Browsing by Author "Castelo Valdueza, Robert"

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  • Castelo Valdueza, Robert; Reymond, Alexandre; Wyss, Carine; Cámara, Francisco; Parra Farré, Genís; Antonarakis, Stylianos E.; Guigó Serra, Roderic; Eyras Jiménez, Eduardo (Oxford University Press, 2005)
    The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene catalog. Here, we show, using ...
  • Abril Ferrando, Josep Francesc; Castelo Valdueza, Robert; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press-CSHL Press, 2005)
    We have carried out an initial analysis of the dynamics of the recent evolution of the splice-sites sequences on a large collection of human, rodent (mouse and rat), and chicken introns. Our results indicate that the ...
  • Hartmann, Britta; Castelo Valdueza, Robert; Miñana Gómez, Belén; Peden, Erin; Blanchette, Marco; Rio, Donald C.; Singh, Ravinder; Valcárcel, J. (Juan) (Cold Spring Harbor Laboratory Press, 2011)
    In Drosophila melanogaster, female-specific expression of Sex-lethal (SXL) and Transformer (TRA) proteins controls sex-specific alternative splicing and/or translation of a handful of regulatory genes responsible for sexual ...
  • Guigó Serra, Roderic; Flicek, Paul; Abril Ferrando, Josep Francesc; Reymond, Alexandre; Lagarde, Julien; Denoeud, France; Antonarakis, Stylianos E.; Ashburner, Michael; Bajic, Vladimir B.; Birney, Ewan; Castelo Valdueza, Robert; Eyras Jiménez, Eduardo; Ucla, Catherine; Gingeras, Thomas R.; Harrow, Jennifer; Hubbard, Tim J.; Lewis, Suzanna E.; Reese, Martin G. (BioMed Central, 2006)
    Background: We present the results of EGASP, a community experiment to assess the state-ofthe-/nart in genome annotation within the ENCODE regions, which span 1% of the human genome/nsequence. The experiment had two major ...
  • Esnaola, Mikel; Puig, Pedro; González, David; Castelo Valdueza, Robert; González Ruiz, Juan Ramón (BioMed Central, 2013)
    Background: High-throughput RNA sequencing (RNA-seq) offers unprecedented power to capture the real dynamics of gene expression. Experimental designs with extensive biological replication present a unique opportunity to ...
  • Eyras Jiménez, Eduardo; Reymond, Alexandre; Castelo Valdueza, Robert; Bye, Jacqueline M.; Cámara, Francisco; Flicek, Paul; Huckle, Elizabeth J.; Parra Farré, Genís; Shteynberg, David D.; Wyss, Carine; Rogers, Jane; Antonarakis, Stylianos E.; Birney, Ewan; Guigó Serra, Roderic; Brent, Michael R. (BioMed Central, 2005)
    Background: Despite the continuous production of genome sequence for a number of organisms,/nreliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly/ntrue for genomes for which ...
  • Costa, Daniel; Bonet, Núria; Solé, Amanda; González de Aledo-Castillo, José Manuel; Sabidó Aguadé, Eduard, 1981-; Casals López, Ferran; Rovira, Carlota; Nadal, Alfons; Marin, Jose Luis; Cobo, Teresa; Castelo Valdueza, Robert (Wiley, 2021)
    The fetal inflammatory response (FIR) increases the risk of perinatal brain injury, particularly in extremely low gestational age newborns (ELGANs, < 28 weeks of gestation). One of the mechanisms contributing to such a ...
  • Hänzelmann, Sonja, 1981-; Castelo Valdueza, Robert; Guinney, Justin (BioMed Central, 2013)
    Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise ...
  • Costa Coto, Daniel (2021-05-21)
    Preterm birth is the leading cause of neonatal morbidity and mortality worldwide. Preterm newborns require special care for surviving and may develop severe diseases related to prematurity, especially those born very early. ...
  • Puigdevall Costa, Pau (Universitat Pompeu Fabra, 2019-02-20)
    Understanding the molecular basis of human inherited disease is a challenging task due to the complexity of mapping the genotype to the phenotype. The study of diseases running in families has shown that the inheritance ...
  • Lyle, Robert; Prandini, Paola; Osoegawa, Kazutoyo; Ten Hallers, Boudewijn; Humphray, Sean; Zhu, Baoli; Eyras Jiménez, Eduardo; Castelo Valdueza, Robert; Bird, Christine P.; Gagos, Sarantos; Scott, Carol; Cox, Antony; Deutsch, Samuel; Ucla, Catherine; Cruts, Marc; Dahoun, Sophie; She, Xinwei; Bena, Frederique; Wang, Sheng-Yue; Broeckhoven, Christine van; Eichler, Evan E.; Guigó Serra, Roderic; Rogers, Jane; De Jong, Pieter J.; Reymond, Alexandre; Antonarakis, Stylianos E. (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. ...
  • Tur Mongé, Inma (Universitat Pompeu Fabra, 2014-06-19)
    Expression quantitative trait loci (eQTL) mapping constitutes a challenging problem due to the high-dimensional multivariate nature of continuous gene expression traits and discrete genotypes from genetical genomics ...
  • Roverato, Alberto; Castelo Valdueza, Robert (Oxford University Press, 2020)
    A graphical model provides a compact and efficient representation of the association structure in a multivariate distribution by means of a graph. Relevant features of the distribution are represented by vertices, edges ...
  • Hänzelmann, Sonja (Universitat Pompeu Fabra, 2013-03-14)
    In the last decade, molecular biology has expanded from a reductionist view to a systems-wide view that tries to unravel the complex interactions of cellular components. Owing to the emergence of high-throughput technology ...
  • Denoeud, France; Kapranov, Philipp; Ucla, Catherine; Frankish, Adam; Castelo Valdueza, Robert; Drenkow, Jorg; Lagarde, Julien; Alioto, Tyler; Manzano, Caroline; Chrast, Jacqueline; Dike, Sujit; Wyss, Carine; Henrichsen, Charlotte N.; Holroyd, Nancy; Dickson, Mark C.; Taylor, Ruth; Hance, Zahra; Foissac, Sylvain; Myers, Richard M.; Rogers, Jane; Hubbard, Tim J.; Harrow, Jennifer; Guigó Serra, Roderic; Gingeras, Thomas R.; Antonarakis, Stylianos E.; Reymond, Alexandre (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using ...
  • Kannan, Lavanya; Ramos, Marcel; Re, Angela; El-Hachem, Nehme; Safikhani, Zhaleh; Gendoo, Deena M. A.; Davis, Sean; Gomez Cabrero, David; Castelo Valdueza, Robert; Hansen, Kasper D.; Carey, Vicent J.; Morgan, Martin; Culhane, Aedín C.; Haibe-Kains, Benjamin; Waldron, Levi (Oxford University Press, 2016)
    Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and ...
  • Roverato, Alberto; Castelo Valdueza, Robert (Wiley, 2017)
    Genetic interactions confer robustness on cells in response to genetic perturbations. This often occurs through molecular buffering mechanisms that can be predicted by using, among other features, the degree of coexpression ...
  • Baumstark, Rebecca; Hänzelmann, Sonja, 1981-; Tsuru, Saburo; Schaerli, Yolanda; Francesconi, Mirko; Mancuso, Francesco M.; Castelo Valdueza, Robert; Isalan, Mark (Nature Publishing Group, 2015)
    What happens to gene expression when you add new links to a gene regulatory network? To answer this question, we profile 85 network rewirings in E. coli. Here we report that concerted patterns of differential expression ...
  • Hänzelmann, Sonja, 1981-; Wang, Jinling; Güney, Emre, 1983-; Tang, Yunzhao; Zhang, Enming; Axelsson, Annika S.; Nenonen, Hannah; Salehi, Albert S.; Wollheim, Claes B.; Zetterberg, Eva; Berntorp, Erik; Costa, Ivan G.; Castelo Valdueza, Robert; Rosengren, Anders H. (Taylor & Francis (Routledge), 2015)
    The disease mechanisms underlying type 2 diabetes (T2D) remain poorly defined. Here we aimed to explore the pathophysiology of T2D by analyzing gene co-expression networks in human islets. Using partial correlation networks ...
  • Costa, Daniel; Castelo Valdueza, Robert (Nature Publishing Group, 2016)
    BACKGROUND: The fetal inflammatory response (FIR) in placental membranes to an intrauterine infection often precedes premature birth raising neonatal mortality and morbidity. However, the precise molecular events behind ...

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