Now showing items 1-7 of 7

    • Assembly and Validation of Versatile Transcription Activator-Like Effector Libraries 

      Li, Yi; Ehrhardt, Kristina; Zhang, Michael Q.; Bleris, Leonidas (Nature Publishing Group, 2014-05-06)
      The ability to perturb individual genes in genome-wide experiments has been instrumental in unraveling cellular and disease properties. Here we introduce, describe the assembly, and demonstrate the use of comprehensive and ...
    • Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells 

      Guo, Weilong; Chung, Wen-Yu; Qian, Minping; Pellegrini, Matteo; Zhang, Michael Q. (Oxford University Press, 2013-12-16)
      DNA methylation is an important defense and regulatory mechanism. In mammals, most DNA methylation occurs at CpG sites, and asymmetric non-CpG methylation has only been detected at appreciable levels in a few cell types. ...
    • FastDMA: An Infinium Humanmethylation450 Beadchip Analyzer 

      Wu, D.; Gu, J.; Zhang, Michael Q. (2013-09-05)
      DNA methylation is vital for many essential biological processes and human diseases. Illumina Infinium HumanMethylation450 Beadchip is a recently developed platform studying genome-wide DNA methylation state on more than ...
    • Integrated Omics Study Delineates the Dynamics of Lipid Droplets in Rhodococcus Opacus PD630 

      Chen, Yong; Ding, Yunfeng; Yang, Li; Yu, Jinhai; Liu, Guiming; Wang, Xumin; Zhang, Shuyan; Zhang, Michael Q.; Li, Yanda (Oxford University Press, 2013-10-22)
      Rhodococcus opacus strain PD630 (R. opacus PD630), is an oleaginous bacterium, and also is one of few prokaryotic organisms that contain lipid droplets (LDs). LD is an important organelle for lipid storage but also ...
    • Miror: A Method for Cell-Type Specific MicroRNA Occupancy Rate Prediction 

      Xie, Peng; Liu, Yu; Li, Yanda; Zhang, Michael Q.; Wang, Xiaowo (Royal Soc Chemistry, 2014-03-13)
      MicroRNA (miRNA) regulation is highly cell-type specific. It is sensitive to both the miRNA-mRNA relative abundance and the competitive endogenous RNA (ceRNA) effect. However, almost all existing miRNA target prediction ...
    • ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks 

      Li, GuiPeng; Li, Ming; Zhang, YiWei; Wang, Dong; Li, Rong; Guimera, Roger; Gao, Juntao Tony; Zhang, Michael Q. (Public Library of Science, 2014-05-01)
      Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain ...
    • OLego: Fast and Sensitive Mapping of Spliced mRNA-Seq Reads Using Small Seeds 

      Wu, Jie; Anczuk©w, Olga; Krainer, Adrian R.; Zhang, Michael Q.; Zhang, Chaolin (Oxford University Press, 2013-04)
      A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo ...