structural and functional properties by docking simulations with possible substrates. The results allowed us to propose a classification of the lipoxygenases from diatoms based on their sequence features, which may be reflected in specific structural differences and possible substrate specificity.
    MeSH term(s) Lipoxygenases/chemistry ; Lipoxygenases/genetics ; Diatoms/genetics ; Oxylipins ; Phylogeny ; Molecular Docking Simulation ; Ecosystem ; Computational Biology
    Chemical Substances Lipoxygenases (EC 1.13.11.-) ; Oxylipins
    Language English
    Publishing date 2024-02-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom14030276
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: An investigation into the molecular basis of cancer comorbidities in coronavirus infection.

    Facchiano, Antonio / Facchiano, Francesco / Facchiano, Angelo

    FEBS open bio

    2020  Volume 10, Issue 11, Page(s) 2363–2374

    Abstract: Comorbidities in COVID-19 patients often worsen clinical conditions and may represent death predictors. Here, the expression of five genes, known to encode coronavirus receptors/interactors (ACE2, TMPRSS2, CLEC4M, DPP4 and TMPRSS11D), was investigated in ...

    Abstract Comorbidities in COVID-19 patients often worsen clinical conditions and may represent death predictors. Here, the expression of five genes, known to encode coronavirus receptors/interactors (ACE2, TMPRSS2, CLEC4M, DPP4 and TMPRSS11D), was investigated in normal and cancer tissues, and their molecular relationships with clinical comorbidities were investigated. Using expression data from GENT2 databases, we evaluated gene expression in all anatomical districts from 32 normal tissues in 3902 individuals. Functional relationships with body districts were analyzed by chilibot. We performed DisGeNet, genemania and DAVID analyses to identify human diseases associated with these genes. Transcriptomic expression levels were then analyzed in 31 cancer types and healthy controls from approximately 43 000 individuals, using GEPIA2 and GENT2 databases. By performing receiver operating characteristic analysis, the area under the curve (AUC) was used to discriminate healthy from cancer patients. Coronavirus receptors were found to be expressed in several body districts. Moreover, the five genes were found to associate with acute respiratory syndrome, diabetes, cardiovascular diseases and cancer (i.e. the most frequent COVID-19 comorbidities). Their expression levels were found to be significantly altered in cancer types, including colon, kidney, liver, testis, thyroid and skin cancers (P < 0.0001); AUC > 0.80 suggests that TMPRSS2, CLEC4M and DPP4 are relevant markers of kidney, liver, and thyroid cancer, respectively. The five coronavirus receptors are related to all main COVID-19 comorbidities and three show significantly different expression in cancer versus control tissues. Further investigation into their role may help in monitoring other comorbidities, as well as for follow-up of patients who have recovered from SARS-CoV-2 infection.
    MeSH term(s) Angiotensin-Converting Enzyme 2/genetics ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; Cell Adhesion Molecules/genetics ; Comorbidity ; Databases, Genetic ; Dipeptidyl Peptidase 4/genetics ; Epidemics ; Female ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; Genetic Predisposition to Disease/genetics ; Humans ; Lectins, C-Type/genetics ; Male ; Membrane Proteins/genetics ; Neoplasms/classification ; Neoplasms/epidemiology ; Neoplasms/genetics ; Receptors, Cell Surface/genetics ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/physiology ; Serine Endopeptidases/genetics ; Serine Proteases/genetics
    Chemical Substances CLEC4M protein, human ; Cell Adhesion Molecules ; Lectins, C-Type ; Membrane Proteins ; Receptors, Cell Surface ; Serine Proteases (EC 3.4.-) ; DPP4 protein, human (EC 3.4.14.5) ; Dipeptidyl Peptidase 4 (EC 3.4.14.5) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Serine Endopeptidases (EC 3.4.21.-) ; TMPRSS11D protein, human (EC 3.4.21.-) ; TMPRSS2 protein, human (EC 3.4.21.-)
    Keywords covid19
    Language English
    Publishing date 2020-10-12
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2651702-4
    ISSN 2211-5463 ; 2211-5463
    ISSN (online) 2211-5463
    ISSN 2211-5463
    DOI 10.1002/2211-5463.12984
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Reply to Jakovac: About COVID-19 and vitamin D.

    Facchiano, Angelo / Facchiano, Antonio / Bartoli, Manuela / Ricci, Alberto / Facchiano, Francesco

    American journal of physiology. Endocrinology and metabolism

    2020  Volume 318, Issue 6, Page(s) E838

    MeSH term(s) Betacoronavirus ; COVID-19 ; Coronavirus Infections ; Humans ; Pandemics ; Pneumonia, Viral ; SARS-CoV-2 ; Vitamin D
    Chemical Substances Vitamin D (1406-16-2)
    Keywords covid19
    Language English
    Publishing date 2020-05-20
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 603841-4
    ISSN 1522-1555 ; 0193-1849
    ISSN (online) 1522-1555
    ISSN 0193-1849
    DOI 10.1152/ajpendo.00185.2020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uc I Zs.89: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  8. Article: Molecular dynamics analysis of the structural properties of the transglutaminases of

    Giordano, Deborah / Langini, Cassiano / Caflisch, Amedeo / Marabotti, Anna / Facchiano, Angelo

    Computational and structural biotechnology journal

    2022  Volume 20, Page(s) 3924–3934

    Abstract: The microbial transglutaminase (TGase) ... ...

    Abstract The microbial transglutaminase (TGase) from
    Language English
    Publishing date 2022-07-20
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.07.024
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Food Plant Secondary Metabolites Antiviral Activity and Their Possible Roles in SARS-CoV-2 Treatment

    Deborah Giordano / Angelo Facchiano / Virginia Carbone

    Molecules, Vol 28, Iss 2470, p

    An Overview

    2023  Volume 2470

    Abstract: Natural products and plant extracts exhibit many biological activities, including that related to the defense mechanisms against parasites. Many studies have investigated the biological functions of secondary metabolites and reported evidence of ... ...

    Abstract Natural products and plant extracts exhibit many biological activities, including that related to the defense mechanisms against parasites. Many studies have investigated the biological functions of secondary metabolites and reported evidence of antiviral activities. The pandemic emergencies have further increased the interest in finding antiviral agents, and efforts are oriented to investigate possible activities of secondary plant metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection. In this review, we performed a comprehensive analysis of studies through in silico and in vitro investigations, also including in vivo applications and clinical trials, to evaluate the state of knowledge on the antiviral activities of secondary metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection, with a particular focus on natural compounds present in food plants. Although some of the food plant secondary metabolites seem to be useful in the prevention and as a possible therapeutic management against SARS-CoV-2, up to now, no molecules can be used as a potential treatment for COVID-19; however, more research is needed.
    Keywords phytochemicals ; secondary metabolites ; antiviral activity ; HIV ; SARS-CoV-2 ; COVID-19 ; Organic chemistry ; QD241-441
    Subject code 500
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Bioinformatic resources for the investigation of proteins and proteomes

    Facchiano Angelo

    Peptidomics, Vol 3, Iss 1, Pp 1-

    2017  Volume 10

    Abstract: Experimental techniques in omics sciences need strong support of bioinformatics tools for the data management, analysis and interpretation. Scientific community develops continuously new databases and tools. They make it possible the comparison of new ... ...

    Abstract Experimental techniques in omics sciences need strong support of bioinformatics tools for the data management, analysis and interpretation. Scientific community develops continuously new databases and tools. They make it possible the comparison of new experimental data with the existing ones, to gain new knowledge. Bioinformatics assists proteomics scientists for protein identification from experimental data, management of the huge data produced, investigation of molecular mechanisms of protein functions, their roles in biochemical pathways, and functional interpretation of biological processes. This article introduces the main bioinformatics resources for investigation in the protein world, with references to analyses performed by means of free tools available on the net.
    Keywords Databases ; bioinformatics tools ; experimental interpretation ; computational tools ; Gene Ontology ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2017-02-01T00:00:00Z
    Publisher De Gruyter
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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