Browsing by Author "Eyras Jiménez, Eduardo"

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  • Nucleosome-driven transcription factor binding and gene regulation
    Ballaré, Cecilia Julia; Castellano, Giancarlo; Gaveglia, Laura; Althammer, Sonja Daniela; González-Vallinas Rostes, Juan, 1983-; Eyras Jiménez, Eduardo; Le Dily, François; Zaurín Quer, Roser; Soronellas, Daniel; Vicent, Guillermo Pablo; Beato, Miguel (Elsevier, 2013)
    In fission yeast cells, Cds1 is the effector kinase of the DNA replication checkpoint. We previously showed that when the DNA replication checkpoint is activated, the repressor Yox1 is phosphorylated and inactivated by ...
  • PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
    Acera Mateos, Pablo; Balboa, Renzo F.; Easteal, Simon; Eyras Jiménez, Eduardo; Patel, Hardip R. (Nature Research, 2021)
    Viral co-infections occur in COVID-19 patients, potentially impacting disease progression and severity. However, there is currently no dedicated method to identify viral co-infections in patient RNA-seq data. We developed ...
  • Predictive models of gene regulation from high-throughput epigenomics data
    Althammer, Sonja Daniela; Pagès Pinós, Amadís; Eyras Jiménez, Eduardo (Hindawi, 2012)
    The epigenetic regulation of gene expression involves multiple factors. The synergistic or antagonistic action of these factors has suggested the existence of an epigenetic code for gene regulation. Highthroughput sequencing ...
  • Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
    Althammer, Sonja Daniela; González-Vallinas Rostes, Juan, 1983-; Ballaré, Cecilia Julia; Beato, Miguel; Eyras Jiménez, Eduardo (Oxford University Press, 2011)
    MOTIVATION: High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein-DNA and protein-RNA binding, as well as for measuring RNA expression. With increasing ...
  • RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
    Rubia, Ivan de la; Srivastava, Akanksha; Xue, Wenjing; Indi, Joel A.; Carbonell Sala, Silvia; Lagarde, Julien; Albà Soler, Mar; Eyras Jiménez, Eduardo (BioMed Central, 2022)
    Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a reference genome, which precludes the study ...
  • RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation
    Bechara, Elias; Sebestyén, Endre; Bernardis, Isabella; Eyras Jiménez, Eduardo; Valcárcel, J. (Juan) (Elsevier, 2013)
    RBM5, a regulator of alternative splicing of apoptotic genes, and its highly homologous RBM6 and RBM10 are RNA-binding proteins frequently deleted or mutated in lung cancer. We report that RBM5/6 and RBM10 antagonistically ...
  • Regulation of FAS exon definition and apoptosis by the ewing sarcoma protein
    Paronetto, Maria Paola; Bernardis, Isabella; Volpe, Elisabetta; Bechara, Elias; Sebestyén, Endre; Eyras Jiménez, Eduardo; Valcárcel, J. (Juan) (Elsevier, 2014)
    The Ewing sarcoma protein EWS is an RNA and DNA binding protein implicated in transcription, pre-mRNA splicing, and DNA damage response. Using CLIP-seq, we identified EWS RNA binding sites in exonic regions near 5′ splice ...
  • ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning
    Ruiz Reche, Angel; Srivastava, Akanksha; Indi, Joel A.; de la Rubia, Ivan; Eyras Jiménez, Eduardo (BioMed Central, 2019)
    We describe ReorientExpress, a method to perform reference-free orientation of transcriptomic long sequencing reads. ReorientExpress uses deep learning to correctly predict the orientation of the majority of reads, and in ...
  • Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome
    Reixachs i Solé, Marina; Ruiz Orera, Jorge, 1988-; Albà Soler, Mar; Eyras Jiménez, Eduardo (Nature Research, 2020)
    The differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeline for ...
  • RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae
    Plass Pórtulas, Mireya, 1982-; Codony Servat, Carles; Ferreira, Pedro G.; Vilardell, Josep; Eyras Jiménez, Eduardo (Cold Spring Harbor Laboratory Press (CSHL Press) -- RNA, 2012)
    Alternative splicing is the mechanism by which different combinations of exons in the pre-mRNA give rise to distinct mature mRNAs. This process is mediated by splicing factors that bind the pre-mRNA and affect the recognition ...
  • SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data
    Dotu, Ivan; Scott I. Adamson; Coleman, Benjamin; Fournier, Cyril; Ricart Altimiras, Emma; Eyras Jiménez, Eduardo; Chuang, Jeffrey H. (Public Library of Science (PLoS), 2018)
    RNA-protein binding is critical to gene regulation, controlling fundamental processes including splicing, translation, localization and stability, and aberrant RNA-protein interactions are known to play a role in a wide ...
  • Software development and analysis of high throughput sequencing data for genomic enhancer prediction
    González-Vallinas Rostes, Juan (Universitat Pompeu Fabra, 2014-10-31)
    High Throughput Sequencing technologies (HTS) are becoming the standard in genomic regulation analysis. During my thesis I developed software for the analysis of HTS data. Through collaborations with other research groups, ...
  • Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation
    Fernandez, Noemí; Fernandez Miragall, Olga; Ramajo, Jorge; García Sacristán, Ana; Bellora Pereyra, Nicolás; Eyras Jiménez, Eduardo; Briones, Carlos; Martinez Salas, Encarnación (Oxford University Press, 2011)
    RNA structure plays a fundamental role in internal initiation of translation. Picornavirus internal ribosome entry site (IRES) are long, efficient cis-acting elements that recruit the ribosome to internal mRNA sites. ...
  • SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
    Trincado Alonso, Juan Luis, 1987-; Entizne, Juan Carlos; Hysenaj, Gerald; Singh, Babita, 1986-; Skalic, Miha, 1990-; Elliott, David, 1947-; Eyras Jiménez, Eduardo (BioMed Central, 2018)
    Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses ...
  • Systematic analysis of splice-site-creating mutations in cancer
    Jayasinghe, Reyka G.; Eyras Jiménez, Eduardo; Ding, Li; The Cancer Genome Atlas (TCGA) Research Network (Elsevier, 2018)
    For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale ...
  • Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing
    Yuen, Zaka Wing-Sze; Srivastava, Akanksha; Daniel, Runa; McNevin, Dennis; Jack, Cameron; Eyras Jiménez, Eduardo (Nature Research, 2021)
    DNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy remains largely unknown. ...
  • Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1
    Cifdaloz, Metehan; Osterloh, Lisa; Graña-Castro, Osvaldo; Riveiro-Falkenbach, Erica; Ximénez-Embún, Pilar; Muñoz, Javier; Tejedo, Cristina; Calvo, Tonantzin G.; Karras, Panagiotis; Olmeda, David; Miñana Gómez, Belén; Gómez López, Gonzalo; Cañón, Estela; Eyras Jiménez, Eduardo; Guo, Haihong; Kappes, Ferdinand; Ortíz Romero, Pablo Luis; Rodríguez Peraltó, José Luís; Megías, Diego; Valcárcel, J. (Juan); Soengas, María S. (Nature Publishing Group, 2017)
    Melanomas are well-known for their altered mRNA expression profiles. Yet, the specific contribution of mRNA binding proteins (mRBPs) to melanoma development remains unclear. Here we identify a cluster of melanoma-enriched ...
  • The 5' untranslated region of the serotonin receptor 2C pre-mRNA generates miRNAs and is expressed in non-neuronal cells
    Zhang, Zhaiyi; Falaleeva, Marina; Agranat-Tamir, Lily; Pagès Pinós, Amadís; Eyras Jiménez, Eduardo; Sperling, Joseph; Sperling, Ruth; Stamm, Stefan (Springer Verlag, 2013)
    The serotonin receptor 2C (HTR2C) gene encodes a G protein-coupled receptor that is exclusively expressed in neurons. Here, we report that the 5' untranslated region of the receptor pre-mRNA as well as its hosted miRNAs ...
  • The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators
    Llorian, Miriam; Gooding, Clare; Bellora Pereyra, Nicolás; Hallegger, Martina; Buckroyd, Adrian; Wang, Xiao; Rajgor, Dipen; Kayikci, Melis; Feltham, Jack; Ule, Jernej; Eyras Jiménez, Eduardo; Smith, Christopher, W. J. (Oxford University Press, 2016)
    Alternative splicing (AS) is a key component of gene expression programs that drive cellular differentiation. Smooth muscle cells (SMCs) are important in the function of a number of physiological systems; however, investigation ...
  • The BioMart community portal: an innovative alternative to large, centralized data repositories
    Eyras Jiménez, Eduardo; Smedley, Damian; Pérez Llamas, Christian, 1976-; Kasprzyk, Arek (Oxford University Press, 2015)
    The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects ...

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