Browsing by Author "Armaos, Alexandros, 1989-"

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  • Delli Ponti, Riccardo, 1987-; Broglia, Laura; Vandelli, Andrea; Armaos, Alexandros, 1989-; Torrent Burgas, Marc; Sanchez de Groot, Natalia; Tartaglia, Gian Gaetano (Wiley, 2023)
    RNA molecules undergo a number of chemical modifications whose effects can alter their structure and molecular interactions. Previous studies have shown that RNA editing can impact the formation of ribonucleoprotein complexes ...
  • 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 ...
  • 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 ...
  • Monti, Michele; Armaos, Alexandros, 1989-; Fantini, Marco; Pastore, Annalisa; Tartaglia, Gian Gaetano (Frontiers, 2021)
    Solubility is a requirement for many cellular processes. Loss of solubility and aggregation can lead to the partial or complete abrogation of protein function. Thus, understanding the relationship between protein evolution ...
  • 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 ...
  • Rea, Jessica; Menci, Valentina; Tollis, Paolo; Santini, Tiziana; Armaos, Alexandros, 1989-; Garone, Maria Giovanna; Iberite, Federica; Cipriano, Andrea; Tartaglia, Gian Gaetano; Rosa, Alessandro; Ballarino, Monica; Laneve, Pietro; Caffarelli, Elisa (Nature Research, 2020)
    Neuronal differentiation is a timely and spatially regulated process, relying on precisely orchestrated gene expression control. The sequential activation/repression of genes driving cell fate specification is achieved by ...
  • Cava, Claudia; Armaos, Alexandros, 1989-; Lang, Benjamin; Tartaglia, Gian Gaetano; Castiglioni, Isabella (Nature Research, 2022)
    Breast cancer is a heterogeneous disease classified into four main subtypes with different clinical outcomes, such as patient survival, prognosis, and relapse. Current genetic tests for the differential diagnosis of BC ...
  • Armaos, Alexandros, 1989-; 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 ...
  • Mas, Aina Maria; Goñi, Enrique; Ruiz de Los Mozos, Igor; Arcas Mantas, Aida; Statello, Luisa; González, Jovanna; Blázquez, Lorea; Lee, Wei Ting Chelsea; Gupta, Dipika; Sejas, Álvaro; Hoshina, Shoko; Armaos, Alexandros, 1989-; Tartaglia, Gian Gaetano; Waga, Shou; Ule, Jernej; Rothenberg, Eli; Gómez, María; Huarte, Maite (Nature Research, 2023)
    Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in ...
  • Zacco, Elsa; Kantelberg, Owen; Milanetti, Edoardo; Armaos, Alexandros, 1989-; Panei, Francesco Paolo; Gregory, Jenna; Jeacock, Kiani; Clarke, David J.; Chandran, Siddharthan; Ruocco, Giancarlo; Gustincich, Stefano; Horrocks, Mathew H.; Pastore, Annalisa; Tartaglia, Gian Gaetano (Nature Research, 2022)
    Aptamers are artificial oligonucleotides binding to specific molecular targets. They have a promising role in therapeutics and diagnostics but are often difficult to design. Here, we exploited the catRAPID algorithm to ...
  • Zacco, Elsa; Kantelberg, Owen; Milanetti, Edoardo; Armaos, Alexandros, 1989-; Panei, Francesco Paolo; Gregory, Jenna; Jeacock, Kiani; Clarke, David J.; Chandran, Siddharthan; Ruocco, Giancarlo; Gustincich, Stefano; Horrocks, Mathew H.; Pastore, Annalisa; Tartaglia, Gian Gaetano (Nature Research, 2022)
    Aptamers are artificial oligonucleotides binding to specific molecular targets. They have a promising role in therapeutics and diagnostics but are often difficult to design. Here, we exploited the catRAPID algorithm to ...
  • Sanchez de Groot, Natalia; Armaos, Alexandros, 1989-; Graña-Montes, Ricardo; Alriquet, Marion; Calloni, Giulia; Vabulas, R. Martin; Tartaglia, Gian Gaetano (Nature Research, 2019)
    The combination of high-throughput sequencing and in vivo crosslinking approaches leads to the progressive uncovering of the complex interdependence between cellular transcriptome and proteome. Yet, the molecular determinants ...
  • Lorenzo Gotor, Maria de las Nieves; Armaos, Alexandros, 1989-; Calloni, Giulia; Torrent Burgas, Marc; Vabulas, R. Martin; Sánchez de Groot, Natalia; Tartaglia, Gian Gaetano (Oxford University Press, 2020)
    Proteins and RNAs assemble in membrane-less organelles that organize intracellular spaces and regulate biochemical reactions. The ability of proteins and RNAs to form condensates is encoded in their sequences, yet it is ...
  • Armaos, Alexandros, 1989-; Zacco, Elsa; Sanchez de Groot, Natalia; Tartaglia, Gian Gaetano (Wiley-VCH Verlag, 2021)
    Changes in the abundance of protein and RNA molecules can impair the formation of complexes in the cell leading to toxicity and death. Here we exploit the information contained in protein, RNA and DNA interaction networks ...
  • Lang, Benjamin; Armaos, Alexandros, 1989-; Tartaglia, Gian Gaetano (Oxford University Press, 2019)
    Protein-RNA interactions are implicated in a number of physiological roles as well as diseases, with molecular mechanisms ranging from defects in RNA splicing, localization and translation to the formation of aggregates. ...
  • Vandelli, Andrea; Monti, Michele; Milanetti, Edoardo; Armaos, Alexandros, 1989-; Rupert, Jakob; Zacco, Elsa; Bechara, Elias; Delli Ponti, Riccardo, 1987-; Tartaglia, Gian Gaetano (Oxford University Press, 2020)
    Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100 000 human protein interactions with severe acute ...
  • Guiducci, Giulia; Paone, Alessio; Tramonti, Angela; Giardina, Giorgio; Rinaldo, Serena; Bouzidi, Amani; Magnifico, Maria C.; Marani, Marina; Menendez, Javier A.; Fatica, Alessandro; Macone, Alberto; Armaos, Alexandros, 1989-; Tartaglia, Gian Gaetano; Contestabile, Roberto; Paiardini, Alessandro; Cutruzzolà, Francesca (Oxford University Press, 2019)
    Enzymes of intermediary metabolism are often reported to have moonlighting functions as RNA-binding proteins and have regulatory roles beyond their primary activities. Human serine hydroxymethyltransferase (SHMT) is essential ...
  • Vandelli, Andrea; Arnal, Magdalena; Monti, Michele; Fiorentino, Jonathan; Broglia, Laura; Colantoni, Alessio; Sanchez de Groot, Natalia; Torrent Burgas, Marc; Armaos, Alexandros, 1989-; Tartaglia, Gian Gaetano (Oxford University Press, 2023)
    Biological condensates are membraneless organelles with different material properties. Proteins and RNAs are the main components, but most of their interactions are still unknown. Here, we introduce PRALINE, a database for ...

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