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  1. Article: RhythmicDB: A Database of Predicted Multi-Frequency Rhythmic Transcripts.

    Castellana, Stefano / Biagini, Tommaso / Petrizzelli, Francesco / Cabibbo, Andrea / Mazzoccoli, Gianluigi / Mazza, Tommaso

    Frontiers in genetics

    2022  Volume 13, Page(s) 882044

    Abstract: The physiology and behavior of living organisms are featured by time-related variations driven by molecular clockworks that arose during evolution stochastically and heterogeneously. Over the years, several high-throughput experiments were performed to ... ...

    Abstract The physiology and behavior of living organisms are featured by time-related variations driven by molecular clockworks that arose during evolution stochastically and heterogeneously. Over the years, several high-throughput experiments were performed to evaluate time-dependent gene expression in different cell types across several species and experimental conditions. Here, these were retrieved, manually curated, and analyzed by two software packages, BioCycle and MetaCycle, to infer circadian or ultradian transcripts across different species. These transcripts were stored in RhythmicDB and made publically available.
    Language English
    Publishing date 2022-06-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.882044
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Dystonia as Presenting Feature of Compound Heterozygous PMPCA Gene Variants.

    De Santis, Tiziana / Serpieri, Valentina / Biagini, Tommaso / Lanotte, Michele / Criffò, Carlotta / Mazza, Tommaso / Valente, Enza Maria / Albanese, Alberto

    Movement disorders clinical practice

    2023  Volume 10, Issue 6, Page(s) 1020–1023

    Language English
    Publishing date 2023-04-27
    Publishing country United States
    Document type Journal Article
    ISSN 2330-1619
    ISSN (online) 2330-1619
    DOI 10.1002/mdc3.13749
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Functional Study of SNCA p.V15A Variant: Further Linking α-Synuclein and Glucocerebrosidase.

    Avenali, Micol / Cerri, Silvia / Palmieri, Ilaria / Ongari, Gerardo / Stiuso, Rita / Buongarzone, Gabriele / Tassorelli, Cristina / Biagini, Tommaso / Valente, Marialuisa / Cereda, Cristina / Mazza, Tommaso / Gana, Simone / Pacchetti, Claudio / Valente, Enza Maria

    Movement disorders : official journal of the Movement Disorder Society

    2024  

    Abstract: Background: SNCA p.V15A was reported in five families. In vitro models showed increased aggregation and seeding activity, mitochondrial damage, and apoptosis. Mutant flies had reduced flying ability and survival.: Objectives: To clinically and ... ...

    Abstract Background: SNCA p.V15A was reported in five families. In vitro models showed increased aggregation and seeding activity, mitochondrial damage, and apoptosis. Mutant flies had reduced flying ability and survival.
    Objectives: To clinically and functionally evaluate SNCA p.V15A in a large Italian family with Parkinson's disease (PD).
    Methods: Genetic diagnosis was reached through next-generation sequencing. Pathogenicity was assessed by molecular dynamics simulation and biochemical studies on peripheral blood mononuclear cells (PBMCs).
    Results: Five siblings carried SNCA p.V15A; three developed bradykinetic-rigid PD in their 50s with rapid motor progression and variable cognitive impairment. A fourth sibling had isolated mood disturbance, whereas the fifth was still unaffected at age 47. The mutant protein showed decreased stability and an unstable folded structure. Proband's PBMCs showed elevated total and phosphorylated α-synuclein (α-syn) levels and significantly reduced glucocerebrosidase activity.
    Conclusion: This study demonstrates accumulation of α-syn
    Language English
    Publishing date 2024-03-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 607633-6
    ISSN 1531-8257 ; 0885-3185
    ISSN (online) 1531-8257
    ISSN 0885-3185
    DOI 10.1002/mds.29736
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2555: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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    Zs.MO 238: Show issues

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  4. Article ; Online: Connecting the dots: A practical evaluation of web-tools for describing protein dynamics as networks.

    Petrizzelli, Francesco / Biagini, Tommaso / Bianco, Salvatore Daniele / Liorni, Niccolò / Napoli, Alessandro / Castellana, Stefano / Mazza, Tommaso

    Frontiers in bioinformatics

    2022  Volume 2, Page(s) 1045368

    Abstract: Protein Structure Networks (PSNs) are a well-known mathematical model for estimation and analysis of the three-dimensional protein structure. Investigating the topological architecture of PSNs may help identify the crucial amino acid residues for protein ...

    Abstract Protein Structure Networks (PSNs) are a well-known mathematical model for estimation and analysis of the three-dimensional protein structure. Investigating the topological architecture of PSNs may help identify the crucial amino acid residues for protein stability and protein-protein interactions, as well as deduce any possible mutational effects. But because proteins go through conformational changes to give rise to essential biological functions, this has to be done dynamically over time. The most effective method to describe protein dynamics is molecular dynamics simulation, with the most popular software programs for manipulating simulations to infer interaction networks being RING, MD-TASK, and NAPS. Here, we compare the computational approaches used by these three tools-all of which are accessible as web servers-to understand the pathogenicity of missense mutations and talk about their potential applications as well as their advantages and disadvantages.
    Language English
    Publishing date 2022-10-19
    Publishing country Switzerland
    Document type Journal Article ; Review
    ISSN 2673-7647
    ISSN (online) 2673-7647
    DOI 10.3389/fbinf.2022.1045368
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: KDM6A missense variants hamper H3 histone demethylation in lung squamous cell carcinoma

    Biagini, Tommaso / Petrizzelli, Francesco / Bianco, Salvatore Daniele / Liorni, Niccolò / Napoli, Alessandro / Castellana, Stefano / Luigi Vescovi, Angelo / Carella, Massimo / Caputo, Viviana / Mazza, Tommaso

    Computational and Structural Biotechnology Journal. 2022, v. 20

    2022  

    Abstract: KDM6A is the disease causative gene of type 2 Kabuki Syndrome, a rare multisystem disease; it is also a known cancer driver gene, with multiple somatic mutations found in a few cancer types. In this study, we looked at eleven missense variants in lung ... ...

    Abstract KDM6A is the disease causative gene of type 2 Kabuki Syndrome, a rare multisystem disease; it is also a known cancer driver gene, with multiple somatic mutations found in a few cancer types. In this study, we looked at eleven missense variants in lung squamous cell carcinoma, one of the most common lung cancer subtypes, to see how they affect the KDM6A catalytic mechanisms. We found that they influence the interaction with histone H3 and the exposure of the trimethylated Lys27, which is critical for wild-type physiological function to varying degrees, by altering the conformational transition.
    Keywords biotechnology ; demethylation ; genes ; histones ; lung neoplasms ; lungs ; squamous cell carcinoma
    Language English
    Size p. 3151-3160.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.06.041
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Exploiting

    Cocciadiferro, Dario / Mazza, Tommaso / Vecchio, Davide / Biagini, Tommaso / Petrizzelli, Francesco / Agolini, Emanuele / Villani, Andrea / Minervino, Daniele / Martinelli, Diego / Rizzo, Cristiano / Boenzi, Sara / Panfili, Filippo Maria / Buonuomo, Paola Sabrina / Macchiaiolo, Marina / Bartuli, Andrea / Novelli, Antonio

    Frontiers in genetics

    2024  Volume 14, Page(s) 1307934

    Abstract: Desmosterolosis is a rare sterol biosynthesis disorder characterized by multiple congenital anomalies, failure to thrive, severe developmental delay, progressive epileptic encephalopathy, and elevated levels of desmosterol caused by biallelic mutations ... ...

    Abstract Desmosterolosis is a rare sterol biosynthesis disorder characterized by multiple congenital anomalies, failure to thrive, severe developmental delay, progressive epileptic encephalopathy, and elevated levels of desmosterol caused by biallelic mutations of
    Language English
    Publishing date 2024-01-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1307934
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Further case of enlarged spinal nerve roots in KRAS-related Noonan syndrome.

    Leoni, Chiara / Viscogliosi, Germana / Onesimo, Roberta / Verdolotti, Tommaso / Biagini, Tommaso / Mazza, Tommaso / De Luca, Alessandro / Perri, Lucrezia / Trevisan, Valentina / Flex, Elisabetta / Tartaglia, Marco / Zampino, Giuseppe

    Clinical genetics

    2023  Volume 104, Issue 1, Page(s) 136–138

    Abstract: Noonan syndrome (NS) belongs to RASopathies, a family of disorders caused by unregulated signaling through the RAS-MAPK pathway. Herein, we report on an individual with molecularly confirmed diagnosis of NS showing asymptomatic enlarged spinal nerve ... ...

    Abstract Noonan syndrome (NS) belongs to RASopathies, a family of disorders caused by unregulated signaling through the RAS-MAPK pathway. Herein, we report on an individual with molecularly confirmed diagnosis of NS showing asymptomatic enlarged spinal nerve roots, which are distinctive features of neurofibromatosis type 1. To date, a total of 16 patients with neurogenic tumors resembling neurofibromas/schwannomas and a molecularly confirmed diagnosis of a non-NF1 RASopathy have been reported, adding this further feature shared among RASopathies.
    MeSH term(s) Humans ; Noonan Syndrome/diagnosis ; Noonan Syndrome/genetics ; Proto-Oncogene Proteins p21(ras)/genetics ; Neurofibromatosis 1/complications ; Neurofibromatosis 1/diagnosis ; Neurofibromatosis 1/genetics ; Neurofibromatoses ; Spinal Nerve Roots/diagnostic imaging ; Mutation
    Chemical Substances Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2) ; KRAS protein, human
    Language English
    Publishing date 2023-02-21
    Publishing country Denmark
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 221209-2
    ISSN 1399-0004 ; 0009-9163
    ISSN (online) 1399-0004
    ISSN 0009-9163
    DOI 10.1111/cge.14308
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 413: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  8. Article ; Online: APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants.

    Bianco, Salvatore Daniele / Parca, Luca / Petrizzelli, Francesco / Biagini, Tommaso / Giovannetti, Agnese / Liorni, Niccolò / Napoli, Alessandro / Carella, Massimo / Procaccio, Vincent / Lott, Marie T / Zhang, Shiping / Vescovi, Angelo Luigi / Wallace, Douglas C / Caputo, Viviana / Mazza, Tommaso

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 5058

    Abstract: Mitochondrial dysfunction has pleiotropic effects and is frequently caused by mitochondrial DNA mutations. However, factors such as significant variability in clinical manifestations make interpreting the pathogenicity of variants in the mitochondrial ... ...

    Abstract Mitochondrial dysfunction has pleiotropic effects and is frequently caused by mitochondrial DNA mutations. However, factors such as significant variability in clinical manifestations make interpreting the pathogenicity of variants in the mitochondrial genome challenging. Here, we present APOGEE 2, a mitochondrially-centered ensemble method designed to improve the accuracy of pathogenicity predictions for interpreting missense mitochondrial variants. Built on the joint consensus recommendations by the American College of Medical Genetics and Genomics/Association for Molecular Pathology, APOGEE 2 features an improved machine learning method and a curated training set for enhanced performance metrics. It offers region-wise assessments of genome fragility and mechanistic analyses of specific amino acids that cause perceptible long-range effects on protein structure. With clinical and research use in mind, APOGEE 2 scores and pathogenicity probabilities are precompiled and available in MitImpact. APOGEE 2's ability to address challenges in interpreting mitochondrial missense variants makes it an essential tool in the field of mitochondrial genetics.
    MeSH term(s) Humans ; Mutation, Missense ; Mutation ; Amino Acids ; Machine Learning ; Mitochondria/genetics
    Chemical Substances Amino Acids
    Language English
    Publishing date 2023-08-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-40797-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: A comparative benchmark of classic DNA motif discovery tools on synthetic data.

    Castellana, Stefano / Biagini, Tommaso / Parca, Luca / Petrizzelli, Francesco / Bianco, Salvatore Daniele / Vescovi, Angelo Luigi / Carella, Massimo / Mazza, Tommaso

    Briefings in bioinformatics

    2021  Volume 22, Issue 6

    Abstract: Hundreds of human proteins were found to establish transient interactions with rather degenerated consensus DNA sequences or motifs. Identifying these motifs and the genomic sites where interactions occur represent one of the most challenging research ... ...

    Abstract Hundreds of human proteins were found to establish transient interactions with rather degenerated consensus DNA sequences or motifs. Identifying these motifs and the genomic sites where interactions occur represent one of the most challenging research goals in modern molecular biology and bioinformatics. The last twenty years witnessed an explosion of computational tools designed to perform this task, whose performance has been last compared fifteen years ago. Here, we survey sixteen of them, benchmark their ability to identify known motifs nested in twenty-nine simulated sequence datasets, and finally report their strengths, weaknesses, and complementarity.
    MeSH term(s) Benchmarking ; Computational Biology/methods ; DNA/chemistry ; Humans ; Sequence Analysis, DNA/methods
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2021-08-05
    Publishing country England
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbab303
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 6262: Show issues Location:
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  10. Article: Molecular dynamics analysis of superoxide dismutase 1 mutations suggests decoupling between mechanisms underlying ALS onset and progression.

    Kalia, Munishikha / Miotto, Mattia / Ness, Deborah / Opie-Martin, Sarah / Spargo, Thomas P / Di Rienzo, Lorenzo / Biagini, Tommaso / Petrizzelli, Francesco / Al Khleifat, Ahmad / Kabiljo, Renata / Mazza, Tommaso / Ruocco, Giancarlo / Milanetti, Edoardo / Dobson, Richard Jb / Al-Chalabi, Ammar / Iacoangeli, Alfredo

    Computational and structural biotechnology journal

    2023  Volume 21, Page(s) 5296–5308

    Abstract: Mutations in the superoxide dismutase 1 ( ...

    Abstract Mutations in the superoxide dismutase 1 (
    Language English
    Publishing date 2023-09-17
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2023.09.016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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