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Grant support

Spanish Ministry of Economy and Competitiveness (SAF2011-26211), the European Research Council (ERC Starting Grant to G. G. T) and the RTTIC project (to A.Z.). 'La Caixa' fellowship (to P. K.). Programa de Ayudas FPI del Ministerio de Economia y Competitividad-BES-2012-052457 (to D.M.).

Analysis of institutional authors

Tartaglia, Gian GaetanoCorresponding AuthorAgostini FAuthorZanzoni AAuthorKlus PAuthorMarchese DAuthorCirillo DAuthor

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March 25, 2020
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catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

Publicated to:Bioinformatics. 29 (22): 2928-2930 - 2013-11-15 29(22), DOI: 10.1093/bioinformatics/btt495

Authors: Agostini, F; Zanzoni, A; Klus, P; Marchese, D; Cirillo, D; Tartaglia, GG

Affiliations

CRG, Barcelona 08003, Spain - Author
Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain. - Author
UPF, Barcelona 08003, Spain - Author

Abstract

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 without size restriction; (iii) analysis of nucleic acid binding regions in proteins; and (iv) detection of RNA motifs involved in protein recognition.We developed a web server to allow fast calculation of ribonucleoprotein associations in Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae and Xenopus tropicalis (custom libraries can be also generated). The catRAPID omics was benchmarked on the recently published RNA interactomes of Serine/arginine-rich splicing factor 1 (SRSF1), Histone-lysine N-methyltransferase EZH2 (EZH2), TAR DNA-binding protein 43 (TDP43) and RNA-binding protein FUS (FUS) as well as on the protein interactomes of U1/U2 small nucleolar RNAs, X inactive specific transcript (Xist) repeat A region (RepA) and Crumbs homolog 3 (CRB3) 3'-untranslated region RNAs. Our predictions are highly significant (P < 0.05) and will help the experimentalist to identify candidates for further validation.catRAPID omics can be freely accessed on the Web at http://s.tartaglialab.com/catrapid/omics. Documentation, tutorial and FAQs are available at http://s.tartaglialab.com/page/catrapid_group.

Keywords

DatabaseIdentificationQuantitative predictions

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Bioinformatics due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2013, it was in position 4/52, thus managing to position itself as a Q1 (Primer Cuartil), in the category Mathematical & Computational Biology.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 5.19. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 3.32 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 22.83 (source consulted: Dimensions Aug 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-08-29, the following number of citations:

  • WoS: 217
  • Scopus: 141
  • Europe PMC: 154

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-08-29:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 212.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 210 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 4.25.
  • The number of mentions on the social network X (formerly Twitter): 6 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Agostini, FEDERICO) and Last Author (Tartaglia GG).

the authors responsible for correspondence tasks have been Tartaglia, Gian Gaetano and Tartaglia GG.