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, 1987-; Marti, Stefanie; Armaos, Alexandros, 1989-; 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 ...
  • Ciryam, Prajwal; Antalek, Matthew; Cid Samper, Fernando, 1991-; Tartaglia, Gian Gaetano; Dobson, Christopher M.; Guettsches, Katrin; Eggers, Britta; Vorgerd, Matthias; Marcus, Katrin; Kley, Rudolf A.; Morimoto, Richard I.; Vendruscolo, Michele; Weihl, Conrad C. (BioMed Central, 2019)
    Protein aggregation is a pathological feature of neurodegenerative disorders. We previously demonstrated that protein inclusions in the brain are composed of supersaturated proteins, which are abundant and aggregation-prone, ...
  • Delli Ponti, Riccardo, 1987-; Armaos, Alexandros, 1989-; Marti, Stefanie; Tartaglia, Gian Gaetano (Frontiers, 2018)
    To compare the secondary structure profiles of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict ...
  • 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 ...
  • Cid-Samper, Fernando; Gelabert-Baldrich, Mariona; Lang, Benjamin; Lorenzo Gotor, Maria de las Nieves; Ponti, Riccardo delli; Severijnen, Lies-Anne W.F.M.; Bolognesi, Benedetta; Gelpi, Ellen; Hukema, Renate K.; Botta Orfila, Teresa; Tartaglia, Gian Gaetano (Elsevier, 2018)
    Recent evidence indicates that specific RNAs promote the formation of ribonucleoprotein condensates by acting as scaffolds for RNA-binding proteins (RBPs). We systematically investigated RNA-RBP interaction networks 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 ...
  • Macho Rendón, Javier; Lang, Benjamin; Tartaglia, Gian Gaetano; Torrent Burgas, Marc (Oxford University Press, 2020)
    Bacterial infections have been on the rise world-wide in recent years and have a considerable impact on human well-being in terms of attributable deaths and disability-adjusted life years. Yet many mechanisms underlying ...
  • 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, 1987-; 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 ...
  • Cid Samper, Fernando, 1991- (Universitat Pompeu Fabra, 2020-01-27)
    Ribonucleoprotein granules (RNP granules) are liquid-liquid phase separated complexes composed mainly by proteins and RNA. They are responsible of many processes involved in RNA regulation. Alterations in the dynamics of ...
  • Armaos, Alexandros, 1989- (Universitat Pompeu Fabra, 2020-01-23)
    Despite what was previously considered, the role of RNA is not only to carry the genetic information from DNA to proteins. Indeed, RNA has proven to be implicated in more complex cellular processes. Recent evidence suggests ...
  • 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 ...
  • Delli Ponti, Riccardo, 1987-; Armaos, Alexandros, 1989-; Vandelli, Andrea; Tartaglia, Gian Gaetano (Oxford University Press, 2020)
    MOTIVATION: RNA structure is difficult to predict in vivo due to interactions with enzymes and other molecules. Here we introduce CROSSalive, an algorithm to predict the single- and double-stranded regions of RNAs in vivo ...
  • 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 ...
  • Riemschoss, Katrin; Arndt, Verena; Bolognesi, Benedetta; von Eisenhart-Rothe, Philipp; Liu, Shu; Buravlova, Oleksandra; Duernberger, Yvonne; Paulsen, Lydia; Hornberger, Annika; Hossinger, André; Lorenzo Gotor, Maria de las Nieves; Hogl, Sebastian; Müller, Stephan A.; Tartaglia, Gian Gaetano; Lichtenthaler, Stefan F.; Vorberg, Ina M. (Life Science Alliance, 2019)
    Prions of lower eukaryotes are self-templating protein aggregates that replicate by converting homotypic proteins into stable, tightly packed beta-sheet-rich protein assemblies. Propagation is mediated by prion domains, ...