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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: 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)

    Full text online

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

    Facchiano Angelo

    Peptidomics, Vol 2, Iss

    2016  Volume 1

    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 2016-12-01T00:00:00Z
    Publisher De Gruyter Open
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  6. 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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    In stock of ZB MED Cologne/Königswinter

    Zs.MO 81: Show issues

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  7. 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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  8. Article ; Online: Standardizing macromolecular structure files: further efforts are needed

    D’Arminio, Nancy / Giordano, Deborah / Scafuri, Bernardina / Facchiano, Angelo / Marabotti, Anna

    Trends in Biochemical Sciences. 20232023 July 06, Apr. 06, v. 48, no. 7 p.590-596

    2023  

    Abstract: Investigating large datasets of biological information by automatic procedures may offer chances of progress in knowledge. Recently, tremendous improvements in structural biology have allowed the number of structures in the Protein Data Bank (PDB) ... ...

    Abstract Investigating large datasets of biological information by automatic procedures may offer chances of progress in knowledge. Recently, tremendous improvements in structural biology have allowed the number of structures in the Protein Data Bank (PDB) archive to increase rapidly, in particular those for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated proteins. However, their automatic analysis can be hampered by the nonuniform descriptors used by authors in some records of the PDB and PDBx/mmCIF files. In this opinion article we highlight the difficulties encountered in automating the analysis of hundreds of structures, suggesting that further standardization of the description of these molecular entities and of their attributes, generalized to the macromolecular structures contained in the PDB, might generate files more suitable for automatized analyses of a large number of structures.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; data collection ; databases ; structural biology ; PDB archive ; automatic data analysis ; antibody ; spike protein
    Language English
    Dates of publication 2023-0406
    Size p. 590-596.
    Publishing place Elsevier Ltd
    Document type Article ; Online
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2023.03.002
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 78/716: Show issues

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  9. Article ; Online: Deletion of a Single Lysine Residue at Position 292 of CAMK2A Disrupts Protein Function, Causing Severe Epileptic Encephalopathy and Intellectual Disability

    Lintas, Carla / Facchiano, Angelo / Azzarà, Alessia / Cassano, Ilaria / Tabolacci, Claudio / Galasso, Cinzia / Gurrieri, Fiorella

    Genes (Basel). 2023 June 27, v. 14, no. 7

    2023  

    Abstract: Background: The use of NGS technology has rapidly increased during the last decade, and many new monogenic neurodevelopmental disorders have emerged. Pathogenic variants in the neuronal CAMK2A gene have been recently associated with “intellectual ... ...

    Abstract Background: The use of NGS technology has rapidly increased during the last decade, and many new monogenic neurodevelopmental disorders have emerged. Pathogenic variants in the neuronal CAMK2A gene have been recently associated with “intellectual developmental disorder, autosomal dominant 53″ (OMIM#617798), a syndrome characterized by variable clinical manifestations including mild to severe intellectual disability, delayed psychomotor development, delayed or absent speech, delayed walking, seizures, dysmorphic features and behavioral psychiatric manifestations as autism spectrum disorders, aggressive behavior, and hyperactivity. CAMK2A (OMIM*114078) encodes for a subunit of the calcium/calmodulin-dependent serine/threonine kinase II (CaMKII), which is predominately expressed in the brain, where it plays critical roles in synaptic plasticity, learning, and memory as well as in neuronal migration. Methods and Results: We hereby describe a thirty-five-year-old woman affected by severe intellectual disability with epileptic encephalopathy. We performed exome sequencing and found a de novo heterozygous variant in the CAMK2A gene (NM_171825.2: c.874_876delCTT; p.Lys292del), which was fully correlated with her phenotype. This is the first report of an inframe single amino acid deletion in a patient affected by intellectual developmental disorder autosomal dominant 53. The variant is predicted to affect protein structure and function and interaction with other proteins and hits a crucial functional site. Discussion: We discuss our variant in relation to previously reported variants and with the objective of delineating possible genotype–phenotype correlations.
    Keywords aggression ; amino acid deletion ; autism ; brain ; calcium-calmodulin-dependent protein kinase ; encephalopathy ; genes ; genotype-phenotype correlation ; heterozygosity ; lysine ; memory ; neurons ; neuroplasticity ; patients ; phenotype ; protein structure ; psychomotor development ; serine ; speech ; threonine ; women
    Language English
    Dates of publication 2023-0627
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14071353
    Database NAL-Catalogue (AGRICOLA)

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  10. 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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