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Visualitza Recerca: articles, congressos, llibres per autoria "Tartaglia, Gian Gaetano"

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A computational approach for the discovery of protein-RNA networks

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 ...
A high-throughput approach to predict A-to-I effects on RNA structure indicates a change of double-stranded content in noncoding RNAs

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 ...
A high-throughput approach to profile RNA structure

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 ...
A metastable subproteome underlies inclusion formation in muscle proteinopathies

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, ...
A method for RNA structure prediction shows evidence for structure in lncRNAs

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 ...
Advances in the characterization of RNA-binding proteins

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 ...
Aggregation is a context-dependent constraint on protein evolution

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 ...
An integrative study of protein-RNA condensates identifies scaffolding RNAs and reveals players in fragile X-associated tremor/ataxia syndrome

Cid Samper, Fernando, 1991-; 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 ...
BacFITBase: a database to assess the relevance of bacterial genes during host infection

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 ...
By the company they keep: interaction networks define the binding ability of transcription factors

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 ...
catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

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 ...
catRAPID signature: identification of ribonucleoproteins and RNA-binding regions

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 ...
ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli

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) ...
Characterization of novel paternal ncRNAs at the Plagl1 locus, including Hymai, predicted to interact with regulators of active chromatin

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 ...
Constitutive patterns of gene expression regulated by RNA-binding proteins

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 ...
CROSSalive: a web server for predicting the in vivo structure of RNA molecules

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 ...
Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing

Conrad, Thomas; Ntini, Evgenia; Lang, Benjamin; Cozzuto, Luca; Andersen, Jesper B.; Marquardt, Jens U.; Ponomarenko, Julia; Tartaglia, Gian Gaetano; Vang Ørom, Ulf A. (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)

MicroRNA expression is important for gene regulation and deregulated microRNA expression is often observed in diseases such as cancer. The processing of primary microRNA transcripts is an important regulatory step in ...
Discovering the 3' UTR-mediated regulation of alpha-synuclein

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 ...
DnaK functions as a central hub in the E. colichaperone network

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 ...
DualSeqDB: the host-pathogen dual RNA sequencing database for infection processes

Macho Rendón, Javier; Lang, Benjamin; Ramos Llorens, Marc; Tartaglia, Gian Gaetano; Torrent Burgas, Marc (Oxford University Press, 2020)

Despite antibiotic resistance being a matter of growing concern worldwide, the bacterial mechanisms of pathogenesis remain underexplored, restraining our ability to develop new antimicrobials. The rise of high-throughput ...