Browsing by Author "Djebali, Sarah"

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  • Teng, Mingxiang; Love, Michael I.; Davis, Carrie A.; Djebali, Sarah; Dobin, Alexander; Graveley, Brenton R.; Li, Sheng; Mason, Christopher E.; Olson, Sara; Pervouchine, Dmitri D.; Sloan, Cricket A.; Wei, Xintao; Zhan, Lijun; Irizarry, Rafael A. (BioMed Central, 2016)
    Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, ...
  • 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 ...
  • Stamatoyannopoulos, John A.; Guigó Serra, Roderic; Djebali, Sarah; Lagarde, Julien; Adams, Leslie B. (BioMed Central, 2012)
    To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE ...
  • Rodríguez Martín, Bernardo; Palumbo, Emilio; Marco Sola, Santiago; Griebel, Thasso; Ribeca, Paolo; Alonso, Graciela; Rastrojo, Alberto; Aguado, Begoña; Guigó Serra, Roderic; Djebali, Sarah (BioMed Central, 2017)
    Background: Chimeric transcripts are commonly defined as transcripts linking two or more different genes in the genome, and can be explained by various biological mechanisms such as genomic rearrangement, read-through or ...
  • Gerstein, Mark B.; Djebali, Sarah; Lagarde, Julien; Pervouchine, Dmitri D.; Guigó Serra, Roderic; Tanzer, Andrea; Waterston, Robert (Nature Publishing Group, 2014)
    The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of ...
  • Tilgner, Hagen, 1980-; Knowles, David G.; Johnson, Rory; Davis, Carrie A.; Chakrabortty, Sudipto; Djebali, Sarah; Curado, Joao; Snyder, Michael; Gingeras, Thomas R.; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Splicing remains an incompletely understood process. Recent findings suggest that chromatin structure participates in its regulation. Here, we analyze the RNA from subcellular fractions obtained through RNA-seq in the cell ...
  • Djebali, Sarah; Lagarde, Julien; Denoeud, France; Guigó Serra, Roderic (Nature Research, 2008)
    Rapid amplification of cDNA ends (RACE) is a widely used approach for transcript identification. Random clone selection from the RACE mixture, however, is an ineffective sampling strategy if the dynamic range of transcript ...
  • 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 ...
  • Teng, Mingxiang; Love, Michael I.; Davis, Carrie A.; Djebali, Sarah; Dobin, Alexander; Graveley, Brenton R.; Li, Sheng; Mason, Christopher E.; Olson, Sara; Pervouchine, Dmitri D.; Sloan, Cricket A.; Wei, Xintao; Zhan, Lijun; Irizarry, Rafael A. (BioMed Central, 2016)
    After the publication of this work [1] it was noticed that there were typographical errors in the following equations: equation 5 in column 2, equation 7 in column 2, equation 8 in column 1.
  • Djebali, Sarah; Lagarde, Julien; Lacroix, Vincent; Foissac, Sylvain; Ribeca, Paolo; Martin, David; Guigó Serra, Roderic; Gingeras, Thomas R. (Public Library of Science (PLoS), 2012)
    The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast ...
  • Breschi, Alessandra, 1988-; Djebali, Sarah; Gillis, Jesse; Pervouchine, Dmitri D.; Dobin, Alexander; Davis, Carrie A.; Gingeras, Thomas R.; Guigó Serra, Roderic (BioMed Central, 2016)
    Background: A comparison of transcriptional profiles derived from different tissues in a given species or among different species assumes that commonalities reflect evolutionarily conserved programs and that differences ...
  • Djebali, Sarah; Merkel, Angelika; Tanzer, Andrea; Lagarde, Julien; Röder, Maik; Curado, Joao; Derrien, Thomas; Ferreira, Pedro G.; González, David; Johnson, Rory; Kingswood, Colin; Ribeca, Paolo; Sammeth, Michael; Skancke, Jorgen; Tilgner, Hagen, 1980-; Guigó Serra, Roderic; Gingeras, Thomas R. (Nature Publishing Group, 2012)
    Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic ...
  • Dong, Xianjun; Greven, Melissa C.; Kundaje, Anshul; Djebali, Sarah; Brown, James B.; Cheng, Chao; Gingeras, Thomas R.; Gerstein, Mark B.; Guigó Serra, Roderic; Birney, Ewan; Weng, Zhiping (BioMed Central, 2012)
    BACKGROUND: Previous work has demonstrated that chromatin feature levels correlate with gene expression. The ENCODE project enables us to further explore this relationship using an unprecedented volume of data. Expression ...
  • Derrien, Thomas; Johnson, Rory; Bussotti, Giovanni, 1983-; Tanzer, Andrea; Djebali, Sarah; Tilgner, Hagen, 1980-; Guernec, Gregory; Martin, David; Merkel, Angelika; Knowles, David G.; Lagarde, Julien; Veeravalli, Lavanya; Ruan, Xiaoan; Ruan, Yijun; Lassmann, Timo; Carninci, Piero; Brown, James B.; Lipovich, Leonard; González, José M.; Thomas, Mark; Davis, Carrie A.; Shiekhattar, Ramin; Gingeras, Thomas R.; Hubbard, Tim J.; Notredame, Cedric; Harrow, Jennifer; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to ...
  • Ferreira, Pedro G.; González-Pérez, Abel; Knowles, David G.; Monlong, Jean; Johnson, Rory; Djebali, Sarah; Papasaikas, Panagiotis; Tamborero Noguera, David; Gouin, Anaïs; López Bigas, Núria; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2014)
    Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying ...
  • Cheng, Chao; Alexander, Roger; Min, Renqiang; Leng, Jing; Yip, Kevin Y.; Rozowsky, Joel S.; Yan, Koon-Kiu; Dong, Xianjun; Djebali, Sarah; Ruan, Yijun; Davis, Carrie A.; Carninci, Piero; Lassmann, Timo; Gingeras, Thomas R.; Guigó Serra, Roderic; Birney, Ewan; Weng, Zhiping; Snyder, Michael; Gerstein, Mark B. (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Statistical models have been used to quantify the relationship between gene expression and transcription factor (TF) binding signals. Here we apply the models to the large-scale data generated by the ENCODE project to study ...
  • Durán, Elisa; Djebali, Sarah; González, Santi; Flores, Oscar; Mercader Bigas, Josep Maria; Guigó Serra, Roderic; Torrents, David; Soler López, Montserrat; Orozco, Modesto (Oxford University Press, 2013)
    Although protein recognition of DNA motifs in promoter regions has been traditionally considered as a critical regulatory element in transcription, the location of promoters, and in particular transcription start sites ...