Browsing by Author "Pervouchine, Dmitri D."

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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 ...
  • Breschi, Alessandra, 1988-; Muñoz-Aguirre, Manuel; Wucher, Valentin; Davis, Carrie A.; Garrido Martín, Diego, 1992-; Djebali, Sarah; Gillis, Jesse; Pervouchine, Dmitri D.; Vlasova, Anna; Dobin, Alexander; Zaleski, Chris; Drenkow, Jorg; Danyko, Cassidy; Scavelli, Alexandra; Reverter, Ferran; Snyder, Michael; Gingeras, Thomas R.; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)
    We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, ...
  • 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 ...
  • Frankish, Adam; Uszczynska-Ratajczak, Barbara; Ritchie, Graham R. S.; González, José M.; Pervouchine, Dmitri D.; Petryszak, Robert; Mudge, Jonathan M.; Fonseca, Nuno; Brazma, Alvis; Guigó Serra, Roderic; Harrow, Jennifer (BioMed Central, 2015)
    Background: A vast amount of DNA variation is being identified by increasingly large-scale exome and genome sequencing projects. To be useful, variants require accurate functional annotation and a wide range of tools are ...
  • Kalmykova, Svetlana; Kalinina, Marina; Denisov, Stepan; Mironov, Alexey; Skvortsov, Dmitry; Guigó Serra, Roderic; Pervouchine, Dmitri D. (Nature Research, 2021)
    The ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge on functional RNA structures is focused on locally-occurring base pairs. However, crosslinking ...
  • 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.
  • 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 ...
  • Pervouchine, Dmitri D.; Popov, Yaroslav; Berry, Andy; Borsari, Beatrice, 1992-; Frankish, Adam; Guigó Serra, Roderic (Oxford University Press, 2019)
    Nonsense-mediated decay (NMD) is a eukaryotic mRNA surveillance system that selectively degrades transcripts with premature termination codons (PTC). Many RNA-binding proteins (RBP) regulate their expression levels by a ...
  • Pervouchine, Dmitri D.; Knowles, David G.; Guigó Serra, Roderic (Oxford University Press, 2013)
    MOTIVATION: Novel technologies brought in unprecedented amounts of high-throughput sequencing data along with great challenges in their analysis and interpretation. The percent-spliced-in (PSI, ) metric estimates the ...
  • Ferreira, Pedro G.; Muñoz-Aguirre, Manuel; Reverter, Ferran; Godinho, Caio P. Sá; Sousa, Abel; Amadoz, Alicia; Sodaei, Reza, 1988-; Hidalgo, Marta R.; Pervouchine, Dmitri D.; Carbonell-Caballero, Jose; Nurtdinov, Ramil; Breschi, Alessandra, 1988-; Amador, Raziel; Oliveira, Patrícia; Çubut, Cankut; Curado, Joao; Aguet, François; Oliveira, Carla; Dopazo, Joaquín; Sammeth, Michael; Ardlie, Kristin G.; Guigó Serra, Roderic (Nature Publishing Group, 2018)
    Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA ...

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