Browsing by Author "Tartaglia, Gian Gaetano"

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  • Marchese, Domenica, 1986-; Livi, Carmen Maria; Tartaglia, Gian Gaetano (Humana Press (Springer Imprint), 2016)
    Protein–RNA interactions play important roles in a wide variety of cellular processes, ranging from transcriptional and posttranscriptional regulation of genes to host defense against pathogens. In this chapter we present ...
  • Delli Ponti, Riccardo; Marti, Stefanie; Armaos, Alexandros; Tartaglia, Gian Gaetano (Oxford University Press, 2017)
    Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without ...
  • Marchese, Domenica, 1986-; Sanchez de Groot, Natalia; Lorenzo Gotor, Maria de las Nieves; Livi, Carmen Maria; Tartaglia, Gian Gaetano (Wiley, 2016)
    From transcription, to transport, storage, and translation, RNA depends on association with different RNA-binding proteins (RBPs). Methods based on next-generation sequencing and protein mass-spectrometry have started to ...
  • Delli Ponti, Riccardo, 1987- (Universitat Pompeu Fabra, 2019-01-16)
    The secondary structure of an RNA molecule is fundamental for its function. However, structural conservation and the structure of RNA in vivo are still poorly understood. Data from recent high-throughput experiments can ...
  • Cirillo, Davide; Botta Orfila, Teresa; Tartaglia, Gian Gaetano (Oxford University Press, 2015)
    Access to genome-wide data provides the opportunity to address questions concerning the ability of transcription factors (TFs) to assemble in distinct macromolecular complexes. Here, we introduce the PAnDA (Protein And DNA ...
  • Agostini, Federico, 1985-; Zanzoni, Andreas; Klus, Petr, 1985-; Marchese, Domenica, 1986-; Cirillo, Davide; Tartaglia, Gian Gaetano (Oxford University Press, 2013)
    SUMMARY: Here we introduce catRAPID omics, a server for large-scale calculations of protein-RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences ...
  • Livi, Carmen Maria; Klus, Petr, 1985-; Delli Ponti, Riccardo; Tartaglia, Gian Gaetano (Oxford University Press, 2016)
    MOTIVATION: Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if the RNA-binding domains are not annotated. We introduce catRAPID signature to identify ...
  • Agostini, Federico, 1985-; Cirillo, Davide; Livi, Carmen Maria; Ponti, Riccardo delli; Tartaglia, Gian Gaetano (Oxford University Press, 2014)
    SUMMARY: Here we introduce ccSOL omics, a webserver for large-scale calculations of protein solubility. Our method allows (i) proteome-wide predictions; (ii) identification of soluble fragments within each sequences; (iii) ...
  • Iglesias-Platas, Isabel; Martin-Trujillo, Alex; Cirillo, Davide; Court, Franck; Guillaumet-Adkins, Amy; Camprubí, Cristina; Bourc'his, Deborah; Hata, Kenichiro; Feil, Robert; Tartaglia, Gian Gaetano; Arnaud, Philippe; Monk, David (Public Library of Science (PLoS), 2012)
    Genomic imprinting is a complex epigenetic mechanism of transcriptional control that utilizes DNA methylation and histone modifications to bring about parent-of-origin specific monoallelic expression in mammals. Genes ...
  • Tartaglia, Gian Gaetano; Cirillo, Davide; Marchese, Domenica, 1986-; Agostini, Federico, 1985-; Livi, Carmen Maria; Botta Orfila, Teresa (BioMed Central, 2014)
    Background: RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of ...
  • Marchese, Domenica, 1986-; Botta Orfila, Teresa; Cirillo, Davide; Rodríguez, Juan Antonio; Livi, Carmen Maria; Fernández-Santiago, Ruben; Ezquerra, Mario; Martí, Maria José; Bechara, Elias; Tartaglia, Gian Gaetano; Catalan multiple system atrophy-registry (CMSAR) (Oxford University Press, 2017)
    Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions (3'UTRs). Yet, the post-transcriptional mechanisms regulating SNCA ...
  • Calloni, Giulia; Chen, Taotao; Schermann, Sonya M.; Chang, Hung-chun; Genevaux, Pierre; Agostini, Federico, 1985-; Tartaglia, Gian Gaetano (Elsevier, 2012)
    Cellular chaperone networks prevent potentially toxic protein aggregation and ensure proteome integrity. Here, we used Escherichia coli as a model to understand the organization of these networks, focusing on the cooperation ...
  • Botta Orfila, Teresa; Tartaglia, Gian Gaetano; Michalon, Aubin (Springer, 2016)
    Fragile X-associated tremor/ataxia syndrome (FXTAS) is an inherited neurodegenerative disorder manifesting in carriers of 55 to 200 CGG repeats in the 5' untranslated region (UTR) of the fragile X mental retardation gene ...
  • Klus, Petr, 1985-; Cirillo, Davide; Botta Orfila, Teresa; Tartaglia, Gian Gaetano (Nature Publishing Group, 2015)
    It has been reported that genes up-regulated in cancer are often down-regulated in neurodegenerative disorders and vice versa. The fact that apparently unrelated diseases share functional pathways suggests a link between ...
  • Cirillo, Davide; Agostini, Federico, 1985-; Klus, Petr, 1985-; Marchese, Domenica, 1986-; Rodríguez, Silvia; Bolognesi, Benedetta; Tartaglia, Gian Gaetano (Cold Spring Harbor Laboratory Press (CSHL Press), 2013)
    Increasing evidence indicates that RNA plays an active role in a number of neurodegenerative diseases. We recently introduced a theoretical framework, catRAPID, to predict the binding ability of protein and RNA molecules. ...
  • Lobanov, Michail Yu.; Klus, Petr, 1985-; Sokolovsky, Igor V.; Tartaglia, Gian Gaetano; Galzitskaya, Oxana V. (Nature Publishing Group, 2016)
    The biological function of multiple repetitions of single amino acids, or homo-repeats, is largely unknown, but their occurrence in proteins has been associated with more than 20 hereditary diseases. Analysing 122 bacterial ...
  • Armaos, Alexandros; Cirillo, Davide; Tartaglia, Gian Gaetano (Oxford University Press, 2017)
    SUMMARY: Here we introduce omiXcore, a server for calculations of protein binding to large RNAs (> 500 nucleotides). Our webserver allows (i) use of both protein and RNA sequences without size restriction, (ii) pre-compiled ...
  • Marchese, Domenica, 1986- (Universitat Pompeu Fabra, 2016-11-14)
    The role of RNA processing in the pathogenesis of neurodegenerative diseases is still poorly understood. α-synuclein (SNCA) is a presynaptic neuronal protein known as the major component of Lewy bodies, the pathological ...
  • Zanzoni, Andreas; Spinelli, Lionel; Ribeiro, Diogo M.; Tartaglia, Gian Gaetano; Brun, Christine (Nature Research, 2019)
    The coordination of the synthesis of functionally-related proteins can be achieved at the post-transcriptional level by the action of common regulatory molecules, such as RNA-binding proteins (RBPs). Despite advances in ...
  • Cirillo, Davide (Universitat Pompeu Fabra, 2016-05-09)
    The purpose of my doctoral studies has been the development of bioinformatics methods to quantitatively evaluate associations between proteins and nucleic acids (NAs). This thesis aims at providing insights into molecular ...