Browsing by Author "Snyder, Michael"

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  • 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 ...
  • Zheng, Deyou; Frankish, Adam; Baertsch, Robert; Kapranov, Philipp; Reymond, Alexandre; Choo, Siew Woh; Lu, Yontao; Denoeud, France; Antonarakis, Stylianos E.; Snyder, Michael; Ruan, Yijun; Wei, Chia-Lin; Gingeras, Thomas R.; Guigó Serra, Roderic; Harrow, Jennifer; Gerstein, Mark B. (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an ...
  • 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 ...
  • Rozowsky, Joel S.; Newburger, Daniel; Sayward, Fred; Wu, Jiaqian; Jordan, Greg; Korbel, Jan O.; Nagalakshmi, Ugrappa; Yang, Jing; Zheng, Deyou; Guigó Serra, Roderic; Gingeras, Thomas R.; Weissman, Sherman; Miller, Perry; Snyder, Michael; Gerstein, Mark B. (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    For the ∼1% of the human genome in the ENCODE regions, only about half of the transcriptionally active regions (TARs) identified with tiling microarrays correspond to annotated exons. Here we categorize this large amount ...
  • 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 ...