Browsing by Author "Drenkow, Jorg"

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  • A limited set of transcriptional programs define major cell types
    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, ...
  • Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions
    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 ...
  • Structured RNAs in the ENCODE selected regions of the human genome
    Washietl, Stefan; Pedersen, Jackob S.; Korbel, Jan O.; Stocsits, Claudia; Gruber, Andreas R.; Hackermüller, Jörg; Hertel, Jana; Lindemeyer, Manja; Reiche, Kristin; Tanzer, Andrea; Ucla, Catherine; Wyss, Carine; Antonarakis, Stylianos E.; Denoeud, France; Lagarde, Julien; Drenkow, Jorg; Kapranov, Philipp; Gingeras, Thomas R.; Guigó Serra, Roderic; Snyder, Michael; Gerstein, Mark B.; Reymond, Alexandre; Hofacker, Ivo L.; Stadler, Peter F. (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within ...

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