Browsing by Author "Notredame, Cedric"

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  • Yue, Feng; Breschi, Alessandra, 1988-; Pervouchine, Dmitri D.; Djebali, Sarah; Prieto Barja, Pablo, 1986-; Lagarde, Julien; Bussotti, Giovanni, 1983-; Tanzer, Andrea; Notredame, Cedric; Guigó Serra, Roderic; Ren, Bing; The Mouse Encyclopedia of DNA Elements (ENCODE) Consortium (Nature Publishing Group, 2014)
    The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into ...
  • Quinn, Thomas P.; Erb, Ionas; Gloor, Greg; Notredame, Cedric; Richardson, Mark F.; Crowley, Tamsyn M. (Oxford University Press, 2019)
    Background: Next-generation sequencing (NGS) has made it possible to determine the sequence and relative abundance of all nucleotides in a biological or environmental sample. A cornerstone of NGS is the quantification of ...
  • Davey, Norman E.; Notredame, Cedric; Tosatto, Silvio C.E. (F1000Research, 2019)
    Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments ...
  • Espinosa-Carrasco, José (Universitat Pompeu Fabra, 2016-11-08)
    New high-throughput behavioral systems enable the recording of continuous behavioral sequences with an unprecedented richness of signals and a deep temporal resolution. Automated systems offer neuroscience the opportunity ...
  • Ounzain, Samir; Micheletti, Rudi; Arnan Ros, Carme; Plaisance, Isabelle; Cecchi, Dario; Schroen, Blanche; Reverter, Ferran; Alexanian, Michael; Gonzales, Christine; Ng, Shi Yan; Bussotti, Giovanni, 1983-; Pezzuto, Iole; Notredame, Cedric; Heymans, Stephane; Guigó Serra, Roderic; Johnson, Rory; Pedrazzini, Thierry (Elsevier, 2015)
    Long noncoding RNAs (lncRNAs) are emerging as important regulators of developmental pathways. However, their roles in human cardiac precursor cell (CPC) remain unexplored. To characterize the long noncoding transcriptome ...
  • Catuara Solarz, Silvina, 1986-; Espinosa-Carrasco, José; Erb, Ionas; Langohr, Klaus; Gonzalez, Juan Ramon; Notredame, Cedric; Dierssen, Mara (Society for Neuroscience, 2016)
    Intellectual disability in Down syndrome (DS) is accompanied by altered neuro-architecture, deficient synaptic plasticity, and excitation-inhibition imbalance in critical brain regions for learning and memory. Recently, ...
  • Bussotti, Giovanni, 1983- (Universitat Pompeu Fabra, 2013-01-23)
    In recent years there has been a growing interest in the field of non-coding RNA. This surge is a direct consequence of the discovery of a huge number of new non-coding genes, and of the finding that many of these transcripts ...
  • Pervouchine, Dmitri D.; Djebali, Sarah; Breschi, Alessandra, 1988-; Prieto Barja, Pablo, 1986-; Lagarde, Julien; Bussotti, Giovanni, 1983-; Monlong, Jean; Notredame, Cedric; Guigó Serra, Roderic; Gingeras, Thomas R. (Nature Pub. Group, 2015)
    Mice have been a long-standing model for human biology and disease. Here we characterize, by RNA sequencing, the transcriptional profiles of a large and heterogeneous collection of mouse tissues, augmenting the mouse ...
  • Shiao, Meng-Shin; Chang, Jia-Ming, 1978-; Fan, Wen-Lang; Jade Lu, Mei-Yeh; Notredame, Cedric; Fang, Shu; Kondo, Rumi; Li, Wen-Hsiung (Oxford University Press, 2015)
    Drosophila sechellia relies exclusively on the fruits of Morinda citrifolia, which are toxic to most insects, including its sibling species Drosophila melanogaster and Drosophila simulans. Although several odorant binding ...
  • Burokas, Aurelijus, 1982-; Martín García, Elena, 1975-; Espinosa-Carrasco, José; Erb, Ionas; McDonald, Jerome; Notredame, Cedric; Dierssen, Mara; Maldonado, Rafael, 1961- (Wiley-Blackwell, 2018)
    A major problem in treating obesity is the high rate of relapse to abnormal food-taking habits after maintaining an energy balanced diet. Alterations of eating behavior such as compulsive-like behavior and lack of self-control ...
  • Vlasova, Anna; Capella Gutiérrez, Salvador Jesús, 1985-; Erb, Ionas; Cámara, Francisco; Prieto Barja, Pablo, 1986-; Kedra, Darek; González Navarrete, Irene, 1983-; Cozzuto, Luca; Gómez Garrido, Jèssica; Aguilar Morón, María Asunción; Andreu Somavilla, Núria; Zehnsdorf, Maik; Alioto, Tyler; Notredame, Cedric; Gabaldón Estevan, Juan Antonio, 1973-; Guigó Serra, Roderic (BioMed Central, 2016)
    Background: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million ...
  • Orobitg, Miquel; Guirado, Fernando; Cores, Fernando; Lladós, Jordi; Notredame, Cedric (Elsevier, 2015)
    Multiple Sequence Alignment (MSA) is essential for a wide range of applications in Bioinformatics. Traditionally, the alignment accuracy was the main metric used to evaluate the goodness of MSA tools. However, with the ...
  • Erb, Ionas; Notredame, Cedric (Springer, 2016)
    Correlation is ubiquitously used in gene expression analysis although its validity as an objective criterion is often questionable. If no normalization reflecting the original mRNA counts in the cells is available, correlation ...
  • Bussotti, Giovanni, 1983-; Leonardi, Tommaso; Clark, Michael B.; Mercer, Tim R.; Crawford, Joanna; Malquori, Lorenzo; Notredame, Cedric; Dinger, Marcel E.; Mattick, John S.; Enright, Anton J. (Cold Spring Harbor Laboratory Press (CSHL Press), 2016)
    Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied ...
  • Kemena, Carsten, 1983- (Universitat Pompeu Fabra, 2012-12-12)
    Sequence alignment is one of the basic methods to compare biological sequences and the cornerstone of a wide range of different analyses. Due to this privileged position at the beginning of many studies its accuracy is of ...
  • Chang, Jia-Ming, 1978- (Universitat Pompeu Fabra, 2013-07-25)
    Most evolutionary analyses are based upon pre-estimated multiple sequence alignment models. From a computational point of view, it is too complex to estimate a correct alignment, as it is to derive a correct tree from that ...
  • Chatzou, Maria, 1985- (Universitat Pompeu Fabra, 2016-11-07)
    One of the main and most recent challenges of modern biology is to keep-up with growing amount of biological data coming from next generation sequencing technologies. Keeping up with the growing volumes of experiments will ...
  • Orom, Ulf Andersson; Derrien, Thomas; Beringer, Malte; Gumireddy, Kiranmai; Gardini, Alessandro; Bussotti, Giovanni, 1983-; Lai, Fan; Zytnicki, Matthias; Notredame, Cedric; Huang, Qihong; Guigó Serra, Roderic; Shiekhattar, Ramin (Elsevier, 2010)
    While the long noncoding RNAs (ncRNAs) constitute a large portion of the mammalian transcriptome, their biological functions has remained elusive. A few long ncRNAs that have been studied in any detail silence gene expression ...
  • Prieto Barja, Pablo, 1986- (Universitat Pompeu Fabra, 2017-01-12)
    In this PhD I have used NGS technologies in different organisms and scenarios such as in ENCODE, comparing the conservation and evolution of long non-coding RNA sequences between human and mouse, using experimental evidences ...
  • Espinosa-Carrasco, José; Hermoso Pulido, Antonio; Erb, Ionas; Dierssen, Mara; Ponomarenko, Julia; Notredame, Cedric (Oxford University Press, 2019)
    We present a new web application to query and visualize time-series behavioral data: the Pergola web-server. This server provides a user-friendly interface for exploring longitudinal behavioral data taking advantage of the ...