Rafael Riudavets Puig

Researcher - Department of Medical Genetics

Norwegian version of this page

Email r.r.puig@medisin.uio.no

Username

Visiting address Kirkeveien 166 Laboratoriebygget 0450 Oslo

Postal address Postboks 4956 Nydalen OUS HF Ullevål sykehus 0424 Oslo

Other affiliations Faculty of Mathematics and Natural Sciences (Student)

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Academic interests

Bioinformatics
Gene Expression Regulation
Systems Biology
Omics data integration
Machine Learning

Background

Bachelor in Biomedicine, Master degree in Bioinformatics and Biostatistics.

Positions held

Research Assistant, Martin Kuiper Group, Norwegian University of Science and Technology

Rauluseviciute, Ieva; Riudavets-Puig, Rafael; Blanc-Mathieu, Romain; Castro Mondragon, Jaime Abraham; Ferenc, Katalin Terezia & Kumar, Vipin [Show all 20 contributors for this article] (2023). JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic Acids Research (NAR). ISSN 0305-1048. 52(D1), p. D174–D182. doi: 10.1093/nar/gkad1059. Full text in Research Archive Show summary
JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.
Riudavets Puig, Rafael; Boddie, Paul; Khan, Aziz; Castro Mondragon, Jaime Abraham & Mathelier, Anthony (2021). UniBind: maps of high-confidence direct TF-DNA interactions across nine species. BMC Genomics. ISSN 1471-2164. doi: 10.1186/s12864-021-07760-6.
Castro Mondragon, Jaime Abraham; Riudavets Puig, Rafael; Rauluseviciute, Ieva; Lemma, Roza Berhanu; Turchi, Laura & Blanc-Mathieu, Romain [Show all 23 contributors for this article] (2021). JASPAR 2022: the 9th release of the open-acess database of transcription factor binding profiles. Nucleic Acids Research (NAR). ISSN 0305-1048. doi: 10.1093/nar/gkab1113. Full text in Research Archive
Khan, Aziz; Riudavets Puig, Rafael; Boddie, Paul & Mathelier, Anthony (2020). BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences. Bioinformatics. ISSN 1367-4803. doi: 10.1093/bioinformatics/btaa928. Full text in Research Archive
Holmås, Stian; Riudavets Puig, Rafael; Acencio, Marcio Luis; Mironov, Vladimir & Kuiper, Martin (2019). The Cytoscape BioGateway App: explorative network building from an RDF store. Bioinformatics. ISSN 1367-4803. doi: 10.1093/bioinformatics/btz835. Full text in Research Archive

View all works in Cristin

Riudavets Puig, Rafael (2021). UniBind 2021 poster.
Riudavets Puig, Rafael (2021). UniBind 2021 presentation.

View all works in Cristin

Published Aug. 28, 2019 12:07 PM - Last modified Dec. 15, 2023 1:03 PM

Research groups

The Mathelier Group