Recent Submissions

  • Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome 

    Jjingo, Daudi; Wang, Jianrong; Conley, Andrew B.; Lunyak, Victoria V.; Jordan, I. King (Oxford University Press, 2013-10)
    Motivation: It has been suggested that presumably distinct classes of genomic regulatory elements may actually share common sets of features and mechanisms. However, there has been no genome-wide assessment of the prevalence ...
  • Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes 

    Lopes, Fabrício R.; Jjingo, Daudi; R. M. da Silva, Carlos; Andrade, Alan C.; Marraccini, Pierre; Teixeira, Joaõ B.; Carazzolle, Marcelo F.; A. G. Pereira, Gonçalo; Pereira, Luiz Filipe P.; Vanzela, André L. L.; Wang, Lu; Jordan, I. King; Carareto, Claudia M. A. (PLoS ONE (Public Library of Science), 2013-11-11)
    Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under ...
  • Effect of the transposable element environment of human genes on gene length and expression 

    Jjingo, Daudi; Huda, Ahsan; Gundapuneni, Madhumati; Mariño-Ramǐrez, Leonardo; Jordan, I. King (Oxford University Press, 2011-02-28)
    Independent lines of investigation have documented effects of both transposable elements (TEs) and gene length (GL) on gene expression. However, TE gene fractions are highly correlated with GL, suggesting that they cannot ...
  • On the presence and role of human gene-body DNA methylation 

    Jjingo, Daudi; Conley, Andrew B.; Yi, Soojin V.; Lunyak, Victoria V.; Jordan, I. King (International Multidisciplinary Publishing Academy for Computational Technologies, 2012-05-09)
    DNA methylation of promoter sequences is a repressive epigenetic mark that down-regulates gene expression. However, DNA methylation is more prevalent within gene-bodies than seen for promoters, and gene-body methylation ...
  • Flow-dependent epigenetic DNA methylation regulates endothelial gene expression and atherosclerosis 

    Dunn, Jessilyn; Qiu, Haiwei; Kim, Soyeon; Jjingo, Daudi; Hoffman, Ryan; Kim, Chan Woo; Jang, Inhwan; Son, Dong Ju; Kim, Daniel; Pan, Chenyi; Fan, Yuhong; Jordan, I. King; Jo, Hanjoong (American Society for Clinical Investigation, 2014)
    In atherosclerosis, plaques preferentially develop in arterial regions of disturbed blood flow (d-flow), which alters endothelial gene expression and function. Here, we determined that d-flow regulates genome-wide DNA ...
  • Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression 

    Jjingo, Daudi; Conley, Andrew B.; Wang, Jianrong; Mariño-Ramírez, Leonardo; Lunyak, Victoria V.; Jordan, I. King (BioMed Central, 2014)
    Background: Mammalian-wide interspersed repeats (MIRs) are the most ancient family of transposable elements (TEs) in the human genome. The deep conservation of MIRs initially suggested the possibility that they had been ...
  • Computational identification of transposable elements in the mouse genome 

    Jjingo, Daudi; Makalowski, Wojciech (2007)
    Repeat sequences cover about 39 percent of the mouse genome and completion of sequencing of the mouse genome [1] has enabled extensive research on the role of repeat sequences in mammalian genomics. This research covers ...
  • Prediction of transposable element derived enhancers using chromatin modification profiles 

    Huda, Ahsan; Tyagi, Eishita; Marino-Ramırez, Leonardo; Bowen, Nathan J.; Jjingo, Daudi; King Jordan, I. (PLoS ONE (Public Library of Science), 2011-11-07)
    Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for several different histone modifications. We modelled these enhancer chromatin profiles in the human ...