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Browsing by Author "González-Vallinas Rostes, Juan, 1983-"

Browsing by Author "González-Vallinas Rostes, Juan, 1983-"

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  • A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells
    González-Vallinas Rostes, Juan, 1983-; Pagès Pinós, Amadís; Singh, Babita, 1986-; Eyras Jiménez, Eduardo (BioMed Central, 2015)
    Background. Transcriptional enhancers are generally known to regulate gene transcription from afar. Their activation involves a series of changes in chromatin marks and recruitment of protein factors. These enhancers may ...
  • AVISPA: a web tool for the prediction and analysis of alternative splicing
    Barash, Yoseph; Vaquero-Garcia, Jorge; González-Vallinas Rostes, Juan, 1983-; Xiong, Hui Yuan; Gao, Weijun; Lee, Leo J.; Frey, Brendan J. (BioMed Central, 2013)
    Transcriptome complexity and its relation to numerous diseases underpins the need to predict in silico splice variants and the regulatory elements that affect them. Building upon our recently described splicing code, we ...
  • Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling
    Nadal Ribelles, Mariona, 1984-; Conde Pueyo, Núria, 1983-; Flores, Oscar; González-Vallinas Rostes, Juan, 1983-; Eyras Jiménez, Eduardo; Nadal Clanchet, Eulàlia de; Posas Garriga, Francesc (BioMed Central, 2012)
    Cells are subjected to dramatic changes of gene expression upon environmental changes. Stress/ncauses a general down-regulation of gene expression together with the induction of a set of stress-responsive/ngenes. The ...
  • 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 ...
  • 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 ...
  • Use of ChIP-Seq data for the design of a multiple promoter-alignment method
    Erb, Ionas; González-Vallinas Rostes, Juan, 1983-; Bussotti, Giovanni, 1983-; Blanco, Enrique; Eyras Jiménez, Eduardo; Notredame, Cedric (Oxford University Press, 2012)
    We address the challenge of regulatory sequence alignment with a new method, Pro-Coffee, a multiple aligner specifically designed for homologous promoter regions. Pro-Coffee uses a dinucleotide substitution matrix estimated ...

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